Matthew T. Weirauch, Ph.D. - Publications

Affiliations: 
2009 University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
Bioinformatics Biology, Genetics, Biostatistics Biology

49 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
2018 Boni AC, Ambrósio DL, Cupertino FB, Montenegro-Montero A, Virgilio S, Freitas FZ, Corrocher FA, Gonçalves RD, Yang A, Weirauch MT, Hughes TR, Larrondo LF, Bertolini MC. Neurospora crassa developmental control mediated by the FLB-3 transcription factor. Fungal Biology. 122: 570-582. PMID 29801802 DOI: 10.1016/j.funbio.2018.01.004  0.44
2017 Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR. Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biology. 18: 167. PMID 28877740 DOI: 10.1186/s13059-017-1287-y  0.44
2016 Khund-Sayeed S, He X, Holzberg T, Wang J, Rajagopal D, Upadhyay S, Durell SR, Mukherjee S, Weirauch MT, Rose R, Vinson C. 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 27485769 DOI: 10.1039/c6ib00079g  0.4
2016 Mao AP, Constantinides MG, Mathew R, Zuo Z, Chen X, Weirauch MT, Bendelac A. Multiple layers of transcriptional regulation by PLZF in NKT-cell development. Proceedings of the National Academy of Sciences of the United States of America. PMID 27325774 DOI: 10.1073/pnas.1601504113  0.4
2016 Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, ... ... Weirauch MT, et al. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nature Communications. 7: 10165. PMID 26836814 DOI: 10.1038/ncomms10165  0.4
2015 Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, ... ... Weirauch MT, et al. DREAMTools: a Python package for scoring collaborative challenges. F1000research. 4: 1030. PMID 27134723 DOI: 10.12688/f1000research.7118.1  0.4
2015 Chen X, Ernst K, Soman F, Borowczak M, Weirauch MT. CressInt: a user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana. Current Plant Biology. 3: 48-55. PMID 26855883 DOI: 10.1016/j.cpb.2015.09.001  0.4
2015 Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Affinity regression predicts the recognition code of nucleic acid-binding proteins. Nature Biotechnology. PMID 26571099 DOI: 10.1038/nbt.3343  0.4
2015 Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC. Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. Journal of Immunology (Baltimore, Md. : 1950). 195: 2683-95. PMID 26268651 DOI: 10.4049/jimmunol.1500510  0.4
2015 Hass MR, Liow HH, Chen X, Sharma A, Inoue YU, Inoue T, Reeb A, Martens A, Fulbright M, Raju S, Stevens M, Boyle S, Park JS, Weirauch MT, Brent MR, et al. SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. Molecular Cell. 59: 685-97. PMID 26257285 DOI: 10.1016/j.molcel.2015.07.008  0.4
2015 Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 33: 831-8. PMID 26213851 DOI: 10.1038/nbt.3300  0.4
2015 He X, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C. GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays. G3 (Bethesda, Md.). 5: 1909-18. PMID 26185160 DOI: 10.1534/g3.115.020248  0.4
2015 Pan W, Zhu S, Dai D, Liu Z, Li D, Li B, Gagliani N, Zheng Y, Tang Y, Weirauch MT, Chen X, Zhu W, Wang Y, Chen B, Qian Y, et al. MiR-125a targets effector programs to stabilize Treg-mediated immune homeostasis. Nature Communications. 6: 7096. PMID 25963922 DOI: 10.1038/ncomms8096  0.4
2015 Yucesoy B, Kaufman KM, Lummus ZL, Weirauch MT, Zhang G, Cartier A, Boulet LP, Sastre J, Quirce S, Tarlo SM, Cruz MJ, Munoz X, Harley JB, Bernstein DI. Genome-Wide Association Study Identifies Novel Loci Associated With Diisocyanate-Induced Occupational Asthma. Toxicological Sciences : An Official Journal of the Society of Toxicology. 146: 192-201. PMID 25918132 DOI: 10.1093/toxsci/kfv084  0.4
