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Marcin P. Joachimiak, Ph.D. - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
protein folding
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20/53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2012 Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. Bmc Genomics. 13: 138. PMID 22507456 DOI: 10.1186/1471-2164-13-138  0.32
2012 Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. The Journal of Biological Chemistry. 287: 7945-55. PMID 22253435 DOI: 10.1074/Jbc.M111.302653  0.363
2012 Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. 78: 1168-77. PMID 22156435 DOI: 10.1128/Aem.05666-11  0.305
2011 Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, et al. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. Plos One. 6: e21470. PMID 21738675 DOI: 10.1371/Journal.Pone.0021470  0.356
2011 Sundararajan A, Kurowski J, Yan T, Klingeman DM, Joachimiak MP, Zhou J, Naranjo B, Gralnick JA, Fields MW. Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth. Applied and Environmental Microbiology. 77: 4647-56. PMID 21602393 DOI: 10.1128/Aem.03003-10  0.354
2011 Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research. 39: 2344-56. PMID 21071404 DOI: 10.1093/Nar/Gkq1046  0.323
2010 He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/Aem.02141-09  0.324
2010 Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. 38: D396-400. PMID 19906701 DOI: 10.1093/Nar/Gkp919  0.38
2010 Burns A, Joachimiak M, Deutschbauer A, Arkin A, Bender K. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough Lawrence Berkeley National Laboratory. DOI: 10.2172/985922  0.35
2010 Timberlake S, Joachimiak M, Joyner D, Chakraborty R, Baumohl J, Dehal P, Arkin A, Hazen T, Alm E. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress Lawrence Berkeley National Laboratory. DOI: 10.2172/985921  0.319
2010 Rajeev L, Luning E, Dehal P, Joachimiak M, Mukhopadhyay A. Mapping the Two-component Regulatory Networks in Desulfovibrio vulgaris Lawrence Berkeley National Laboratory. DOI: 10.2172/985735  0.304
2009 Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, Keasling JD, Wall JD. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research. 37: 2926-39. PMID 19293273 DOI: 10.1093/Nar/Gkp164  0.346
2007 Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology. 189: 8944-52. PMID 17921288 DOI: 10.1128/Jb.00284-07  0.308
2007 Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, ... Joachimiak MP, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/Journal.Pbio.0050016  0.4
2003 Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology. 4: R9. PMID 12620119 DOI: 10.1186/Gb-2003-4-2-R9  0.493
2002 Joachimiak MP, Cohen FE. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biology. 3: RESEARCH0077. PMID 12537566 DOI: 10.1186/Gb-2002-3-12-Research0077  0.525
2001 Joachimiak MP, Chang C, Rosenthal PJ, Cohen FE. The impact of whole genome sequence data on drug discovery--a malaria case study. Molecular Medicine (Cambridge, Mass.). 7: 698-710. PMID 11713369 DOI: 10.1007/Bf03401960  0.495
2000 Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. Co-evolution of proteins with their interaction partners. Journal of Molecular Biology. 299: 283-93. PMID 10860738 DOI: 10.1006/Jmbi.2000.3732  0.559
1999 Gerloff DL, Cannarozzi GM, Joachimiak M, Cohen FE, Schreiber D, Benner SA. Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins. Biochemical and Biophysical Research Communications. 254: 70-6. PMID 9920734 DOI: 10.1006/Bbrc.1998.9884  0.495
1998 Gerloff DL, Joachimiak M, Cohen FE, Cannarozzi GM, Chamberlin SG, Benner SA. Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family. Biochemical and Biophysical Research Communications. 251: 173-81. PMID 9790926 DOI: 10.1006/Bbrc.1998.9198  0.52
Low-probability matches (unlikely to be authored by this person)
2012 Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA. Functional responses of methanogenic archaea to syntrophic growth. The Isme Journal. 6: 2045-55. PMID 22739494 DOI: 10.1038/Ismej.2012.60  0.3
2010 Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, et al. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 12: 2645-57. PMID 20482586 DOI: 10.1111/J.1462-2920.2010.02234.X  0.294
2010 He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin AP, Hazen TC, et al. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. The Isme Journal. 4: 1386-97. PMID 20445634 DOI: 10.1038/Ismej.2010.59  0.292
2013 Cardinale S, Joachimiak MP, Arkin AP. Effects of genetic variation on the E. coli host-circuit interface. Cell Reports. 4: 231-7. PMID 23871664 DOI: 10.1016/J.Celrep.2013.06.023  0.291
2009 Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. Bmc Genomics. 10: 131. PMID 19321007 DOI: 10.1186/1471-2164-10-131  0.287
2010 Joachimiak M. Revisiting Modes of energy generation in sulfate reducing bacteria Lawrence Berkeley National Laboratory. DOI: 10.2172/985244  0.286
1997 Joachimiak M, Tevzadze G, Podkowinski J, Haselkorn R, Gornicki P. Wheat cytosolic acetyl-CoA carboxylase complements an ACC1 null mutation in yeast. Proceedings of the National Academy of Sciences of the United States of America. 94: 9990-5. PMID 11038571 DOI: 10.1073/Pnas.94.18.9990  0.285
2012 Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. 194: 5783-93. PMID 22904289 DOI: 10.1128/Jb.00749-12  0.281
