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<title>Publications — FDI Lab</title>
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<h1>Publications</h1>
<p>FDI Lab publications from 2008 to present — 202 records.</p>
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<p style="color:var(--gray-text); font-size:0.9rem; margin-bottom:1rem;">Citations aggregated from ORCID records of FDI Lab principal investigators and senior staff. Formatted in <a href="https://www.nlm.nih.gov/bsd/uniform_requirements.html" target="_blank" rel="noopener" style="color:var(--accent);">NLM citation style</a>.</p>
<h2 style="margin-top:2.5rem;">2026 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(10)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Bandrowski A, Namburi A, Ferguson A, Floyd CL, Martone ME. Rigor and Transparency in two neurotrauma-publishing journals: editorial policies improve transparent reporting [Preprint]. bioRxiv; 2026. doi:<a href="https://doi.org/10.64898/2026.01.16.699952" target="_blank" rel="noopener">10.64898/2026.01.16.699952</a>.</li>
<li>Eckmann P, Barnett A, Bannach-Brown A, Bascunan Atria EP, Cabanac G, Owen Franzen LD, Gazda MA, Hair K, Howison J, Kilicoglu H, Labbe C, McCann S, Nachev V, Roelandse M, Salholz-Hillel M, Schulz R, ter Riet G, Vorland C, Bandrowski A, Weissgerber T. Use as directed? A comparison of software tools intended to check rigor and transparency of published work. PLoS One. 2026;21(2):e0342225. doi:<a href="https://doi.org/10.1371/journal.pone.0342225" target="_blank" rel="noopener">10.1371/journal.pone.0342225</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41686823/" target="_blank" rel="noopener">41686823</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12904390/" target="_blank" rel="noopener">PMC12904390</a>.</li>
<li>Ferguson A, Radabaugh HL, Huie JR, LaPlaca MC, Dixon CE, Surles-Zeigler MC, Harris NG, Catherine J, Rojas LV, Espin AT, Grethe JS, Bandrowski A, Maryann M, Gurkoff GG. Towards creating an injury severity index for experimental traumatic brain injury (TBI): data-driven and knowledge-driven approaches. . 2026. doi:<a href="https://doi.org/10.5281/zenodo.18472747" target="_blank" rel="noopener">10.5281/zenodo.18472747</a>.</li>
<li>Fond KA, Radabaugh HL, Vavrek R, Axtman PJ, Huie JR, Fedor BA, Gensel JC, Fouad K, Grethe JS, Martone ME, Ferguson AR, Torres-Espin A. Improving data quality in neurotrauma data sharing: The Open Data Commons minimal data standards and a data tool for compliance [Preprint]. Zenodo (CERN European Organization for Nuclear Research); 2026. doi:<a href="https://doi.org/10.5281/zenodo.18603759" target="_blank" rel="noopener">10.5281/zenodo.18603759</a>.</li>
<li>Hovhannisyan AH, Alfaro J, Aldape J, Mecklenburg JM, Zou Y, Lai Z, Guo W, Yang J, Boada MD, Ernberg M, Ren K, Akopian A, Allen K, Almarza A, Arenkiel B, Ayaz B, Bae Y, Paula BBD, Bandrowski A, Boada MD, Boccanfuso J, Boline J, Carpio DL, Cai D, Caudle R, Cela R, Chen R, Chen Y, Constantinescu B, Cortez I, Cruz-Almeida Y, Dolwick MF, Donnelly C, Dou Z, Emrick J, Ernberg M, Freburg-Hoffmeister D, Fullam S, Gaire J, Gandhi A, Goolsby B, Greene S, Haelterman N, Iadarola M, Ishihara S, Ishola A, Jayachandran S, Jin Y, Jin Z, Ko F, Kulkarni P, Lai Z, Lee B, Levites Y, Li J, Lotz M, Macpherson L, Maerz T, Majano C, Malfait AM, Martone M, Mehta B, Miller R, Miller R, Muhammad A, Newton M, Obeidat A, Olmer M, Orange D, Otero M, Otto K, Patterson F, Pela M, Perry S, Price T, Priester S, Prieto H, Ray R, Ren D, Dasilva MR, Roberts A, Ronan E, Ruiz O, Smith S, Gonzalez MS, Southern K, Stover J, Strinden M, Swahn H, Tappan S, Sanchez LT, Tumanov A, Vivanco-Estela A, Wagenaar J, Wang E, Wang L, Worley K, Wythe J, Yan J, Zou Y, Akopian AN. Masticatory myalgia to headache-like secondary hypersensitivity induces gene plasticity at dura mater. J Headache Pain. 2026;27(1). doi:<a href="https://doi.org/10.1186/s10194-026-02361-8" target="_blank" rel="noopener">10.1186/s10194-026-02361-8</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41987013/" target="_blank" rel="noopener">41987013</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC13085479/" target="_blank" rel="noopener">PMC13085479</a>.</li>
<li>LaPlaca MC, Harris NV, Surles-Zeigler MC, Gurkoff GG, Ferguson A, Dixon CE, Lyeth BG, VandeVord PJ, Johnson CE, Crawford F, Ferguson S, Bondi C, Huie JR, E. MM, Grethe JS, Torres-Espin A, Cheng WH(, Wanner IB, Jasmin S, Kobaissy F, Boutté AM, Agoston D, Moro F, Febo M, Smith GD, Duncan D, Obenaus A, Allendorfer JB, Korotcov A, Floyd CL. Enhancing Data Sharing for Preclinical Traumatic Brain Injury Research with Common Data Elements [Preprint]. Open MIND; 2026. doi:<a href="https://doi.org/10.5281/zenodo.18624818" target="_blank" rel="noopener">10.5281/zenodo.18624818</a>.</li>
<li>Li R, Das A, Yang Y, Li Z, Hong N, Xu H, Martone M, Zheng WJ. A birth certificate for data to improve findability, accountability, and traceability. NAR Genomics and Bioinformatics. 2026;8(2). doi:<a href="https://doi.org/10.1093/nargab/lqag037" target="_blank" rel="noopener">10.1093/nargab/lqag037</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41972008/" target="_blank" rel="noopener">41972008</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC13069677/" target="_blank" rel="noopener">PMC13069677</a>.</li>
<li>Maryann M, Huie JR, Axtman PJ, Davis AM, Gurkoff GG, Espín AT, Grethe JS, Ferguson A, PRECISE-TBI. The Open Data Commons for Traumatic Brain Injury: an Interagency Community Platform for Pre-clinical Data Management and Sharing. . 2026. doi:<a href="https://doi.org/10.5281/zenodo.18616679" target="_blank" rel="noopener">10.5281/zenodo.18616679</a>.</li>
<li>Stover JD, Bowles RD, Cruz-Almeida Y, Caudle RM, Allen KD, Akopian A, Arenkiel B, Ayaz B, Bae Y, de Paula BB, Bandrowski A, Boada MD, Boccanfuso J, Boline J, Cai D, Carpio, Lane D, Caudle R, Cela R, Chen Y, Chen R, Constantinescu B, Cortez, Ibdanelo, Franklin Dolwick M, Donnelly C, Dou Z, Emrick J, Ernberg M, Freburg-Hoffmeister D, Fullam S, Gaire J, Gandhi A, Goolsby B, Greene S, Haelterman N, Iadarola M, Ishihara S, Ishola A, Jayachandran S, Jin Z, Ko F, Kulkarni P, Lai Z, Lee B, Levites Y, Leynes C, Li J, Lotz M, Macpherson L, Maerz T, Majano C, Malfait AM, Martone M, Mehta B, Miller R, Miller R, Newton M, Obeidat A, Olmer M, Orange D, Otero M, Otto K, Patterson F, Pela M, Perry S, Price T, Prieto H, Ray R, Ren D, Dasilva MR, Roberts A, deLavor JR, Ronan E, Ruiz O, Smith S, Socorro M, Southern K, Stover J, Strinden M, Swahn H, Tantry E, Tappan S, Sanchez LT, Vivanco-Estela A, Wagenaar J, Wang L, Worley K, Wythe J, Yan J, Younis J, Almarza AJ. CRISPR Epigenome Editing of IL1R1 Expression of Neurons that Innervate the Temporomandibular Joint or Knee Causes Reduced Sensitization to Osteoarthritic Environment. Ann Biomed Eng. 2026. doi:<a href="https://doi.org/10.1007/s10439-026-04047-3" target="_blank" rel="noopener">10.1007/s10439-026-04047-3</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41949727/" target="_blank" rel="noopener">41949727</a>.</li>
<li>Surles-Zeigler MC, Holmes L, Sincomb T, Martone ME, Grethe JS, Ferguson AR, Dixon CE. PRECISE TBI Model Catalog: Increasing Accessibility and Reproducibility in TBI research [Preprint]. bioRxiv; 2026. doi:<a href="https://doi.org/10.64898/2026.02.10.704562" target="_blank" rel="noopener">10.64898/2026.02.10.704562</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41727021/" target="_blank" rel="noopener">41727021</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12918779/" target="_blank" rel="noopener">PMC12918779</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2025 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(13)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Adams MCB, Bann CM, Bayman EO, Chao M, Hergenroeder GW, Knott C, Lindquist MA, Luo ZD, Martin R, Martone ME, McCarthy J, McCumber M, Meropol SB, Ridenour TA, Saavedra LM, Sarker A, Anstrom KJ, Thompson WK. Building community through data: the value of a researcher driven open science ecosystem. Pain Medicine. 2025;26(6):295-298. doi:<a href="https://doi.org/10.1093/pm/pnaf003" target="_blank" rel="noopener">10.1093/pm/pnaf003</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39836639/" target="_blank" rel="noopener">39836639</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12130680/" target="_blank" rel="noopener">PMC12130680</a>.</li>
<li>Alfaro JJ, Wang E, Allen K, Almarza A, Arenkiel B, Ayaz B, Bae Y, de Paula BB, Bandrowski A, Boada MD, Boccanfuso J, Boline J, Carpio DL, Cai D, Caudle R, Cela R, Chen R, Chen Y, Constantinescu B, Cortez I, Cruz-Almeida Y, Dolwick MF, Donnelly C, Dou Z, Emrick J, Ernberg M, Freburg-Hoffmeister D, Fullam S, Gaire J, Gandhi A, Goolsby B, Greene S, Haelterman N, Iadarola M, Ishihara S, Ishola A, Jayachandran S, Jin Y, Jin Z, Ko F, Kulkarni P, Lai Z, Lee B, Levites Y, Li J, Lotz M, Macpherson L, Maerz T, Majano C, Malfait AM, Martone M, Mehta B, Miller R, Miller R, Muhammad A, Newton M, Obeidat A, Olmer M, Orange D, Otero M, Otto K, Patterson F, Pela M, Perry S, Price T, Priester S, Prieto H, Ray R, Ren D, Dasilva MR, Roberts A, Ronan E, Ruiz O, Smith S, Gonzalez MS, Southern K, Stover J, Strinden M, Swahn H, Tappan S, Sanchez LT, Tumanov A, Vivanco-Estela A, Wagenaar J, Wang L, Worley K, Wythe J, Yan J, Zou Y, Akopian AN. Identification of sensory fiber types in mouse temporomandibular joint tissues. Sci Rep. 2025;15(1). doi:<a href="https://doi.org/10.1038/s41598-025-17508-x" target="_blank" rel="noopener">10.1038/s41598-025-17508-x</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40890331/" target="_blank" rel="noopener">40890331</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12402272/" target="_blank" rel="noopener">PMC12402272</a>.</li>
<li>Copits BA, Curatolo M, Dougherty PM, Gereau RW, Luo W, Martone M, Olausson H, Price TJ, Renthal W, Woolf CJ, Zhao G. Human pain neuroscience and the next generation of pain therapeutics. Neuron. 2025;113(9):1304-1306. doi:<a href="https://doi.org/10.1016/j.neuron.2025.04.005" target="_blank" rel="noopener">10.1016/j.neuron.2025.04.005</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40339567/" target="_blank" rel="noopener">40339567</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12279253/" target="_blank" rel="noopener">PMC12279253</a>.</li>
<li>Fedor BA, Torres-Espin A, Vavrek R, Martone ME, Bixby JL, Gensel JC, Lemmon V, Grethe JS, Huie JR, Ferguson AR, Fouad K. A Community Effort to Develop Common Data Elements for Pre-Clinical Spinal Cord Injury Research. Neurotrauma Reports. 2025;6(1):391-401. doi:<a href="https://doi.org/10.1089/neur.2025.0021" target="_blank" rel="noopener">10.1089/neur.2025.0021</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40918992/" target="_blank" rel="noopener">40918992</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12408885/" target="_blank" rel="noopener">PMC12408885</a>.</li>
<li>Goth F, Alves R, Braun M, Castro LJ, Chourdakis G, Christ S, Cohen J, Druskat S, Erxleben F, Grad JN, Hagdorn M, Hodges T, Juckeland G, Kempf D, Lamprecht AL, Linxweiler J, Löffler F, Martone M, Schwarzmeier M, Seibold H, Thiele JP, von Waldow H, Wittke S. Foundational Competencies and Responsibilities of a Research Software Engineer: Current State and Suggestions for Future Directions. F1000Res. 2025;13:1429. doi:<a href="https://doi.org/10.12688/f1000research.157778.2" target="_blank" rel="noopener">10.12688/f1000research.157778.2</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40950244/" target="_blank" rel="noopener">40950244</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12426816/" target="_blank" rel="noopener">PMC12426816</a>.</li>
<li>Haelterman NA, Akopian AN, Allen KD, Cruz-Almeida Y, Donnelly CR, Lee B, Lenzi R, Malfait AM, Mancini M, Martone ME, Wagenaar JB, Worley KC. Designing and implementing solution-oriented team science initiatives—a chronic pain example. Front. Pain Res.. 2025;6. doi:<a href="https://doi.org/10.3389/fpain.2025.1669072" target="_blank" rel="noopener">10.3389/fpain.2025.1669072</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41477302/" target="_blank" rel="noopener">41477302</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12748165/" target="_blank" rel="noopener">PMC12748165</a>.</li>