2015 Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 4. PMID 25905672 DOI: 10.7554/eLife.06967  0.4
2015 Lu X, Zoller EE, Weirauch MT, Wu Z, Namjou B, Williams AH, Ziegler JT, Comeau ME, Marion MC, Glenn SB, Adler A, Shen N, Nath SK, Stevens AM, Freedman BI, et al. Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression. American Journal of Human Genetics. 96: 731-9. PMID 25865496 DOI: 10.1016/j.ajhg.2015.03.002  0.4
2015 Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnology. 33: 555-62. PMID 25690854 DOI: 10.1038/nbt.3128  0.4
2015 Makashir SB, Kottyan LC, Weirauch MT. Meta-analysis of differential gene co-expression: application to lupus. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 443-54. PMID 25592603  0.4
2015 Kottyan LC, Weirauch MT, Rothenberg ME. Making it big in allergy. The Journal of Allergy and Clinical Immunology. 135: 43-5. PMID 25567041 DOI: 10.1016/j.jaci.2014.10.041  0.4
2015 Kottyan LC, Zoller EE, Bene J, Lu X, Kelly JA, Rupert AM, Lessard CJ, Vaughn SE, Marion M, Weirauch MT, Namjou B, Adler A, Rasmussen A, Glenn S, Montgomery CG, et al. The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Human Molecular Genetics. 24: 582-96. PMID 25205108 DOI: 10.1093/hmg/ddu455  0.4
2014 Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, ... ... Weirauch MT, et al. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife. 3: e02626. PMID 25279814 DOI: 10.7554/eLife.02626  0.4
2014 Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Reports. 8: 2015-30. PMID 25220462 DOI: 10.1016/j.celrep.2014.08.019  0.4
2014 Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 158: 1431-43. PMID 25215497 DOI: 10.1016/j.cell.2014.08.009  0.4
2014 Fang J, Barker B, Bolanos L, Liu X, Jerez A, Makishima H, Christie S, Chen X, Rao DS, Grimes HL, Komurov K, Weirauch MT, Cancelas JA, Maciejewski JP, Starczynowski DT. Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network. Cell Reports. 8: 1328-38. PMID 25199827 DOI: 10.1016/j.celrep.2014.07.062  0.4
2014 Martin LJ, Pilipenko V, Kaufman KM, Cripe L, Kottyan LC, Keddache M, Dexheimer P, Weirauch MT, Benson DW. Whole exome sequencing for familial bicuspid aortic valve identifies putative variants. Circulation. Cardiovascular Genetics. 7: 677-83. PMID 25085919 DOI: 10.1161/CIRCGENETICS.114.000526  0.4
2014 Kottyan LC, Davis BP, Sherrill JD, Liu K, Rochman M, Kaufman K, Weirauch MT, Vaughn S, Lazaro S, Rupert AM, Kohram M, Stucke EM, Kemme KA, Magnusen A, He H, et al. Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease. Nature Genetics. 46: 895-900. PMID 25017104 DOI: 10.1038/ng.3033  0.4
2014 Qian Y, Johnson JA, Connor JA, Valencia CA, Barasa N, Schubert J, Husami A, Kissell D, Zhang G, Weirauch MT, Filipovich AH, Zhang K. The 253-kb inversion and deep intronic mutations in UNC13D are present in North American patients with familial hemophagocytic lymphohistiocytosis 3. Pediatric Blood & Cancer. 61: 1034-40. PMID 24470399 DOI: 10.1002/pbc.24955  0.4
2014 Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Research. 42: 153-62. PMID 24068555 DOI: 10.1093/nar/gkt858  0.4
2013 Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I. Early evolution of the T-box transcription factor family. Proceedings of the National Academy of Sciences of the United States of America. 110: 16050-5. PMID 24043797 DOI: 10.1073/pnas.1309748110  0.4
2013 Meir YJ, Lin A, Huang MF, Lin JR, Weirauch MT, Chou HC, Lin SJ, Wu SC. A versatile, highly efficient, and potentially safer piggyBac transposon system for mammalian genome manipulations. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 27: 4429-43. PMID 23896728 DOI: 10.1096/fj.12-223586  0.4