2010 Zhou A, Hillesland K, He Z, Joachimiak M, Zane G, Dehal P, Arkin A, Stahl D, Wall J, Hazen T, Zhou J, Baidoo E, Benke P, Mukhopadhyay A. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough Lawrence Berkeley National Laboratory. DOI: 10.2172/985929  0.274
2013 Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The Isme Journal. 7: 1790-802. PMID 23575373 DOI: 10.1038/Ismej.2013.60  0.273
2012 Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T. Application of phenotypic microarrays to environmental microbiology. Current Opinion in Biotechnology. 23: 41-8. PMID 22217654 DOI: 10.1016/J.Copbio.2011.12.006  0.267
2007 Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, et al. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 189: 5996-6010. PMID 17545284 DOI: 10.1128/Jb.00368-07  0.257
2006 Joachimiak MP, Weisman JL, May BCh. JColorGrid: software for the visualization of biological measurements. Bmc Bioinformatics. 7: 225. PMID 16640789 DOI: 10.1186/1471-2105-7-225  0.244
2020 Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP, et al. How many rare diseases are there? Nature Reviews. Drug Discovery. 19: 77-78. PMID 32020066 DOI: 10.1038/D41573-019-00180-Y  0.197
2018 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, ... ... Joachimiak MP, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/Nbt.4163  0.189
2023 Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. Arxiv. PMID 37292480  0.186
2024 Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Frontiers in Microbiology. 15: 1351678. PMID 38638909 DOI: 10.3389/fmicb.2024.1351678  0.146
2024 Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, et al. An open source knowledge graph ecosystem for the life sciences. Scientific Data. 11: 363. PMID 38605048 DOI: 10.1038/s41597-024-03171-w  0.14
2019 Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, ... ... Joachimiak M, et al. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. PMID 31701156 DOI: 10.1093/nar/gkz997  0.139
2022 Beranová L, Joachimiak MP, Kliegr T, Rabby G, Sklenák V. Why was this cited? Explainable machine learning applied to COVID-19 research literature. Scientometrics. 1-37. PMID 35431364 DOI: 10.1007/s11192-022-04314-9  0.119
2019 Zhang XA, Yates A, Vasilevsky N, Gourdine JP, Callahan TJ, Carmody LC, Danis D, Joachimiak MP, Ravanmehr V, Pfaff ER, Champion J, Robasky K, Xu H, Fecho K, Walton NA, et al. Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. Npj Digital Medicine. 2. PMID 31119199 DOI: 10.1038/s41746-019-0110-4  0.106
2021 Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, et al. Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. Nar Genomics and Bioinformatics. 3: lqab113. PMID 34888523 DOI: 10.1093/nargab/lqab113  0.101
2021 Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, ... ... Joachimiak MP, et al. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. Msystems. 6. PMID 33622857 DOI: 10.1128/mSystems.01194-20  0.096
2020 Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, ... ... Joachimiak MP, et al. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Patterns (New York, N.Y.). 100155. PMID 33196056 DOI: 10.1016/j.patter.2020.100155  0.091
2020 Reese J, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Robinson PN, Joachimiak MP, Mungall CJ. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Biorxiv : the Preprint Server For Biology. PMID 32839776 DOI: 10.1101/2020.08.17.254839  0.09
2023 Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, ... ... Joachimiak MP, et al. KG-Hub - Building and Exchanging Biological Knowledge Graphs. Bioinformatics (Oxford, England). PMID 37389415 DOI: 10.1093/bioinformatics/btad418  0.088
2023 Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS. A bacterial sensor taxonomy across earth ecosystems for machine learning applications. Msystems. e0002623. PMID 38078749 DOI: 10.1128/msystems.00026-23  0.084
2023 Taneja SB, Callahan TJ, Paine MF, Kane-Gill SL, Kilicoglu H, Joachimiak MP, Boyce RD. Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions. Journal of Biomedical Informatics. 140: 104341. PMID 36933632 DOI: 10.1016/j.jbi.2023.104341  0.083
2023 Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G. GRAPE for fast and scalable graph processing and random-walk-based embedding. Nature Computational Science. 3: 552-568. PMID 38177435 DOI: 10.1038/s43588-023-00465-8  0.078
2024 Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, Kim H, Moxon S, Reese JT, Haendel MA, Robinson PN, Mungall CJ. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinformatics (Oxford, England). PMID 38383067 DOI: 10.1093/bioinformatics/btae104  0.077
2021 Joachimiak MP. Zinc against COVID-19? Symptom surveillance and deficiency risk groups. Plos Neglected Tropical Diseases. 15: e0008895. PMID 33395417 DOI: 10.1371/journal.pntd.0008895  0.065
2021 Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, ... ... Joachimiak MP, et al. Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities". Msystems. 6. PMID 33947809 DOI: 10.1128/mSystems.00273-21  0.053
2024 Ladau J, Brodie EL, Falco N, Bansal I, Hoffman EB, Joachimiak MP, Mora AM, Walker AM, Wainwright HM, Wu Y, Pavicic M, Jacobson D, Hess M, Brown JB, Abuabara K. Estimating geographic variation of infection fatality ratios during epidemics. Infectious Disease Modelling. 9: 634-643. PMID 38572058 DOI: 10.1016/j.idm.2024.02.009  0.021
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