<li>Imam FT, Gillespie TH, Ziogas I, Surles-Zeigler MC, Tappan S, Ozyurt BI, Boline J, de Bono B, Grethe JS, Martone ME. Developing a multiscale neural connectivity knowledgebase of the autonomic nervous system. Front. Neuroinform.. 2025;19. doi:<a href="https://doi.org/10.3389/fninf.2025.1541184" target="_blank" rel="noopener">10.3389/fninf.2025.1541184</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40162160/" target="_blank" rel="noopener">40162160</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11949889/" target="_blank" rel="noopener">PMC11949889</a>.</li>
<li>Kohrs FE, Drude N, Bandrowski A, Weissgerber TL. Ten simple rules for being a co-author on a many-author non-empirical paper. PLoS Comput Biol. 2025;21(8):e1013317. doi:<a href="https://doi.org/10.1371/journal.pcbi.1013317" target="_blank" rel="noopener">10.1371/journal.pcbi.1013317</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40811760/" target="_blank" rel="noopener">40811760</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12352870/" target="_blank" rel="noopener">PMC12352870</a>.</li>
<li>Newton MD, Lammlin L, Gonzalez-Nolde S, Howser S, Smith I, Stasikelis L, Knights AJ, Akopian A, Allen K, Almarza A, Arenkiel B, Aslam M, Ayaz B, Bae Y, Paula BBD, Bandrowski A, Boada MD, Boccanfuso J, Boline J, Cai D, Carpio DL, Caudle R, Cela R, Chen Y, Chen R, Constantinescu B, Cruz-Almeida Y, Dolwick MF, Donnelly C, Dou Z, Emrick J, Ernberg M, Freburg-Hoffmeister D, Friedman J, Fullam S, Gaire J, Gandhi A, Geraghty T, Goolsby B, Greene S, Haelterman N, Huo Z, Iadarola M, Ishihara S, Jayachandran S, Jin Z, Johnson A, Ko F, Lai Z, Lee B, Levites Y, Leynes C, Li J, Lotz M, Macpherson L, Maerz T, Majano C, Malfait AM, Martone M, Mears S, Mehta B, Miley E, Miller R, Miller R, Newton M, Obeidat A, Oh S, Olmer M, Orange D, Otero M, Otto K, Patterson F, Pela M, Perez D, Perry S, Price T, Prieto H, Ray R, Ren D, Ribeiro Dasilva M, Roberts A, Ronan E, Ruiz O, Smith S, Soccorro Gonzalez M, Southern K, Stover J, Strinden M, Swahn H, Tantry E, Tappan S, Villalba Silva C, Vivanco-Estella A, Vroman R, Wagenaar J, Wang L, Worley K, Wythe J, Yan J, Younis J, Maerz T. A standardized, open-source, portable model for noninvasive joint injury in mice. Osteoarthritis and Cartilage Open. 2025;7(4):100679. doi:<a href="https://doi.org/10.1016/j.ocarto.2025.100679" target="_blank" rel="noopener">10.1016/j.ocarto.2025.100679</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/41333522/" target="_blank" rel="noopener">41333522</a>.</li>
<li>Ozyurt IB, Bandrowski A. Automatic detection and extraction of key resources from tables in biomedical papers. BioData Mining. 2025;18(1). doi:<a href="https://doi.org/10.1186/s13040-025-00438-9" target="_blank" rel="noopener">10.1186/s13040-025-00438-9</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40114222/" target="_blank" rel="noopener">40114222</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11924859/" target="_blank" rel="noopener">PMC11924859</a>.</li>
<li>Piekniewska A, Roelandse M, Lloyd KCK, Korf I, Voss SR, de Castro G, Magnani DM, Varga Z, James-Zorn C, Horb M, Grethe JS, Bandrowski A. Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact. PLoS One. 2025;20(8):e0327344. doi:<a href="https://doi.org/10.1371/journal.pone.0327344" target="_blank" rel="noopener">10.1371/journal.pone.0327344</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40802618/" target="_blank" rel="noopener">40802618</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12349098/" target="_blank" rel="noopener">PMC12349098</a>.</li>
<li>Ruiz OE, Wagenaar JB, Mehta B, Ziogas I, Swanson L, Worley KC, Cruz-Almeida Y, Johnson AJ, Boline J, Boccanfuso J, Martone ME, Haelterman NA. A guide to developing harmonized research workflows in a team science context. Experimental Neurology. 2025;392:115333. doi:<a href="https://doi.org/10.1016/j.expneurol.2025.115333" target="_blank" rel="noopener">10.1016/j.expneurol.2025.115333</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40482901/" target="_blank" rel="noopener">40482901</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12233188/" target="_blank" rel="noopener">PMC12233188</a>.</li>
<li>Sheoran A, Fond KA, Davis LM, Huie JR, Vavrek R, Axtman PJ, Lemmon V, Bixby JL, Visser U, Gensel JC, Fouad K, Ferguson AR, Grethe JS, Bandrowski A, Martone ME, Torres-Espin A. Data reporting quality and semantic interoperability increase with community-based data elements (CoDEs). Analysis of the open data commons for spinal cord injury (ODC-SCI). Experimental Neurology. 2025;385:115100. doi:<a href="https://doi.org/10.1016/j.expneurol.2024.115100" target="_blank" rel="noopener">10.1016/j.expneurol.2024.115100</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39647573/" target="_blank" rel="noopener">39647573</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12308985/" target="_blank" rel="noopener">PMC12308985</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2024 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(14)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Ayoubi R, Ryan J, Gonzalez Bolivar S, Alende C, Ruiz Moleon V, Fotouhi M, Alqazzaz M, Southern K, Alshafie W, Baker MR, Ball AR, Callahan D, Cooper JA, Crosby K, Harvey KJ, Houston DW, Kumaran R, Rego M, Schofield C, Wu H, Biddle MS, Brown CM, Kahn RA, Bandrowski A, Virk HS, Edwards AM, McPherson PS, Laflamme C. A consensus platform for antibody characterization. Nat Protoc. 2024;20(6):1509-1545. doi:<a href="https://doi.org/10.1038/s41596-024-01095-8" target="_blank" rel="noopener">10.1038/s41596-024-01095-8</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39690206/" target="_blank" rel="noopener">39690206</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC13054593/" target="_blank" rel="noopener">PMC13054593</a>.</li>
<li>Biddle M, Stylianou P, Rekas M, Wright A, Sousa J, Ruddy D, Stefana MI, Kmiecik K, Bandrowski A, Kahn RA, Laflamme C, Krockow EM, Virk HS. Improving the integrity and reproducibility of research that uses antibodies: a technical, data sharing, behavioral and policy challenge. mAbs. 2024;16(1). doi:<a href="https://doi.org/10.1080/19420862.2024.2323706" target="_blank" rel="noopener">10.1080/19420862.2024.2323706</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38444344/" target="_blank" rel="noopener">38444344</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10936606/" target="_blank" rel="noopener">PMC10936606</a>.</li>
<li>Cruz-Almeida Y, Mehta B, Haelterman NA, Johnson AJ, Heiting C, Ernberg M, Orange D, Lotz M, Boccanfuso J, Smith SB, Pela M, Boline J, Otero M, Allen K, Perez D, Donnelly C, Almarza A, Olmer M, Balkhi H, Wagenaar J, Martone M. Clinical and biobehavioral phenotypic assessments and data harmonization for the RE-JOIN research consortium: Recommendations for common data element selection. Neurobiology of Pain. 2024;16:100163. doi:<a href="https://doi.org/10.1016/j.ynpai.2024.100163" target="_blank" rel="noopener">10.1016/j.ynpai.2024.100163</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39281853/" target="_blank" rel="noopener">39281853</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11399706/" target="_blank" rel="noopener">PMC11399706</a>.</li>
<li>Fouad K, Vavrek R, Surles-Zeigler MC, Huie JR, Radabaugh HL, Gurkoff GG, Visser U, Grethe JS, Martone ME, Ferguson AR, Gensel JC, Torres-Espin A. A practical guide to data management and sharing for biomedical laboratory researchers. Experimental Neurology. 2024;378:114815. doi:<a href="https://doi.org/10.1016/j.expneurol.2024.114815" target="_blank" rel="noopener">10.1016/j.expneurol.2024.114815</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38762093/" target="_blank" rel="noopener">38762093</a>.</li>
<li>Imam FT, Gillespie TH, Ziogas I, Surles-Zeigler MC, Tappan S, Ozyurt BI, Boline J, de Bono B, Grethe JS, Martone ME. Developing a Multiscale Neural Connectivity Knowledgebase of the Autonomic Nervous System [Preprint]. bioRxiv; 2024. doi:<a href="https://doi.org/10.1101/2024.10.25.620360" target="_blank" rel="noopener">10.1101/2024.10.25.620360</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39651195/" target="_blank" rel="noopener">39651195</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11623530/" target="_blank" rel="noopener">PMC11623530</a>.</li>
<li>Kahn RA, Virk H, Laflamme C, Houston DW, Polinski NK, Meijers R, Levey AI, Saper CB, Errington TM, Turn RE, Bandrowski A, Trimmer JS, Rego M, Freedman LP, Ferrara F, Bradbury AR, Cable H, Longworth S. Antibody characterization is critical to enhance reproducibility in biomedical research. eLife. 2024;13. doi:<a href="https://doi.org/10.7554/elife.100211" target="_blank" rel="noopener">10.7554/elife.100211</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39140332/" target="_blank" rel="noopener">39140332</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11324233/" target="_blank" rel="noopener">PMC11324233</a>.</li>
<li>Martone ME. The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR. Front. Neuroinform.. 2024;17. doi:<a href="https://doi.org/10.3389/fninf.2023.1276407" target="_blank" rel="noopener">10.3389/fninf.2023.1276407</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38250019/" target="_blank" rel="noopener">38250019</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10796549/" target="_blank" rel="noopener">PMC10796549</a>.</li>
<li>Ozyurt IB, Bandrowski A. Automatic Detection and Extraction of Key Resources from Tables in Biomedical Papers [Preprint]. bioRxiv; 2024. doi:<a href="https://doi.org/10.1101/2024.10.15.618379" target="_blank" rel="noopener">10.1101/2024.10.15.618379</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39464155/" target="_blank" rel="noopener">39464155</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11507667/" target="_blank" rel="noopener">PMC11507667</a>.</li>
<li>Piekniewska A, Anderson N, Roelandse M, Lloyd KCK, Korf I, Voss SR, de Castro G, Magnani DM, Varga Z, James-Zorn C, Horb M, Grethe JS, Bandrowski A. Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact [Preprint]. bioRxiv; 2024. doi:<a href="https://doi.org/10.1101/2024.01.15.575636" target="_blank" rel="noopener">10.1101/2024.01.15.575636</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38293091/" target="_blank" rel="noopener">38293091</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10827057/" target="_blank" rel="noopener">PMC10827057</a>.</li>
<li>Puebla I, Ascoli G, Blume J, Chodacki J, Finnell J, Kennedy DN, Mair B, Martone ME, Wittenberg J, Poline JB. Ten simple rules for recognizing data and software contributions in hiring, promotion and tenure [Preprint]. Center for Open Science; 2024. doi:<a href="https://doi.org/10.31219/osf.io/u3c4y" target="_blank" rel="noopener">10.31219/osf.io/u3c4y</a>.</li>
<li>Puebla I, Ascoli GA, Blume J, Chodacki J, Finnell J, Kennedy DN, Mair B, Martone ME, Wittenberg J, Poline JB. Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. PLoS Comput Biol. 2024;20(8):e1012296. doi:<a href="https://doi.org/10.1371/journal.pcbi.1012296" target="_blank" rel="noopener">10.1371/journal.pcbi.1012296</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39116028/" target="_blank" rel="noopener">39116028</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11309403/" target="_blank" rel="noopener">PMC11309403</a>.</li>
<li>Schrade L, Mah N, Bandrowski A, Chen Y, Dewender J, Diecke S, Hiepen C, Lancaster MA, Marques-Bonet T, Martinez S, Mueller SC, Navara C, Prigione A, Seltmann S, Sochacki J, Sutcliffe MA, Zywitza V, Hildebrandt TB, Kurtz A. A Standardized Nomenclature Design for Systematic Referencing and Identification of Animal Cellular Material. Animals. 2024;14(11):1541. doi:<a href="https://doi.org/10.3390/ani14111541" target="_blank" rel="noopener">10.3390/ani14111541</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38891588/" target="_blank" rel="noopener">38891588</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11171381/" target="_blank" rel="noopener">PMC11171381</a>.</li>
<li>Tom G, Anita B. Do Organisms Need an Impact Factor? Other Use Cases for PIDs. 2024. doi:<a href="https://doi.org/10.48813/975a-pd17" target="_blank" rel="noopener">10.48813/975a-pd17</a>.</li>
