| KBase: the United States department of energy systems biology knowledgebase AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ... Nature biotechnology 36 (7), 566-569, 2018 | 1242 | 2018 |
| The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families S Yooseph, G Sutton, DB Rusch, AL Halpern, SJ Williamson, ... PLoS biology 5 (3), e16, 2007 | 1021 | 2007 |
| Co-evolution of proteins with their interaction partners CS Goh, AA Bogan, M Joachimiak, D Walther, FE Cohen Journal of molecular biology 299 (2), 283-293, 2000 | 564 | 2000 |
| MicrobesOnline: an integrated portal for comparative and functional genomics PS Dehal, MP Joachimiak, MN Price, JT Bates, JK Baumohl, D Chivian, ... Nucleic acids research 38 (suppl_1), D396-D400, 2010 | 537 | 2010 |
| Expression profiling of the schizont and trophozoite stages of Plasmodium falciparumwith a long-oligonucleotide microarray Z Bozdech, J Zhu, MP Joachimiak, FE Cohen, B Pulliam, JL DeRisi Genome biology 4, 1-15, 2003 | 493 | 2003 |
| The National COVID Cohort Collaborative (N3C): rationale, design, infrastructure, and deployment MA Haendel, CG Chute, TD Bennett, DA Eichmann, J Guinney, WA Kibbe, ... Journal of the American Medical Informatics Association 28 (3), 427-443, 2021 | 478 | 2021 |
| How many rare diseases are there? M Haendel, N Vasilevsky, D Unni, C Bologa, N Harris, H Rehm, ... Nature reviews drug discovery 19 (2), 77-78, 2020 | 403 | 2020 |
| The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species KA Shefchek, NL Harris, M Gargano, N Matentzoglu, D Unni, M Brush, ... Nucleic acids research 48 (D1), D704-D715, 2020 | 235 | 2020 |
| Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough A Mukhopadhyay, AM Redding, MP Joachimiak, AP Arkin, SE Borglin, ... Journal of bacteriology 189 (16), 5996-6010, 2007 | 132 | 2007 |
| JColorGrid: software for the visualization of biological measurements MP Joachimiak, JL Weisman, BCH May BMC bioinformatics 7, 1-5, 2006 | 123 | 2006 |
| Zinc against COVID-19? Symptom surveillance and deficiency risk groups MP Joachimiak PLoS neglected tropical diseases 15 (1), e0008895, 2021 | 102 | 2021 |
| Effects of genetic variation on the E. coli host-circuit interface S Cardinale, MP Joachimiak, AP Arkin Cell reports 4 (2), 231-237, 2013 | 101 | 2013 |
| KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response JT Reese, D Unni, TJ Callahan, L Cappelletti, V Ravanmehr, S Carbon, ... Patterns 2 (1), 2021 | 99 | 2021 |
| Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris Q He, Z He, DC Joyner, M Joachimiak, MN Price, ZK Yang, HCB Yen, ... The ISME Journal 4 (11), 1386-1397, 2010 | 87 | 2010 |
| Functional responses of methanogenic archaea to syntrophic growth CB Walker, AM Redding-Johanson, EE Baidoo, L Rajeev, Z He, ... The ISME journal 6 (11), 2045-2055, 2012 | 81 | 2012 |
| Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state ME Clark, Z He, AM Redding, MP Joachimiak, JD Keasling, JZ Zhou, ... BMC genomics 13, 1-17, 2012 | 80 | 2012 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 79 | 2016 |
| Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning JH Caufield, H Hegde, V Emonet, NL Harris, MP Joachimiak, ... Bioinformatics 40 (3), btae104, 2024 | 73 | 2024 |
| Hydrogen peroxide‐induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough A Zhou, Z He, AM Redding‐Johanson, A Mukhopadhyay, CL Hemme, ... Environmental Microbiology 12 (10), 2645-2657, 2010 | 70 | 2010 |
| Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation Z He, A Zhou, E Baidoo, Q He, MP Joachimiak, P Benke, R Phan, ... Applied and Environmental Microbiology 76 (5), 1574-1586, 2010 | 70 | 2010 |
Adam Paul ArkinDepartment of Bioengineering, University of California, Berkeley, Physical Biosciences Division, E.OVerified email at lbl.gov