2013 Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499: 172-7. PMID 23846655 DOI: 10.1038/nature12311  0.4
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/eLife.00675  0.4
2013 Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, et al. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Molecular Cell. 51: 116-27. PMID 23791784 DOI: 10.1016/j.molcel.2013.05.018  0.4
2013 Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C. CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Research. 23: 988-97. PMID 23590861 DOI: 10.1101/gr.146654.112  0.4
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/nbt.2486  0.4
2012 Ochs SM, Thumann S, Richau R, Weirauch MT, Lowe TM, Thomm M, Hausner W. Activation of archaeal transcription mediated by recruitment of transcription factor B. The Journal of Biological Chemistry. 287: 18863-71. PMID 22496454 DOI: 10.1074/jbc.M112.365742  0.4
2011 Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J. Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 10690-5. PMID 21673140 DOI: 10.1073/pnas.1102544108  0.4
2011 Weirauch MT, Hughes TR. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Sub-Cellular Biochemistry. 52: 25-73. PMID 21557078 DOI: 10.1007/978-90-481-9069-0_3  0.4
2011 Meir YJ, Weirauch MT, Yang HS, Chung PC, Yu RK, Wu SC. Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy. Bmc Biotechnology. 11: 28. PMID 21447194 DOI: 10.1186/1472-6750-11-28  0.4
2011 Weirauch MT. Gene Coexpression Networks for the Analysis of DNA Microarray Data Applied Statistics For Network Biology: Methods in Systems Biology. 1: 215-250. DOI: 10.1002/9783527638079.ch11  0.4
2010 Weirauch MT, Hughes TR. Dramatic changes in transcription factor binding over evolutionary time. Genome Biology. 11: 122. PMID 20519030 DOI: 10.1186/gb-2010-11-6-122  0.4
2010 Wang BD, Kline CL, Pastor DM, Olson TL, Frank B, Luu T, Sharma AK, Robertson G, Weirauch MT, Patierno SR, Stuart JM, Irby RB, Lee NH. Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NF kappaB and microRNA network. Molecular Cancer. 9: 98. PMID 20433755 DOI: 10.1186/1476-4598-9-98  0.4
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Weirauch MT, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/science.1180823  0.4
2010 Weirauch MT, Hughes TR. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends in Genetics : Tig. 26: 66-74. PMID 20083321 DOI: 10.1016/j.tig.2009.12.002  0.4
2009 Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Journal of Bacteriology. 191: 782-794. PMID 19047344 DOI: 10.1128/JB.00965-08  0.4
2008 Liu GE, Weirauch MT, Van Tassell CP, Li RW, Sonstegard TS, Matukumalli LK, Connor EE, Hanson RW, Yang J. Identification of Conserved Regulatory Elements in Mammalian Promoter Regions: A Case Study Using the PCK1 Promoter Genomics, Proteomics and Bioinformatics. 6: 129-143. PMID 19329064 DOI: 10.1016/S1672-0229(09)60001-2  0.4
2007 Byrne AB, Weirauch MT, Wong V, Koeva M, Dixon SJ, Stuart JM, Roy PJ. A global analysis of genetic interactions in Caenorhabditis elegans. Journal of Biology. 6: 8. PMID 17897480 DOI: 10.1186/jbiol58  0.4
2007 Chen C, Weirauch MT, Powell CC, Zambon AC, Stuart JM. A search engine to identify pathway genes from expression data on multiple organisms. Bmc Systems Biology. 1: 20. PMID 17477880 DOI: 10.1186/1752-0509-1-20  0.4
2006 Khatib F, Weirauch MT, Rohl CA. Rapid knot detection and application to protein structure prediction. Bioinformatics (Oxford, England). 22: e252-9. PMID 16873480 DOI: 10.1093/bioinformatics/btl236  0.4
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