<li>Weissgerber TL, Gazda MA, Nilsonne G, ter Riet G, Cobey KD, Prieß-Buchheit J, Noro J, Schulz R, Tijdink JK, Bobrov E, Bannach-Brown A, Franzen DL, Moschini U, Naudet F, Mansmann U, Salholz-Hillel M, Bandrowski A, Macleod MR. Understanding the provenance and quality of methods is essential for responsible reuse of FAIR data. Nat Med. 2024;30(5):1220-1221. doi:<a href="https://doi.org/10.1038/s41591-024-02879-x" target="_blank" rel="noopener">10.1038/s41591-024-02879-x</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38514869/" target="_blank" rel="noopener">38514869</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12939560/" target="_blank" rel="noopener">PMC12939560</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2023 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(7)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D’Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023;21(6):e3002133. doi:<a href="https://doi.org/10.1371/journal.pbio.3002133" target="_blank" rel="noopener">10.1371/journal.pbio.3002133</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37390046/" target="_blank" rel="noopener">37390046</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10313015/" target="_blank" rel="noopener">PMC10313015</a>.</li>
<li>Kleven H, Gillespie TH, Zehl L, Dickscheid T, Bjaalie JG, Martone ME, Leergaard TB. AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures [Preprint]. bioRxiv; 2023. doi:<a href="https://doi.org/10.1101/2023.01.22.525049" target="_blank" rel="noopener">10.1101/2023.01.22.525049</a>.</li>
<li>Kleven H, Gillespie TH, Zehl L, Dickscheid T, Bjaalie JG, Martone ME, Leergaard TB. AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Sci Data. 2023;10(1). doi:<a href="https://doi.org/10.1038/s41597-023-02389-4" target="_blank" rel="noopener">10.1038/s41597-023-02389-4</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37495585/" target="_blank" rel="noopener">37495585</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10372146/" target="_blank" rel="noopener">PMC10372146</a>.</li>
<li>Piękniewska A, Haak LL, Henderson D, McNeill K, Bandrowski A, Seger Y. Establishing an early indicator for data sharing and reuse. Learned Publishing. 2023;37(1):22-29. doi:<a href="https://doi.org/10.1002/leap.1586" target="_blank" rel="noopener">10.1002/leap.1586</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40800001/" target="_blank" rel="noopener">40800001</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12341665/" target="_blank" rel="noopener">PMC12341665</a>.</li>
<li>Roelandse M, Ozyurt IB, Evanko D, Bandrowski A. Assessing the Effectiveness of SciScore in Supporting the Reproducibility of Scientific Research. Sci Editor. 2023. doi:<a href="https://doi.org/10.36591/se-d-4602-15" target="_blank" rel="noopener">10.36591/se-d-4602-15</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40791864/" target="_blank" rel="noopener">40791864</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12338114/" target="_blank" rel="noopener">PMC12338114</a>.</li>
<li>Sheoran A, Martone M, Torres-Espin A. Protocol for Systematic Analysis Data Elements v1 [Preprint]. ZappyLab, Inc.; 2023. doi:<a href="https://doi.org/10.17504/protocols.io.5qpvo3wodv4o/v1" target="_blank" rel="noopener">10.17504/protocols.io.5qpvo3wodv4o/v1</a>.</li>
<li>Surles-Zeigler MC, Sincomb T, Dixon CE, Imam F, Gillespie T, Grethe JS, Ferguson AR, Martone ME. Brain Injury Knowledge Ontology (BIKO) for traumatic brain injury: Formalizing concepts and methods used in translational traumatic brain injury research [Preprint]. bioRxiv; 2023. doi:<a href="https://doi.org/10.1101/2023.10.29.564650" target="_blank" rel="noopener">10.1101/2023.10.29.564650</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2022 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(20)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Abrams MB, Bjaalie JG, Das S, Egan GF, Ghosh SS, Goscinski WJ, Grethe JS, Kotaleski JH, Ho ETW, Kennedy DN, Lanyon LJ, Leergaard TB, Mayberg HS, Milanesi L, Mouček R, Poline JB, Roy PK, Strother SC, Tang TB, Tiesinga P, Wachtler T, Wójcik DK, Martone ME. Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinform. 2022;20(1):37-38. doi:<a href="https://doi.org/10.1007/s12021-021-09522-x" target="_blank" rel="noopener">10.1007/s12021-021-09522-x</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/33851344/" target="_blank" rel="noopener">33851344</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9629304/" target="_blank" rel="noopener">PMC9629304</a>.</li>
<li>Abrams MB, Bjaalie JG, Das S, Egan GF, Ghosh SS, Goscinski WJ, Grethe JS, Kotaleski JH, Ho ETW, Kennedy DN, Lanyon LJ, Leergaard TB, Mayberg HS, Milanesi L, Mouček R, Poline JB, Roy PK, Strother SC, Tang TB, Tiesinga P, Wachtler T, Wójcik DK, Martone ME. A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinform. 2022;20(1):25-36. doi:<a href="https://doi.org/10.1007/s12021-020-09509-0" target="_blank" rel="noopener">10.1007/s12021-020-09509-0</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/33506383/" target="_blank" rel="noopener">33506383</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9036053/" target="_blank" rel="noopener">PMC9036053</a>.</li>
<li>Bandrowski A, Pairish M, Eckmann P, Grethe J, Martone ME. The Antibody Registry: ten years of registering antibodies. Nucleic Acids Research. 2022;51(D1):D358-D367. doi:<a href="https://doi.org/10.1093/nar/gkac927" target="_blank" rel="noopener">10.1093/nar/gkac927</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36370112/" target="_blank" rel="noopener">36370112</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9825422/" target="_blank" rel="noopener">PMC9825422</a>.</li>
<li>Chou A, Torres-Espín A, Huie JR, Krukowski K, Lee S, Nolan A, Guglielmetti C, Hawkins BE, Chaumeil MM, Manley GT, Beattie MS, Bresnahan JC, Martone ME, Grethe JS, Rosi S, Ferguson AR. Empowering Data Sharing and Analytics through the Open Data Commons for Traumatic Brain Injury Research. Neurotrauma Reports. 2022;3(1). doi:<a href="https://doi.org/10.1089/neur.2021.0061" target="_blank" rel="noopener">10.1089/neur.2021.0061</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35403104/" target="_blank" rel="noopener">35403104</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC8985540/" target="_blank" rel="noopener">PMC8985540</a>.</li>
<li>Ellisman M, Bushong E, Kim KY, Martone M. Mouse Heart Perfusion - Ultrastructural Analysis (Using Karnovsky&#39;s Fixative) v1 [Preprint]. Springer Science and Business Media LLC; 2022. doi:<a href="https://doi.org/10.17504/protocols.io.4r3l2o7k3v1y/v1" target="_blank" rel="noopener">10.17504/protocols.io.4r3l2o7k3v1y/v1</a>.</li>
<li>Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Ahooyi TM, Jenkins SL, Taylor D, Bologa CG, Yang JJ, Binder JL, Kumar P, Lambert CG, Grethe JS, Wenger E, Oprea TI, de Bono B, Ma’ayan A. ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects [Preprint]. bioRxiv; 2022. doi:<a href="https://doi.org/10.1101/2022.09.15.508198" target="_blank" rel="noopener">10.1101/2022.09.15.508198</a>.</li>
<li>Gillespie TH, Tripathy SJ, Sy MF, Martone ME, Hill SL. The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. Neuroinform. 2022;20(3):793-809. doi:<a href="https://doi.org/10.1007/s12021-022-09566-7" target="_blank" rel="noopener">10.1007/s12021-022-09566-7</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35267146/" target="_blank" rel="noopener">35267146</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9547803/" target="_blank" rel="noopener">PMC9547803</a>.</li>
<li>Hawrylycz MJ, Martone ME, Hof PR, Lein ES, Regev A, Ascoli GAA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Kim Y, Liu Y, Miller JA, Mitra PP, Mukamel E, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Ropelewski A, Scheuermann RH, Tan SZK, Tickle T, Tilgner H, Varghese M, Wester B, White O, Aevermann B, Allemang D, Ament S, Athey TL, Baker PM, Baker C, Baker KS, Bandrowski A, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Halchenko YO, Harris N, Herb BR, Hintiryan H, Hood G, Horvath S, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Markuhar A, Mathews J, Mathews KL, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Ng L, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Thompson CL, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zeng H, Zhang GQ, Zhang YR, Zheng JW, Zingg B. The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide [Preprint]. bioRxiv; 2022. doi:<a href="https://doi.org/10.1101/2022.10.26.513573" target="_blank" rel="noopener">10.1101/2022.10.26.513573</a>.</li>
<li>Kumar A, Crowley A, Queder N, Poline J, Ghosh SS, Kennedy D, Grethe JS, Helmer KG, Keator DB. The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project [version 2; peer review: 1 approved with reservations, 1 not approved]. F1000Res. 2022;11:228. doi:<a href="https://doi.org/10.12688/f1000research.108008.2" target="_blank" rel="noopener">10.12688/f1000research.108008.2</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39185142/" target="_blank" rel="noopener">39185142</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11344200/" target="_blank" rel="noopener">PMC11344200</a>.</li>
<li>Kumar A, Crowley A, Queder N, Poline J, Ghosh SS, Kennedy D, Grethe JS, Helmer KG, Keator DB. The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project. F1000Res. 2022;11:228. doi:<a href="https://doi.org/10.12688/f1000research.108008.1" target="_blank" rel="noopener">10.12688/f1000research.108008.1</a>.</li>
<li>Martone ME, Nakamura R. Changing the Culture on Data Management and Sharing: Overview and Highlights from a Workshop Held by the National Academies of Sciences, Engineering, and Medicine. Harvard Data Science Review. 2022;4(3). doi:<a href="https://doi.org/10.1162/99608f92.44975b62" target="_blank" rel="noopener">10.1162/99608f92.44975b62</a>.</li>
<li>Martone ME. A decade of GigaScience: the importance of community organizations for open and FAIR efforts in neuroinformatics. GigaScience. 2022;11. doi:<a href="https://doi.org/10.1093/gigascience/giac060" target="_blank" rel="noopener">10.1093/gigascience/giac060</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35701370/" target="_blank" rel="noopener">35701370</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9197677/" target="_blank" rel="noopener">PMC9197677</a>.</li>
<li>Menke J, Eckmann P, Ozyurt IB, Roelandse M, Anderson N, Grethe J, Gamst A, Bandrowski A. Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality. J Med Internet Res. 2022;24(6):e37324. doi:<a href="https://doi.org/10.2196/37324" target="_blank" rel="noopener">10.2196/37324</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35759334/" target="_blank" rel="noopener">35759334</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9274430/" target="_blank" rel="noopener">PMC9274430</a>.</li>
<li>Menke J, Eckmann P, Ozyurt IB, Roelandse M, Anderson N, Grethe J, Gamst A, Bandrowski A. Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality (Preprint) [Preprint]. JMIR Publications Inc.; 2022. doi:<a href="https://doi.org/10.2196/preprints.37324" target="_blank" rel="noopener">10.2196/preprints.37324</a>.</li>
<li>Ochsner SA, Pillich RT, Rawool D, Grethe JS, McKenna NJ. Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience. 2022;25(7):104581. doi:<a href="https://doi.org/10.1016/j.isci.2022.104581" target="_blank" rel="noopener">10.1016/j.isci.2022.104581</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35832893/" target="_blank" rel="noopener">35832893</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9272393/" target="_blank" rel="noopener">PMC9272393</a>.</li>
<li>Poline JB, Kennedy DN, Sommer FT, Ascoli GA, Van Essen DC, Ferguson AR, Grethe JS, Hawrylycz MJ, Thompson PM, Poldrack RA, Ghosh SS, Keator DB, Athey TL, Vogelstein JT, Mayberg HS, Martone ME. Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. Neuroinform. 2022;20(2):507-512. doi:<a href="https://doi.org/10.1007/s12021-021-09557-0" target="_blank" rel="noopener">10.1007/s12021-021-09557-0</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35061216/" target="_blank" rel="noopener">35061216</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9300762/" target="_blank" rel="noopener">PMC9300762</a>.</li>
<li>Surles-Zeigler MC, Sincomb T, Gillespie TH, de Bono B, Bresnahan J, Mawe GM, Grethe JS, Tappan S, Heal M, Martone ME. Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Front. Neuroinform.. 2022;16. doi:<a href="https://doi.org/10.3389/fninf.2022.819198" target="_blank" rel="noopener">10.3389/fninf.2022.819198</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36090663/" target="_blank" rel="noopener">36090663</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9449460/" target="_blank" rel="noopener">PMC9449460</a>.</li>
<li>Tabak L, Jorgenson L, Martone M, Nakamura R. Conversation with Dr. Lawrence Tabak and Dr. Lyric Jorgenson on the NIH Perspective on Data Sharing and Management. Harvard Data Science Review. 2022. doi:<a href="https://doi.org/10.1162/99608f92.b9e4ceec" target="_blank" rel="noopener">10.1162/99608f92.b9e4ceec</a>.</li>
<li>Torres-Espín A, Almeida CA, Chou A, Huie JR, Chiu M, Vavrek R, Sacramento J, Orr MB, Gensel JC, Grethe JS, Martone ME, Fouad K, Ferguson AR, Alilain W, Bacon M, Batty N, Beattie M, Bresnahan J, Burnside E, Busch S, Carpenter R, Quijorna IF, Guo X, Haggerty A, Haroon S, Harris J, Jakeman L, Jones L, Kleitman N, Kopper T, Lane M, Magana F, Magnuson D, Maldonado I, May V, McFarlane K, Morioka K, Oudega M, Pascual PL, Poline JB, Rosenzweig E, Schmidt E, Tetzlaff W, Zholudeva L. Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). Neuroinform. 2022;20(1):203-219. doi:<a href="https://doi.org/10.1007/s12021-021-09533-8" target="_blank" rel="noopener">10.1007/s12021-021-09533-8</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/34347243/" target="_blank" rel="noopener">34347243</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9537193/" target="_blank" rel="noopener">PMC9537193</a>.</li>
<li>de Bono B, Gillespie T, Surles-Zeigler MC, Kokash N, Grethe JS, Martone M. Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. Front. Physiol.. 2022;13. doi:<a href="https://doi.org/10.3389/fphys.2022.795303" target="_blank" rel="noopener">10.3389/fphys.2022.795303</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35547570/" target="_blank" rel="noopener">35547570</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC9083405/" target="_blank" rel="noopener">PMC9083405</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2021 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(8)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Bandrowski A, Grethe JS, Pilko A, Gillespie T, Pine G, Patel B, Surles-Zeigler M, Martone ME. SPARC Data Structure: Rationale and Design of a FAIR Standard for Biomedical Research Data [Preprint]. bioRxiv; 2021. doi:<a href="https://doi.org/10.1101/2021.02.10.430563" target="_blank" rel="noopener">10.1101/2021.02.10.430563</a>.</li>
<li>Chou A, Espin AT, Huie JR, Krukowski K, Lee S, Nolan A, Guglielmetti C, Hawkins BE, Chaumeil MM, Manley GT, Beattie MS, Bresnahan JC, Martone ME, Grethe JS, Rosi S, Ferguson AR. Open Data Commons for Preclinical Traumatic Brain Injury Research: Empowering Data Sharing and Big Data Analytics [Preprint]. bioRxiv; 2021. doi:<a href="https://doi.org/10.1101/2021.03.15.435178" target="_blank" rel="noopener">10.1101/2021.03.15.435178</a>.</li>
<li>Hsu CN, Chang CH, Poopradubsil T, Lo A, William KA, Lin KW, Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput Biol. 2021;17(5):e1008967. doi:<a href="https://doi.org/10.1371/journal.pcbi.1008967" target="_blank" rel="noopener">10.1371/journal.pcbi.1008967</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/34043624/" target="_blank" rel="noopener">34043624</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC8189493/" target="_blank" rel="noopener">PMC8189493</a>.</li>
<li>Murphy F, Bar-Sinai M, Martone ME. A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles. PLoS ONE. 2021;16(7):e0253538. doi:<a href="https://doi.org/10.1371/journal.pone.0253538" target="_blank" rel="noopener">10.1371/journal.pone.0253538</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/34242248/" target="_blank" rel="noopener">34242248</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC8270168/" target="_blank" rel="noopener">PMC8270168</a>.</li>
<li>Murphy F, Bar-Sinai M, Martone ME. A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles [Preprint]. bioRxiv; 2021. doi:<a href="https://doi.org/10.1101/2021.01.19.427362" target="_blank" rel="noopener">10.1101/2021.01.19.427362</a>.</li>
<li>Osanlouy M, Bandrowski A, de Bono B, Brooks D, Cassarà AM, Christie R, Ebrahimi N, Gillespie T, Grethe JS, Guercio LA, Heal M, Lin M, Kuster N, Martone ME, Neufeld E, Nickerson DP, Soltani EG, Tappan S, Wagenaar JB, Zhuang K, Hunter PJ. The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. Front. Physiol.. 2021;12. doi:<a href="https://doi.org/10.3389/fphys.2021.693735" target="_blank" rel="noopener">10.3389/fphys.2021.693735</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/34248680/" target="_blank" rel="noopener">34248680</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC8265045/" target="_blank" rel="noopener">PMC8265045</a>.</li>
<li>Osanlouy M, Bandrowski A, de Bono B, Brooks D, Cassarà AM, Christie R, Ebrahimi N, Gillespie T, Grethe JS, Guercio LA, Heal M, Lin M, Kuster N, Martone ME, Neufeld E, Nickerson DP, Soltani EG, Tappan S, Wagenaar JB, Zhuang K, Hunter PJ. The SPARC DRC: Building a resource for the autonomic nervous system community [Preprint]. bioRxiv; 2021. doi:<a href="https://doi.org/10.1101/2021.04.01.438136" target="_blank" rel="noopener">10.1101/2021.04.01.438136</a>.</li>
<li>Surles-Zeigler MC, Sincomb T, Gillespie TH, de Bono B, Bresnahan J, Mawe GM, Grethe JS, Tappan S, Heal M, Martone ME. Extending and using anatomical vocabularies in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program [Preprint]. bioRxiv; 2021. doi:<a href="https://doi.org/10.1101/2021.11.15.467961" target="_blank" rel="noopener">10.1101/2021.11.15.467961</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2020 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(10)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Adkins RS, Aldridge AI, Allen S, Ament SA, An X, Armand E, Ascoli GA, Bakken TE, Bandrowski A, Banerjee S, Barkas N, Bartlett A, Bateup HS, Behrens MM, Berens P, Berg J, Bernabucci M, Bernaerts Y, Bertagnolli D, Biancalani T, Boggeman L, Booeshaghi AS, Bowman I, Bravo HC, Cadwell CR, Callaway EM, Carlin B, O'Connor C, Carter R, Casper T, Castanon RG, Castro JR, Chance RK, Chatterjee A, Chen H, Chun J, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, D'Orazi FD, Daigle TL, Dalley R, Dee N, Degatano K, Dichter B, Diep D, Ding L, Ding SL, Dominguez B, Dong HW, Dong W, Dougherty EL, Dudoit S, Ecker JR, Eichhorn SW, Fang R, Felix V, Feng G, Feng Z, Fischer S, Fitzpatrick C, Fong O, Foster NN, Galbavy W, Gee JC, Ghosh SS, Giglio M, Gillespie TH, Gillis J, Goldman M, Goldy J, Gong H, Gou L, Grauer M, Halchenko YO, Harris JA, Hartmanis L, Hatfield JT, Hawrylycz M, Helba B, Herb BR, Hertzano R, Hintiryan H, Hirokawa KE, Hockemeyer D, Hodge RD, Hood G, Horwitz GD, Hou X, Hu L, Hu Q, Huang ZJ, Huo B, Ito-Cole T, Jacobs M, Jia X, Jiang S, Jiang T, Jiang X, Jin X, Jorstad NL, Kalmbach BE, Kancherla J, Keene CD, Kelly K, Khajouei F, Kharchenko PV, Kim G, Ko AL, Kobak D, Konwar K, Kramer DJ, Krienen FM, Kroll M, Kuang X, Kuo HC, Lake BB, Larsen R, Lathia K, Laturnus S, Lee AY, Lee CT, Lee KF, Lein ES, Lesnar P, Li A, Li X, Li X, Li YE, Li Y, Li Y, Lim B, Linnarsson S, Liu CS, Liu H, Liu L, Lucero JD, Luo C, Luo Q, Macosko EZ, Mahurkar A, Martone ME, Matho KS, McCarroll SA, McCracken C, McMillen D, Miranda E, Mitra PP, Miyazaki PA, Mizrachi J, Mok S, Mukamel EA, Mulherkar S, Nadaf NM, Naeemi M, Narasimhan A, Nery JR, Ng L, Ngai J, Nguyen TN, Nickel L, Nicovich PR, Niu SY, Ntranos V, Nunn M, Olley D, Orvis J, Osteen JK, Osten P, Owen SF, Pachter L, Palaniswamy R, Palmer CR, Pang Y, Peng H, Pham T, Pinto-Duarte A, Plongthongkum N, Poirion O, Preissl S, Purdom E, Qu L, Rashid M, Reed NM, Regev A, Ren B, Ren M, Rimorin C, Risso D, Rivkin AC, Muñoz-Castañeda R, Romanow WJ, Ropelewski AJ, Roux de Bézieux H, Ruan Z, Sandberg R, Savoia S, Scala F, Schor M, Shen E, Siletti K, Smith JB, Smith K, Somasundaram S, Song Y, Sorensen SA, Stafford DA, Street K, Sulc J, Sunkin S, Svensson V, Tan P, Tan ZH, Tasic B, Thompson C, Tian W, Tickle TL, Tieu M, Ting JT, Tolias AS, Torkelson A, Tung H, Vaishnav ED, Van den Berge K, van Velthoven CTJ, Vanderburg CR, Veldman MB, Vu M, Wakeman W, Wang P, Wang Q, Wang X, Wang Y, Wang Y, Welch JD, White O, Williams E, Xie F, Xie P, Xiong F, Yang XW, Yanny AM, Yao Z, Yin L, Yu Y, Yuan J, Zeng H, Zhang K, Zhang M, Zhang Z, Zhao S, Zhao X, Zhou J, Zhuang X, Zingg B. A multimodal cell census and atlas of the mammalian primary motor cortex. . 2020. doi:<a href="https://doi.org/10.1101/2020.10.19.343129" target="_blank" rel="noopener">10.1101/2020.10.19.343129</a>.</li>
<li>Fouad K, Bixby JL, Callahan A, Grethe JS, Jakeman LB, Lemmon VP, Magnuson DSK, Martone ME, Nielson JL, Schwab JM, Taylor-Burds C, Tetzlaff W, Torres-Espin A, Ferguson AR, Alam S, Bacon M, Bambrick L, Basso M, Beattie M, Bresnahan J, Gensel J, Graham D, Grethe J, Russell Huie J, Jones L, Kabitzke P, Kleitman N, Kusiak A, Kwon B, Lederer R, MacLeod M, May V, Neff E, Rabchevsky S. FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research. Journal of Neurotrauma. 2020;37(6):831-838. doi:<a href="https://doi.org/10.1089/neu.2019.6674" target="_blank" rel="noopener">10.1089/neu.2019.6674</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/31608767/" target="_blank" rel="noopener">31608767</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7071068/" target="_blank" rel="noopener">PMC7071068</a>.</li>
<li>Garijo D, Ménager H, Hwang L, Trisovic A, Hucka M, Morrell T, Allen A. Nine Best Practices for Research Software Registries and Repositories: A Concise Guide. 2020 Dec.</li>
<li>Gillespie TH, Tripathy S, Sy MF, Martone ME, Hill SL. The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types [Preprint]. bioRxiv; 2020. doi:<a href="https://doi.org/10.1101/2020.09.01.278879" target="_blank" rel="noopener">10.1101/2020.09.01.278879</a>.</li>
<li>Hsu CN, Bandrowski AE, Gillespie TH, Udell J, Lin KW, Ozyurt IB, Grethe JS, Martone ME. Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts. Comput. Sci. Eng.. 2020;22(2):22-32. doi:<a href="https://doi.org/10.1109/mcse.2019.2952838" target="_blank" rel="noopener">10.1109/mcse.2019.2952838</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/40791297/" target="_blank" rel="noopener">40791297</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12338378/" target="_blank" rel="noopener">PMC12338378</a>.</li>
<li>Hsu CN, Chang CH, Poopradubsil T, Lo A, William KA, Lin KW, Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. Antibody Watch: Text Mining Antibody Specificity from the Literature. 2020 Aug.</li>
<li>Menke J, Roelandse M, Ozyurt B, Martone M, Bandrowski A. The Rigor and Transparency Index Quality Metric for Assessing Biological and Medical Science Methods. iScience. 2020;23(11):101698. doi:<a href="https://doi.org/10.1016/j.isci.2020.101698" target="_blank" rel="noopener">10.1016/j.isci.2020.101698</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/33196023/" target="_blank" rel="noopener">33196023</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7644557/" target="_blank" rel="noopener">PMC7644557</a>.</li>
<li>Menke J, Roelandse M, Ozyurt B, Martone M, Bandrowski A. Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods [Preprint]. bioRxiv; 2020. doi:<a href="https://doi.org/10.1101/2020.01.15.908111" target="_blank" rel="noopener">10.1101/2020.01.15.908111</a>.</li>
<li>Ozyurt IB, Bandrowski A, Grethe JS. Bio-AnswerFinder: A system to find answers to questions from biomedical texts. Database. 2020;2020. doi:<a href="https://doi.org/10.1093/database/baz137" target="_blank" rel="noopener">10.1093/database/baz137</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/31925435/" target="_blank" rel="noopener">31925435</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7053013/" target="_blank" rel="noopener">PMC7053013</a>.</li>
<li>Ozyurt IB. On the effectiveness of small, discriminatively pre-trained language representation models for biomedical text mining [Preprint]. bioRxiv; 2020. doi:<a href="https://doi.org/10.1101/2020.05.20.107003" target="_blank" rel="noopener">10.1101/2020.05.20.107003</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2019 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(14)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Abrams M, Bjaalie JG, Das S, Egan GF, Ghosh SS, Goscinski WJ, Grethe JS, Kotaleski JH, Ho ETW, Kennedy DN, Lanyon LJ, Leergaard TB, Mayberg H, Milanesi L, Mouček R, Poline JB, Roy PK, Tang TB, Tiesinga P, Wachtler T, Wójcik DK, Martone ME. A standards organization for Open and FAIR neuroscience: the International Neuroinformatics Coordinating Facility [Preprint]. Center for Open Science; 2019. doi:<a href="https://doi.org/10.31219/osf.io/3rt9b" target="_blank" rel="noopener">10.31219/osf.io/3rt9b</a>.</li>
<li>Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE. Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. eLife. 2019;8. doi:<a href="https://doi.org/10.7554/elife.41676" target="_blank" rel="noopener">10.7554/elife.41676</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30693867/" target="_blank" rel="noopener">30693867</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6351100/" target="_blank" rel="noopener">PMC6351100</a>.</li>
<li>Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. A data citation roadmap for scholarly data repositories. Sci Data. 2019;6(1). doi:<a href="https://doi.org/10.1038/s41597-019-0031-8" target="_blank" rel="noopener">10.1038/s41597-019-0031-8</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30971690/" target="_blank" rel="noopener">30971690</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6472386/" target="_blank" rel="noopener">PMC6472386</a>.</li>
<li>Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot [Preprint]. PLoS Computational Biology; 2019. doi:10.1371/journal.pcbi.1007128.</li>
<li>Hsu C, Bandrowski A, Gillespie T, Udell J, Lin K, Özyurt İB, Grethe JS, Martone ME. Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software and Other Digital Artifacts. . 2019. doi:<a href="https://doi.org/10.5281/zenodo.3241632" target="_blank" rel="noopener">10.5281/zenodo.3241632</a>.</li>
<li>Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. Everything matters: The repronim perspective on reproducible neuroimaging. Front. Neuroinform.. 2019;13. doi:<a href="https://doi.org/10.3389/fninf.2019.00001" target="_blank" rel="noopener">10.3389/fninf.2019.00001</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30792636/" target="_blank" rel="noopener">30792636</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6374302/" target="_blank" rel="noopener">PMC6374302</a>.</li>
<li>Lin KW, Bandrowski A, Gillespie T, Go J, Hagstrom S, Hsu CN, Ozyurt I, Grethe J, Martone M. MON-176 Making Informed Decisions on the Selection of Antibodies Using dkNET (NIDDK Information Network). Journal of the Endocrine Society. 2019 Apr.</li>
<li>Martone M, Aghazarian M. The Scholarly Commons. The Serials Librarian. 2019;76(1-4):220-224. doi:<a href="https://doi.org/10.1080/0361526x.2019.1587699" target="_blank" rel="noopener">10.1080/0361526x.2019.1587699</a>.</li>
<li>Ozyurt IB, Grethe J. Iterative document retrieval via deep learning approaches for biomedical question answering. In: 2019 15th International Conference on eScience (eScience). 2019:533-538. doi:<a href="https://doi.org/10.1109/escience.2019.00072" target="_blank" rel="noopener">10.1109/escience.2019.00072</a>.</li>
<li>Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C. Improving transparency and scientific rigor in academic publishing. Brain and Behavior. 2019;9(1). doi:<a href="https://doi.org/10.1002/brb3.1141" target="_blank" rel="noopener">10.1002/brb3.1141</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30506879/" target="_blank" rel="noopener">30506879</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6346653/" target="_blank" rel="noopener">PMC6346653</a>.</li>
<li>Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C. Improving transparency and scientific rigor in academic publishing. Cancer Reports. 2019;2(1). doi:<a href="https://doi.org/10.1002/cnr2.1150" target="_blank" rel="noopener">10.1002/cnr2.1150</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/32721132/" target="_blank" rel="noopener">32721132</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7941525/" target="_blank" rel="noopener">PMC7941525</a>.</li>
<li>Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C. Improving transparency and scientific rigor in academic publishing. J of Neuroscience Research. 2019;97(4):377-390. doi:<a href="https://doi.org/10.1002/jnr.24340" target="_blank" rel="noopener">10.1002/jnr.24340</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30506706/" target="_blank" rel="noopener">30506706</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC12990824/" target="_blank" rel="noopener">PMC12990824</a>.</li>
<li>Van Horn J, Abe S, Ambite JL, Attwood TK, Beard N, Bellis L, Bhattrai A, Bui A, Burns G, Fierro L, Gordon J, Grethe J, Kamdar J, Lei X, Lerman K, McGrath A, Mulder N, O'Driscoll C, Stewart C, Tyagi S. Advancing the international data science workforce through shared training and education [version 1; referees: awaiting peer review]. F1000Res. 2019;8:251. doi:<a href="https://doi.org/10.12688/f1000research.18357.1" target="_blank" rel="noopener">10.12688/f1000research.18357.1</a>.</li>
<li>Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC’, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. Erratum: Addendum: The FAIR Guiding Principles for scientific data management and stewardship (Scientific data (2016) 3 (160018)). Sci Data. 2019;6(1). doi:<a href="https://doi.org/10.1038/s41597-019-0009-6" target="_blank" rel="noopener">10.1038/s41597-019-0009-6</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30890711/" target="_blank" rel="noopener">30890711</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6427092/" target="_blank" rel="noopener">PMC6427092</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2018 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(7)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>AE Bandrowski, TH Gillespie, ME Martone. Research Resource IDentifiers for Key Biological Resources. 2018. doi:<a href="https://doi.org/10.5281/zenodo.1411569" target="_blank" rel="noopener">10.5281/zenodo.1411569</a>.</li>
<li>Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H. DataMed - an open source discovery index for finding biomedical datasets. Journal of the American Medical Informatics Association. 2018;25(3):300-308. doi:<a href="https://doi.org/10.1093/jamia/ocx121" target="_blank" rel="noopener">10.1093/jamia/ocx121</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/29346583/" target="_blank" rel="noopener">29346583</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7378878/" target="_blank" rel="noopener">PMC7378878</a>.</li>
<li>Kennedy DN, Ghosh SS, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Jarecka D, Kaczmarzyk JR, Keator D, Meyer K, Martone ME, Poline JB, Preuss N, Abraham SA, Bates JF, Crowley A, Haselgrove C, Hodge SM, Padhy S, Sincomb T. Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging [Preprint]. Center for Open Science; 2018. doi:<a href="https://doi.org/10.31219/osf.io/u78a6" target="_blank" rel="noopener">10.31219/osf.io/u78a6</a>.</li>
<li>Martone ME, Garcia-Castro A, VandenBos GR. Data sharing in psychology. American Psychologist. 2018;73(2):111-125. doi:<a href="https://doi.org/10.1037/amp0000242" target="_blank" rel="noopener">10.1037/amp0000242</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/29481105/" target="_blank" rel="noopener">29481105</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5920518/" target="_blank" rel="noopener">PMC5920518</a>.</li>
<li>Ozyurt IB, Grethe JS. Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database. 2018;2018. doi:<a href="https://doi.org/10.1093/database/bay130" target="_blank" rel="noopener">10.1093/database/bay130</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/30576493/" target="_blank" rel="noopener">30576493</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6301337/" target="_blank" rel="noopener">PMC6301337</a>.</li>
<li>Staines H, Martone ME. Community feedback on scholarly content: why it is important and why it should be preserved. Insights the UKSG journal. 2018;31. doi:<a href="https://doi.org/10.1629/uksg.418" target="_blank" rel="noopener">10.1629/uksg.418</a>.</li>
<li>Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T. Uniform resolution of compact identifiers for biomedical data. Sci Data. 2018;5(1). doi:<a href="https://doi.org/10.1038/sdata.2018.29" target="_blank" rel="noopener">10.1038/sdata.2018.29</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/29737976/" target="_blank" rel="noopener">29737976</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5944906/" target="_blank" rel="noopener">PMC5944906</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2017 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(10)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Callahan A, Anderson KD, Beattie MS, Bixby JL, Ferguson AR, Fouad K, Jakeman LB, Nielson JL, Popovich PG, Schwab JM, Lemmon VP. Developing a data sharing community for spinal cord injury research. Experimental Neurology. 2017;295:135-143. doi:<a href="https://doi.org/10.1016/j.expneurol.2017.05.012" target="_blank" rel="noopener">10.1016/j.expneurol.2017.05.012</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28576567/" target="_blank" rel="noopener">28576567</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6448396/" target="_blank" rel="noopener">PMC6448396</a>.</li>
<li>Cousijn H, Kenall A, Ganley E, Harrison M, Kernohan D, Lemberger T, Murphy F, Polischuk P, Taylor S, Martone M, Clark T. A data citation roadmap for scientific publishers [Preprint]. bioRxiv; 2017. doi:<a href="https://doi.org/10.1101/100784" target="_blank" rel="noopener">10.1101/100784</a>.</li>
<li>Denham S, Poirazi P, De Schutter E, Friston K, Chan HK, Nowotny T, Han D, Hong S, Rosay S, Wernle T, Treves A, Goethals S, Brette R, Van Pottelbergh T, Sepulchre R, Bird AD, Cuntz H, Gonçalves PJ, Lueckmann JM, Bassetto G, Nonnenmacher M, Macke JH, Sederberg AJ, MacLean JN, Palmer SE, Ferrari U, Gardella C, Marre O, Mora T, Ibrahimovic E, Müller M, Pfister JP, Chauhan T, Masquelier T, Montlibert A, Cottereau BR, Helias M, Schuecker J, Dahmen D, Goedeke S, Hyafil A, Hermoso-Mendizabal A, Rueda-Orozco PE, Jaramillo S, Robbe D, de la Rocha J, Rooy M, Koukouli F, DiGregorio D, Maskos U, Gutkin B, Verisokin AY, Verveyko DV, Postnov DE, Wong W, Talakoub O, Chen R, Popovic M, Lisitsyn D, Drebitz E, Grothe I, Mandon S, Kreiter A, Ernst U, Robinson PA, Zhao X, Aquino KM, Griffiths JD, Mehta-Pandejee G, Gabay N, MacLaurin J, Sarkar S, Kunze T, Haueisen J, Knösche TR, Ahmad S, Cui Y, Lewis M, Hawkins J, Olmi S, Petkoski S, Bartolomei F, Guye M, Jirsa V, Toutounji H, Durstewitz D, Cantarelli M, Quintana A, Marin B, Earnshaw M, Gleeson P, Court R, McDougal R, Angus Silver R, Dura-Bernal S, Larson S, Lytton WW, Idili G, Posani L, Cocco S, Ježek K, Monasson R. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3. BMC neuroscience. 2017 Jan.</li>
<li>Hasan MS, Dean T, Imam FT, Garcia F, Leblanc SP, Zulkernine M. A constraint-based intrusion detection system. In: ECBS '17: Fifth European Conference on the Engineering of Computer Based Systems. 2017:1-10. doi:<a href="https://doi.org/10.1145/3123779.3123812" target="_blank" rel="noopener">10.1145/3123779.3123812</a>.</li>
<li>Hsu CN, Bandrowski A, Grethe JS, Martone ME. Assessing value of biomedical digital repositories. . 2017. doi:<a href="https://doi.org/10.7287/peerj.preprints.2688v2" target="_blank" rel="noopener">10.7287/peerj.preprints.2688v2</a>.</li>
<li>Hsu CN, Bandrowski A, Grethe JS, Martone ME. Assessing value of biomedical digital repositories. . 2017. doi:<a href="https://doi.org/10.7287/peerj.preprints.2688" target="_blank" rel="noopener">10.7287/peerj.preprints.2688</a>.</li>
<li>Hsu CN, Bandrowski A, Grethe JS, Martone M. Assessing value of biomedical digital repositories. . 2017. doi:<a href="https://doi.org/10.7287/peerj.preprints.2688v1" target="_blank" rel="noopener">10.7287/peerj.preprints.2688v1</a>.</li>
<li>McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol. 2017;15(6):e2001414. doi:<a href="https://doi.org/10.1371/journal.pbio.2001414" target="_blank" rel="noopener">10.1371/journal.pbio.2001414</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28662064/" target="_blank" rel="noopener">28662064</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5490878/" target="_blank" rel="noopener">PMC5490878</a>.</li>
<li>Ohno-Machado L, Sansone SA, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj AE, Bell E, Soysal E, Zong N, Kim HE. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet. 2017;49(6):816-819. doi:<a href="https://doi.org/10.1038/ng.3864" target="_blank" rel="noopener">10.1038/ng.3864</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28546571/" target="_blank" rel="noopener">28546571</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6460922/" target="_blank" rel="noopener">PMC6460922</a>.</li>
<li>Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L. DATS, the data tag suite to enable discoverability of datasets. Sci Data. 2017;4(1). doi:<a href="https://doi.org/10.1038/sdata.2017.59" target="_blank" rel="noopener">10.1038/sdata.2017.59</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28585923/" target="_blank" rel="noopener">28585923</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5460592/" target="_blank" rel="noopener">PMC5460592</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2016 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(11)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova‐Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. Brain and Behavior. 2016;6(1). doi:<a href="https://doi.org/10.1002/brb3.417" target="_blank" rel="noopener">10.1002/brb3.417</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/27110440/" target="_blank" rel="noopener">27110440</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4834942/" target="_blank" rel="noopener">PMC4834942</a>.</li>
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova‐Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. J of Comparative Neurology. 2016;524(1):8-22. doi:<a href="https://doi.org/10.1002/cne.23913" target="_blank" rel="noopener">10.1002/cne.23913</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26599696/" target="_blank" rel="noopener">26599696</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4684178/" target="_blank" rel="noopener">PMC4684178</a>.</li>
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SS, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A Cultural Shift in Publishing. Neuroinform. 2016;14(2):169-182. doi:<a href="https://doi.org/10.1007/s12021-015-9284-3" target="_blank" rel="noopener">10.1007/s12021-015-9284-3</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26589523/" target="_blank" rel="noopener">26589523</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5072392/" target="_blank" rel="noopener">PMC5072392</a>.</li>
<li>Bandrowski A, Martone ME. RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods. Neuron. 2016;90(3):434-436. doi:10.1016/j.neuron.2016.04.030.</li>
<li>Fenner M, Crosas M, Grethe J, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. A Data Citation Roadmap for Scholarly Data Repositories [Preprint]. bioRxiv; 2016. doi:<a href="https://doi.org/10.1101/097196" target="_blank" rel="noopener">10.1101/097196</a>.</li>
<li>Hastings J, Frishkoff G, Smith B, Jensen M, Poldrack R, Lomax J, Bandrowski A, Imam F, Turner J, Martone M, Nowakowski P. Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych. AVANT. 2016;VII(3):101-117. doi:<a href="https://doi.org/10.26913/70302016.0109.0007" target="_blank" rel="noopener">10.26913/70302016.0109.0007</a>.</li>
<li>Jeffrey G, Anita B, Michael C, Tom G, James G, Yueling L, Ibrahim O, Maryann M. SciCrunch: A Cooperative And Collaborative Data, Information, And Resource Discovery Portal For Scientific Communities. Front. Neuroinform.. 2016;10. doi:<a href="https://doi.org/10.3389/conf.fninf.2016.20.00063" target="_blank" rel="noopener">10.3389/conf.fninf.2016.20.00063</a>.</li>
<li>Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS ONE. 2016;11(1):e0146300. doi:<a href="https://doi.org/10.1371/journal.pone.0146300" target="_blank" rel="noopener">10.1371/journal.pone.0146300</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26730820/" target="_blank" rel="noopener">26730820</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5156472/" target="_blank" rel="noopener">PMC5156472</a>.</li>
<li>Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 2016;3(1):160018-160018. doi:10.1038/sdata.2016.18.</li>
<li>Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. Comment: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3(1). doi:<a href="https://doi.org/10.1038/sdata.2016.18" target="_blank" rel="noopener">10.1038/sdata.2016.18</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26978244/" target="_blank" rel="noopener">26978244</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4792175/" target="_blank" rel="noopener">PMC4792175</a>.</li>
<li>Özyurt İB, Grethe JS, Martone ME, Bandrowski A. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS ONE. 2016;11(1):e0146300-e0146300. doi:10.1371/journal.pone.0146300.</li>
</ol>
<h2 style="margin-top:2.5rem;">2015 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(5)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova‐Seinstra E, Vasilevsky N. The Resource Identification Initiative: A Cultural Shift in Publishing. 2015 Nov.</li>
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. F1000Res. 2015;4:134. doi:<a href="https://doi.org/10.12688/f1000research.6555.1" target="_blank" rel="noopener">10.12688/f1000research.6555.1</a>.</li>
<li>Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing [version 2; referees: 2 approved]. F1000Res. 2015;4:134. doi:<a href="https://doi.org/10.12688/f1000research.6555.2" target="_blank" rel="noopener">10.12688/f1000research.6555.2</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26594330/" target="_blank" rel="noopener">26594330</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4648211/" target="_blank" rel="noopener">PMC4648211</a>.</li>
<li>Whetzel PL, Grethe JS, Banks DE, Martone ME. The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PLOS ONE. 2015 Sep;10(9):e0136206. doi:10.1371/journal.pone.0136206.</li>
<li>Whetzel PL, Grethe JS, Banks DE, Martone ME. The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PLoS ONE. 2015;10(9):e0136206. doi:<a href="https://doi.org/10.1371/journal.pone.0136206" target="_blank" rel="noopener">10.1371/journal.pone.0136206</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/26393351/" target="_blank" rel="noopener">26393351</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4578941/" target="_blank" rel="noopener">PMC4578941</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2014 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(10)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Carnevale T, Majumdar A, Sivagnanam S, Yoshimoto K, Astakhov V, Bandrowski A, Martone M. The neuroscience gateway portal: high performance computing made easy. BMC Neurosci. 2014;15(S1). doi:<a href="https://doi.org/10.1186/1471-2202-15-s1-p101" target="_blank" rel="noopener">10.1186/1471-2202-15-s1-p101</a>. PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4124975/" target="_blank" rel="noopener">PMC4124975</a>.</li>
<li>Chaudhri VK, Elenius D, Goldenkranz A, Gong A, Martone ME, Webb W, Yorke-Smith N. Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. Journal of Biomedical Semantics. 2014;5(1):51. doi:<a href="https://doi.org/10.1186/2041-1480-5-51" target="_blank" rel="noopener">10.1186/2041-1480-5-51</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/25785183/" target="_blank" rel="noopener">25785183</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4362633/" target="_blank" rel="noopener">PMC4362633</a>.</li>
<li>Ferguson AR, Nielson JL, Cragin MH, Bandrowski AE, Martone ME. Big data from small data: data-sharing in the 'long tail' of neuroscience. Nat Neurosci. 2014;17(11):1442-1447. doi:<a href="https://doi.org/10.1038/nn.3838" target="_blank" rel="noopener">10.1038/nn.3838</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/25349910/" target="_blank" rel="noopener">25349910</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4728080/" target="_blank" rel="noopener">PMC4728080</a>.</li>
<li>Friedrich S, Thomas W, Andrew D, Michael D, Jeffrey G, Sonja G, Kenneth H, Colin I, Marja-Leena L, Bengt L, John M, Roman M, Hyrum S, Gordon S, Leslie S, Jeff T, Shiro U. Mission and activities of the INCF Electrophysiology Data Sharing Task Force. Front. Neuroinform.. 2014;8. doi:<a href="https://doi.org/10.3389/conf.fninf.2014.08.00088" target="_blank" rel="noopener">10.3389/conf.fninf.2014.08.00088</a>.</li>
<li>Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME. Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. Front. Neuroinform.. 2014;8. doi:<a href="https://doi.org/10.3389/fninf.2014.00062" target="_blank" rel="noopener">10.3389/fninf.2014.00062</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24999329/" target="_blank" rel="noopener">24999329</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4064452/" target="_blank" rel="noopener">PMC4064452</a>.</li>
<li>Jeffrey G, Anita B, Davis B, Christopher C, Amarnath G, Stephen L, Yueling L, Ibrahim O, Andrea S, Patricia W, Luis M, Perry M, Rixin W, Gordon S, Maryann M. SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities. In: Frontiers in Neuroinformatics. 2014. doi:10.3389/conf.fninf.2014.18.00069.</li>
<li>Jeffrey G, Anita B, Davis B, Christopher C, Amarnath G, Stephen L, Yueling L, Ibrahim O, Andrea S, Patricia W, Luis M, Perry M, Rixin W, Gordon S, Maryann M. SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities. Front. Neuroinform.. 2014;8. doi:<a href="https://doi.org/10.3389/conf.fninf.2014.18.00069" target="_blank" rel="noopener">10.3389/conf.fninf.2014.18.00069</a>.</li>
<li>Jeffrey G, Anita B, Jonathan C, Amarnath G, Fahim I, Stephen L, Luis M, Perry M, Gordon S, Maryann M, NIF C. The Neuroscience Information Framework (NIF): A Unified Semantic Framework and Associated Tools for Discovery, Integration, and Utilization of Biomedical Data and Resources on the Web. Front. Neuroinform.. 2014;8. doi:<a href="https://doi.org/10.3389/conf.fninf.2014.08.00115" target="_blank" rel="noopener">10.3389/conf.fninf.2014.08.00115</a>.</li>
<li>Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL. Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. Front. Neuroinform.. 2014;8. doi:<a href="https://doi.org/10.3389/fninf.2014.00058" target="_blank" rel="noopener">10.3389/fninf.2014.00058</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/25018728/" target="_blank" rel="noopener">25018728</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4071641/" target="_blank" rel="noopener">PMC4071641</a>.</li>
<li>Nichols B, Mejino JL, Detwiler LT, Nilsen TT, Martone ME, Turner JA, Rubin DL, Brinkley JF. Neuroanatomical domain of the foundational model of anatomy ontology. J Biomed Sem. 2014;5(1):1. doi:<a href="https://doi.org/10.1186/2041-1480-5-1" target="_blank" rel="noopener">10.1186/2041-1480-5-1</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24398054/" target="_blank" rel="noopener">24398054</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3944952/" target="_blank" rel="noopener">PMC3944952</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2013 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(12)</span></h2>
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<ol class="pub-list">
<li>Anita B, Yueling L, Davis B, Jeffrey G, Maryann M. A Unified Research Resource Layer; Experiences from the Neuroscience Information Framework. Front. Neuroinform.. 2013;7. doi:<a href="https://doi.org/10.3389/conf.fninf.2013.09.00075" target="_blank" rel="noopener">10.3389/conf.fninf.2013.09.00075</a>.</li>
<li>Cobb JN, DeClerck G, Greenberg AJ, Clark R, McCouch SR. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement. Theoretical and Applied Genetics. 2013;126(4):867-887. doi:10.1007/s00122-013-2066-0.</li>
<li>Cone AC, Ambrosi C, Scemes E, Martone ME, Sosinsky GE. A comparative antibody analysis of pannexin1 expression in four rat brain regions reveals varying subcellular localizations. Front. Pharmacol.. 2013;4. doi:<a href="https://doi.org/10.3389/fphar.2013.00006" target="_blank" rel="noopener">10.3389/fphar.2013.00006</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/23390418/" target="_blank" rel="noopener">23390418</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3565217/" target="_blank" rel="noopener">PMC3565217</a>.</li>
<li>Gupta A, Bandrowski A, Condit C, Qian X, Grethe JS, Martone ME. Semantic query reformulation. In: SSDBM '13: Conference on Scientific and Statistical Database Management. 2013:1-4. doi:<a href="https://doi.org/10.1145/2484838.2484839" target="_blank" rel="noopener">10.1145/2484838.2484839</a>.</li>
<li>Jeffrey G, Anita B, Davis B, Jonathan C, Jing C, Christopher C, Amarnath G, Fahim I, Stephen L, Yueling L, Ibrahim O, Andrea S, Luis M, Perry M, Rixin W, Gordon S, Giorgio A, Maryann M. The Neuroscience Information Framework (NIF): A Unified Semantic Framework and Associated Tools for Discovery, Integration, and Utilization of Biomedical Data and Resources on the Web. Front. Neuroinform.. 2013;7. doi:<a href="https://doi.org/10.3389/conf.fninf.2013.09.00073" target="_blank" rel="noopener">10.3389/conf.fninf.2013.09.00073</a>.</li>
<li>Larson SD, Martone ME. NeuroLex.org: an online framework for neuroscience knowledge. Front. Neuroinform.. 2013;7. doi:<a href="https://doi.org/10.3389/fninf.2013.00018" target="_blank" rel="noopener">10.3389/fninf.2013.00018</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24009581/" target="_blank" rel="noopener">24009581</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3757470/" target="_blank" rel="noopener">PMC3757470</a>.</li>
<li>Martone ME, Ascoli GA. Connecting Connectomes. Neuroinform. 2013;11(4):389-392. doi:<a href="https://doi.org/10.1007/s12021-013-9207-0" target="_blank" rel="noopener">10.1007/s12021-013-9207-0</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24096724/" target="_blank" rel="noopener">24096724</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3858843/" target="_blank" rel="noopener">PMC3858843</a>.</li>
<li>Martone ME. Brain and Behavior : we want you to share your data. Brain and Behavior. 2013;4(1):1-3. doi:<a href="https://doi.org/10.1002/brb3.192" target="_blank" rel="noopener">10.1002/brb3.192</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24653948/" target="_blank" rel="noopener">24653948</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3937699/" target="_blank" rel="noopener">PMC3937699</a>.</li>
<li>Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front. Neuroinform.. 2013;7. doi:<a href="https://doi.org/10.3389/fninf.2013.00007" target="_blank" rel="noopener">10.3389/fninf.2013.00007</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/23717278/" target="_blank" rel="noopener">23717278</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3653101/" target="_blank" rel="noopener">PMC3653101</a>.</li>
<li>Orloff DN, Iwasa JH, Martone ME, Ellisman MH, Kane CM. The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Research. 2013;41(D1):D1241-D1250. doi:<a href="https://doi.org/10.1093/nar/gks1257" target="_blank" rel="noopener">10.1093/nar/gks1257</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/23203874/" target="_blank" rel="noopener">23203874</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3531121/" target="_blank" rel="noopener">PMC3531121</a>.</li>
<li>Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J. The Gene Ontology (GO) Cellular Component Ontology: Integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Sem. 2013;4(1):20. doi:<a href="https://doi.org/10.1186/2041-1480-4-20" target="_blank" rel="noopener">10.1186/2041-1480-4-20</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/24093723/" target="_blank" rel="noopener">24093723</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3852282/" target="_blank" rel="noopener">PMC3852282</a>.</li>
<li>Vouimba RM, Richter-Levin G. A knowledge based approach to matching human neurodegenerative disease and animal models. Front. Neural Circuits. 2013;7. doi:<a href="https://doi.org/10.3389/fncir.2013.00080" target="_blank" rel="noopener">10.3389/fncir.2013.00080</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/23653594/" target="_blank" rel="noopener">23653594</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3642501/" target="_blank" rel="noopener">PMC3642501</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2012 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(11)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molin T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M. Prototype of Kepler processing workflows for microscopy and neuroinformatics. 2012:1595-1603. doi:<a href="https://doi.org/10.1016/j.procs.2012.04.175" target="_blank" rel="noopener">10.1016/j.procs.2012.04.175</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/28479932/" target="_blank" rel="noopener">28479932</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5415345/" target="_blank" rel="noopener">PMC5415345</a>.</li>
<li>Bandrowski AE, Cachat J, Li Y, Muller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database. 2012;2012(0):bas005-bas005. doi:<a href="https://doi.org/10.1093/database/bas005" target="_blank" rel="noopener">10.1093/database/bas005</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22434839/" target="_blank" rel="noopener">22434839</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3308161/" target="_blank" rel="noopener">PMC3308161</a>.</li>
<li>Burette AC, Lesperance T, Crum J, Martone M, Volkmann N, Ellisman MH, Weinberg RJ. Electron tomographic analysis of synaptic ultrastructure. J of Comparative Neurology. 2012;520(12):2697-2711. doi:<a href="https://doi.org/10.1002/cne.23067" target="_blank" rel="noopener">10.1002/cne.23067</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22684938/" target="_blank" rel="noopener">22684938</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3856703/" target="_blank" rel="noopener">PMC3856703</a>.</li>
<li>Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME. A Survey of the Neuroscience Resource Landscape. Perspectives from the Neuroscience Information Framework. In: International Review of Neurobiology. Elsevier; 2012:39-68. doi:<a href="https://doi.org/10.1016/b978-0-12-388408-4.00003-4" target="_blank" rel="noopener">10.1016/b978-0-12-388408-4.00003-4</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/23195120/" target="_blank" rel="noopener">23195120</a>.</li>
<li>Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods. 2012;9(7):697-710. doi:<a href="https://doi.org/10.1038/nmeth.2084" target="_blank" rel="noopener">10.1038/nmeth.2084</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22743775/" target="_blank" rel="noopener">22743775</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3659807/" target="_blank" rel="noopener">PMC3659807</a>.</li>
<li>Giuly RJ, Martone ME, Ellisman MH. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. BMC Bioinformatics. 2012;13(1). doi:<a href="https://doi.org/10.1186/1471-2105-13-29" target="_blank" rel="noopener">10.1186/1471-2105-13-29</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22321695/" target="_blank" rel="noopener">22321695</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3293777/" target="_blank" rel="noopener">PMC3293777</a>.</li>
<li>Hamilton DJ, Shepherd GM, Martone ME, Ascoli GA. An ontological approach to describing neurons and their relationships. Front. Neuroinform.. 2012;6. doi:<a href="https://doi.org/10.3389/fninf.2012.00015" target="_blank" rel="noopener">10.3389/fninf.2012.00015</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22557965/" target="_blank" rel="noopener">22557965</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3338117/" target="_blank" rel="noopener">PMC3338117</a>.</li>
<li>Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. Front. Gene.. 2012;3. doi:<a href="https://doi.org/10.3389/fgene.2012.00111" target="_blank" rel="noopener">10.3389/fgene.2012.00111</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22737162/" target="_blank" rel="noopener">22737162</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3381282/" target="_blank" rel="noopener">PMC3381282</a>.</li>
<li>Imam Fahim T., Larson Stephen, Bandrowski Anita, Grethe Jeffrey S., Gupta Amarnath, Martone Maryann E.. Maturation of neuroscience information framework: An ontology driven information system for neuroscience. In: Frontiers in Artificial Intelligence and Applications. IOS Press; 2012. doi:<a href="https://doi.org/10.3233/978-1-61499-084-0-15" target="_blank" rel="noopener">10.3233/978-1-61499-084-0-15</a>.</li>
<li>Le Franc Y, Davison AP, Gleeson P, Imam FT, Kriener B, Larson SD, Ray S, Schwabe L, Hill S, De Schutter E. Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models. BMC Neurosci. 2012;13(S1). doi:<a href="https://doi.org/10.1186/1471-2202-13-s1-p149" target="_blank" rel="noopener">10.1186/1471-2202-13-s1-p149</a>. PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3403625/" target="_blank" rel="noopener">PMC3403625</a>.</li>
<li>MUMCUOGLU EU, HASSANPOUR R, TASEL SF, PERKINS G, MARTONE ME, GURCAN MN. Computerized detection and segmentation of mitochondria on electron microscope images. Journal of Microscopy. 2012;246(3):248-265. doi:<a href="https://doi.org/10.1111/j.1365-2818.2012.03614.x" target="_blank" rel="noopener">10.1111/j.1365-2818.2012.03614.x</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/22506967/" target="_blank" rel="noopener">22506967</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2011 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(11)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Akil H, Martone ME, Van Essen DC. Challenges and opportunities in mining neuroscience data. Science. 2011;331(6018):708-712. doi:<a href="https://doi.org/10.1126/science.1199305" target="_blank" rel="noopener">10.1126/science.1199305</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21311009/" target="_blank" rel="noopener">21311009</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3102049/" target="_blank" rel="noopener">PMC3102049</a>.</li>
<li>Berlanga ML, Phan S, Bushong EA, Wu S, Kwon O, Phung BS, Lamont S, Terada M, Tasdizen T, Martone ME, Ellisman MH. Three-dimensional reconstruction of serial mouse brain sections: solution for flattening high-resolution large-scale mosaics. Front. Neuroanat.. 2011;5. doi:<a href="https://doi.org/10.3389/fnana.2011.00017" target="_blank" rel="noopener">10.3389/fnana.2011.00017</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21629828/" target="_blank" rel="noopener">21629828</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3096995/" target="_blank" rel="noopener">PMC3096995</a>.</li>
<li>Berlanga ML, Price DL, Phung BS, Giuly R, Terada M, Yamada N, Cyr M, Caron MG, Laakso A, Martone ME, Ellisman MH. Multiscale imaging characterization of dopamine transporter knockout mice reveals regional alterations in spine density of medium spiny neurons. Brain Research. 2011;1390:41-49. doi:<a href="https://doi.org/10.1016/j.brainres.2011.03.044" target="_blank" rel="noopener">10.1016/j.brainres.2011.03.044</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21439946/" target="_blank" rel="noopener">21439946</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3104025/" target="_blank" rel="noopener">PMC3104025</a>.</li>
<li>Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S. XCEDE: An Extensible Schema for Biomedical Data. Neuroinform. 2011;10(1):19-32. doi:<a href="https://doi.org/10.1007/s12021-011-9119-9" target="_blank" rel="noopener">10.1007/s12021-011-9119-9</a>. PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3836560/" target="_blank" rel="noopener">PMC3836560</a>.</li>
<li>Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larsen SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J. Digital atlasing and standardization in the mouse brain. PLoS Comput Biol. 2011;7(2):e1001065. doi:<a href="https://doi.org/10.1371/journal.pcbi.1001065" target="_blank" rel="noopener">10.1371/journal.pcbi.1001065</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21304938/" target="_blank" rel="noopener">21304938</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3033370/" target="_blank" rel="noopener">PMC3033370</a>.</li>
<li>Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larsen SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J. Correction: Digital Atlasing and Standardization in the Mouse Brain. 2011 Feb.</li>
<li>Imam FT, Larson S, Grethe JS, Gupta A, Bandrowski A, Martone ME. NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement.. In: ICBO. 2011.</li>
<li>Jeff G. The Neuroimaging Informatics Tools and Resources Clearinghouse: Year 4 Update. Front. Neuroinform.. 2011;5. doi:<a href="https://doi.org/10.3389/conf.fninf.2011.08.00125" target="_blank" rel="noopener">10.3389/conf.fninf.2011.08.00125</a>.</li>
<li>Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D. Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. Stand. Genomic Sci.. 2011;4(2):286-292. doi:<a href="https://doi.org/10.4056/sigs.1344279" target="_blank" rel="noopener">10.4056/sigs.1344279</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21677865/" target="_blank" rel="noopener">21677865</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3111990/" target="_blank" rel="noopener">PMC3111990</a>.</li>
<li>Mungall C, Anderson DA, Bandrowski A, Canada BA, Chatyr-Aryamontri A, Cheng KC, et al. An ontology-based approach to linking model organisms and resources to human diseases. 2011.</li>
<li>Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Research. 2011;39(Database):D546-D551. doi:<a href="https://doi.org/10.1093/nar/gkq1102" target="_blank" rel="noopener">10.1093/nar/gkq1102</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21045053/" target="_blank" rel="noopener">21045053</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3013694/" target="_blank" rel="noopener">PMC3013694</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2010 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(11)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Altintas I, Chen J, Sedova M, Gupta A, Sun S, Lin AW, Gujral M, Anand MK, Li W, Grethe JS, Ellisman M. Extending the Data Model for Data-Centric Metagenomics Analysis Using Scientific Workflows in CAMERA. In: 2010 Sixth IEEE International Conference on E-Science Workshops. 2010:49-56. doi:<a href="https://doi.org/10.1109/esciencew.2010.18" target="_blank" rel="noopener">10.1109/esciencew.2010.18</a>.</li>
<li>Altintas I, Lin AW, Chen J, Churas C, Gujral M, Sun S, Li W, Manansala R, Sedova M, Grethe JS, Ellisman M. CAMERA 2.0: A Data-centric Metagenomics Community Infrastructure Driven by Scientific Workflows. In: 2010 IEEE Congress on Services (SERVICES). 2010:352-359. doi:<a href="https://doi.org/10.1109/services.2010.89" target="_blank" rel="noopener">10.1109/services.2010.89</a>.</li>
<li>Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J. Modeling biomedical experimental processes with OBI. J Biomed Semant. 2010;1(S1). doi:<a href="https://doi.org/10.1186/2041-1480-1-s1-s7" target="_blank" rel="noopener">10.1186/2041-1480-1-s1-s7</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/20626927/" target="_blank" rel="noopener">20626927</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2903726/" target="_blank" rel="noopener">PMC2903726</a>.</li>
<li>Jeff G. The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). Front. Neurosci.. 2010;4. doi:<a href="https://doi.org/10.3389/conf.fnins.2010.13.00027" target="_blank" rel="noopener">10.3389/conf.fnins.2010.13.00027</a>.</li>
<li>Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME. Dimensionality Reduction on Multi-Dimensional Transfer Functions for Multi-Channel Volume Data Sets. Information Visualization. 2010;9(3):167-180. doi:<a href="https://doi.org/10.1057/ivs.2010.6" target="_blank" rel="noopener">10.1057/ivs.2010.6</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/21841914/" target="_blank" rel="noopener">21841914</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3153355/" target="_blank" rel="noopener">PMC3153355</a>.</li>
<li>Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME. Multi-Channel Transfer Function with Dimensionality Reduction. SPIE Proceedings. 2010;7530:75300A. doi:<a href="https://doi.org/10.1117/12.839526" target="_blank" rel="noopener">10.1117/12.839526</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/20582228/" target="_blank" rel="noopener">20582228</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2891081/" target="_blank" rel="noopener">PMC2891081</a>.</li>
<li>Kola J(, Harris J, Lawrie S, Rector A, Goble C, Martone M. Towards an ontology for psychosis. Cognitive Systems Research. 2010;11(1):42-52. doi:<a href="https://doi.org/10.1016/j.cogsys.2008.08.005" target="_blank" rel="noopener">10.1016/j.cogsys.2008.08.005</a>.</li>
<li>Maryann M. Activities of the US INCF Node. Front. Neurosci.. 2010;4. doi:<a href="https://doi.org/10.3389/conf.fnins.2010.13.00083" target="_blank" rel="noopener">10.3389/conf.fnins.2010.13.00083</a>.</li>
<li>Maryann M. The possibility and probability of a global neuroscience information framework. Front. Neurosci.. 2010;4. doi:<a href="https://doi.org/10.3389/conf.fnins.2010.13.00013" target="_blank" rel="noopener">10.3389/conf.fnins.2010.13.00013</a>.</li>
<li>Ozyurt IB, Keator DB, Wei D, Fennema-Notestine C, Pease KR, Bockholt J, Grethe JS. Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database. Neuroinform. 2010;8(4):231-249. doi:<a href="https://doi.org/10.1007/s12021-010-9078-6" target="_blank" rel="noopener">10.1007/s12021-010-9078-6</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/20567938/" target="_blank" rel="noopener">20567938</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2974931/" target="_blank" rel="noopener">PMC2974931</a>.</li>
<li>Turner. Application of neuroanatomical ontologies for neuroimaging data annotation. Front. Neuroinform.. 2010. doi:<a href="https://doi.org/10.3389/fninf.2010.00010" target="_blank" rel="noopener">10.3389/fninf.2010.00010</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/20725521/" target="_blank" rel="noopener">20725521</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2912099/" target="_blank" rel="noopener">PMC2912099</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2009 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(6)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Grethe JS, Ross E, Little D, Sanders B, Gupta A, Astakhov V. Mediator Infrastructure for Information Integration and Semantic Data Integration Environment for Biomedical Research. In: Methods in Molecular Biology. Humana Press; 2009:33-53. doi:<a href="https://doi.org/10.1007/978-1-59745-524-4_3" target="_blank" rel="noopener">10.1007/978-1-59745-524-4_3</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/19623485/" target="_blank" rel="noopener">19623485</a>.</li>
<li>Keator DB. Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid. Front. Neuroinform.. 2009;3. doi:<a href="https://doi.org/10.3389/neuro.11.030.2009" target="_blank" rel="noopener">10.3389/neuro.11.030.2009</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/19826494/" target="_blank" rel="noopener">19826494</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2759340/" target="_blank" rel="noopener">PMC2759340</a>.</li>
<li>Kennedy DN, Haselgrove C, Buccigrossi R, Grethe J. Software development for neuroimaging: Promoting community access and best practices through NITRC. In: 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI). 2009:1146-1149. doi:<a href="https://doi.org/10.1109/isbi.2009.5193260" target="_blank" rel="noopener">10.1109/isbi.2009.5193260</a>.</li>
<li>Larson S, Maynard S, Imam FT, Martone ME. NeuroLex.org - A semantic wiki for neuroinformatics based on the NIF Standard Ontology. In: Frontiers in Neuroinformatics. 2009. doi:10.3389/conf.neuro.11.2009.08.078.</li>
<li>Larson SD. Ontologies for Neuroscience: What are they and What are they Good for?. Front. Neurosci.. 2009;3(1). doi:<a href="https://doi.org/10.3389/neuro.01.007.2009" target="_blank" rel="noopener">10.3389/neuro.01.007.2009</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/19753098/" target="_blank" rel="noopener">19753098</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2695392/" target="_blank" rel="noopener">PMC2695392</a>.</li>
<li>Young L, Tu SW, Tennakoon L, Vismer D, Astakhov V, Gupta A, Grethe JS, Martone ME, Das AK, McAuliffe MJ. Ontology driven data integration for autism research. In: 2009 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS). 2009:1-7. doi:<a href="https://doi.org/10.1109/cbms.2009.5255362" target="_blank" rel="noopener">10.1109/cbms.2009.5255362</a>.</li>
</ol>
<h2 style="margin-top:2.5rem;">2008 <span style="font-size:0.8rem; font-weight:normal; color:var(--gray-text);">(12)</span></h2>
<div class="divider"></div>
<ol class="pub-list">
<li>Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME. The NIFSTD and BIRNLex vocabularies: Building comprehensive ontologies for neuroscience. Neuroinform. 2008;6(3):175-194. doi:<a href="https://doi.org/10.1007/s12021-008-9032-z" target="_blank" rel="noopener">10.1007/s12021-008-9032-z</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18975148/" target="_blank" rel="noopener">18975148</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2743139/" target="_blank" rel="noopener">PMC2743139</a>.</li>
<li>David K. The neuroimaging informatics tools and resources clearinghouse (NITRC). Frontiers in Neuroinformatics. 2008;2. doi:10.3389/conf.neuro.11.2008.01.122.</li>
<li>Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW. The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinform. 2008;6(3):149-160. doi:<a href="https://doi.org/10.1007/s12021-008-9024-z" target="_blank" rel="noopener">10.1007/s12021-008-9024-z</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18946742/" target="_blank" rel="noopener">18946742</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2661130/" target="_blank" rel="noopener">PMC2661130</a>.</li>
<li>Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME. Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinform. 2008;6(3):205-217. doi:<a href="https://doi.org/10.1007/s12021-008-9033-y" target="_blank" rel="noopener">10.1007/s12021-008-9033-y</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18958629/" target="_blank" rel="noopener">18958629</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2689790/" target="_blank" rel="noopener">PMC2689790</a>.</li>
<li>Keator DB, Grethe JS, Marcus D, Ozyurt B, Gadde S, Murphy S, Pieper S, Greve D, Notestine R, Bockholt HJ, Papadopoulos P. A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans. Inform. Technol. Biomed.. 2008;12(2):162-172. doi:<a href="https://doi.org/10.1109/titb.2008.917893" target="_blank" rel="noopener">10.1109/titb.2008.917893</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18348946/" target="_blank" rel="noopener">18348946</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2763494/" target="_blank" rel="noopener">PMC2763494</a>.</li>
<li>Kumar VS, Rutt B, Kurc T, Catalyurek UV, Pan TC, Chow S, Lamont S, Martone M, Saltz JH. Large-scale biomedical image analysis in grid environments. IEEE Trans. Inform. Technol. Biomed.. 2008;12(2):154-161. doi:<a href="https://doi.org/10.1109/titb.2007.908466" target="_blank" rel="noopener">10.1109/titb.2007.908466</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18348945/" target="_blank" rel="noopener">18348945</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC3294419/" target="_blank" rel="noopener">PMC3294419</a>.</li>
<li>Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL. The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers. Neuroinform. 2008;6(3):219-227. doi:<a href="https://doi.org/10.1007/s12021-008-9025-y" target="_blank" rel="noopener">10.1007/s12021-008-9025-y</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18975149/" target="_blank" rel="noopener">18975149</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2704600/" target="_blank" rel="noopener">PMC2704600</a>.</li>
<li>Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL. Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework. Neuroinform. 2008;6(3):229-239. doi:<a href="https://doi.org/10.1007/s12021-008-9035-9" target="_blank" rel="noopener">10.1007/s12021-008-9035-9</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18953674/" target="_blank" rel="noopener">18953674</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2664632/" target="_blank" rel="noopener">PMC2664632</a>.</li>
<li>Mark E. Semantic architecture for data integration and discovery within the biomedical informatics research network. Frontiers in Neuroinformatics. 2008;2. doi:10.3389/conf.neuro.11.2008.01.115.</li>
<li>Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, Ellisman MH. The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. Journal of Structural Biology. 2008;161(3):220-231. doi:<a href="https://doi.org/10.1016/j.jsb.2007.10.003" target="_blank" rel="noopener">10.1016/j.jsb.2007.10.003</a>. PubMed PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/18054501/" target="_blank" rel="noopener">18054501</a>; PubMed Central PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC2367257/" target="_blank" rel="noopener">PMC2367257</a>.</li>
<li>Maryann M. A spatial framework for multi-scale computational neuroanatomy. Front. Neuroinform.. 2008;2. doi:<a href="https://doi.org/10.3389/conf.neuro.11.2008.01.134" target="_blank" rel="noopener">10.3389/conf.neuro.11.2008.01.134</a>.</li>
<li>Maryann M. Spatial registration, visualization and annotation of mouse brain images at different scales. Front. Neuroinform.. 2008;2. doi:<a href="https://doi.org/10.3389/conf.neuro.11.2008.01.128" target="_blank" rel="noopener">10.3389/conf.neuro.11.2008.01.128</a>.</li>
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