Matthew T. Weirauch, Ph.D. - Publications

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

145 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
2021 Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Frontiers in Immunology. 12: 701924. PMID 34421907 DOI: 10.3389/fimmu.2021.701924  1
2021 Felton JM, Bouffi C, Schwartz JT, Schollaert KL, Malik A, Vallabh S, Wronowski B, Magier AZ, Merlin L, Barski A, Weirauch MT, Fulkerson PC, Rothenberg ME. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. PMID 34341502 DOI: 10.1038/s41385-021-00416-4  1
2021 Felton JM, Vallabh S, Parameswaran S, Edsall LE, Ernst K, Wronowski B, Malik A, Kotliar M, Weirauch MT, Barski A, Fulkerson PC, Rothenberg ME. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of Immunology (Baltimore, Md. : 1950). PMID 34330753 DOI: 10.4049/jimmunol.2000207  1
2021 Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, ... ... Weirauch MT, et al. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. Bmc Biology. 19: 150. PMID 34325695 DOI: 10.1186/s12915-021-01098-x  1
2021 Murrison LB, Ren X, Prusse K, He H, Kroner J, Chen X, Jenkins S, Johansson E, Biagini JM, Weirauch MT, Kopan R, Martin LJ, Khurana Hershey GK. TSLP disease-associated genetic variants combined with airway TSLP expression to influence asthma risk. The Journal of Allergy and Clinical Immunology. PMID 34111451 DOI: 10.1016/j.jaci.2021.05.033  1
2021 Hass MR, Brissette D, Parameswaran S, Pujato M, Donmez O, Kottyan LC, Weirauch MT, Kopan R. Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. Plos Genetics. 17: e1009574. PMID 34111109 DOI: 10.1371/journal.pgen.1009574  1
2021 Johnston ME, Rivas MP, Nicolle D, Gorse A, Gulati R, Kumbaji M, Weirauch MT, Bondoc A, Cairo S, Geller J, Tiao G, Timchenko N. Olaparib Inhibits Tumor Growth of Hepatoblastoma in Patient Derived Xenograft Models. Hepatology (Baltimore, Md.). PMID 34037269 DOI: 10.1002/hep.31919  0.01
2021 Moreno-Fernandez ME, Giles DA, Oates JR, Chan CC, Damen MSMA, Doll JR, Stankiewicz TE, Chen X, Chetal K, Karns R, Weirauch MT, Romick-Rosendale L, Xanthakos SA, Sheridan R, Szabo S, et al. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. PMID 34004162 DOI: 10.1016/j.cmet.2021.04.018  1
2021 Ho JSY, Mok BW, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, ... ... Weirauch MT, et al. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell. PMID 33836156 DOI: 10.1016/j.cell.2021.03.051  1
2021 Chidambaran V, Zhang X, Pilipenko V, Chen X, Wronowski B, Geisler K, Martin LJ, Barski A, Weirauch MT, Ji H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics. PMID 33820434 DOI: 10.2217/epi-2020-0424  1
2021 Santiago IJ, Zhang D, Saras A, Pontillo N, Xu C, Chen X, Weirauch MT, Mistry M, Ginty DD, Pecot MY, Peng J. Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33766917 DOI: 10.1073/pnas.2025530118  1
2021 Song R, Gao Y, Dozmorov I, Malladi V, Saha I, McDaniel MM, Parameswaran S, Liang C, Arana C, Zhang B, Wakeland B, Zhou J, Weirauch MT, Kottyan LC, Wakeland EK, et al. IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility. Cell Reports. 34: 108891. PMID 33761354 DOI: 10.1016/j.celrep.2021.108891  1
2021 Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, ... ... Weirauch MT, et al. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. Bmc Biology. 19: 41. PMID 33750380 DOI: 10.1186/s12915-021-00975-9  1
2021 Lu X, Chen X, Forney C, Donmez O, Miller D, Parameswaran S, Hong T, Huang Y, Pujato M, Cazares T, Miraldi ER, Ray JP, de Boer CG, Harley JB, Weirauch MT, et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 12: 1611. PMID 33712590 DOI: 10.1038/s41467-021-21854-5  1
2021 Miraldi ER, Chen X, Weirauch MT. Deciphering cis-regulatory grammar with deep learning. Nature Genetics. 53: 266-268. PMID 33686263 DOI: 10.1038/s41588-021-00814-1  1
2021 Oatman N, Dasgupta N, Arora P, Choi K, Gawali MV, Gupta N, Parameswaran S, Salomone J, Reisz JA, Lawler S, Furnari F, Brennan C, Wu J, Sallans L, Gudelsky G, ... ... Weirauch MT, et al. Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer. Science Advances. 7. PMID 33568479 DOI: 10.1126/sciadv.abd7459  1
2021 Alizada A, Khyzha N, Wang L, Antounians L, Chen X, Khor M, Liang M, Rathnakumar K, Weirauch MT, Medina-Rivera A, Fish JE, Wilson MD. Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals. Nature Communications. 12: 567. PMID 33495464 DOI: 10.1038/s41467-020-20765-1  1
2021 Kottyan LC, Trimarchi MP, Lu X, Caldwell JM, Maddox A, Parameswaran S, Lape M, D'Mello RJ, Bonfield M, Ballaban A, Mukkada V, Putnam PE, Abonia P, Ben-Baruch Morgenstern N, Eapen AA, ... ... Weirauch MT, et al. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. The Journal of Allergy and Clinical Immunology. 147: 255-266. PMID 33446330 DOI: 10.1016/j.jaci.2020.10.018  1
2021 Stone HK, Parameswaran S, Eapen AA, Chen X, Harley JB, Devarajan P, Weirauch MT, Kottyan L. Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk. Kidney International Reports. 6: 187-195. PMID 33426398 DOI: 10.1016/j.ekir.2020.09.048  1
2021 Hou G, Harley ITW, Lu X, Zhou T, Xu N, Yao C, Qin Y, Ouyang Y, Ma J, Zhu X, Yu X, Xu H, Dai D, Ding H, Yin Z, ... ... Weirauch MT, et al. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nature Communications. 12: 135. PMID 33420081 DOI: 10.1038/s41467-020-20460-1  1
2020 Johansson E, Martin LJ, He H, Chen X, Weirauch MT, Kroner JW, Khurana Hershey GK, Biagini JM. Secondhand smoke and NFE2L2 genotype interaction increases pediatric asthma risk and severity. Clinical and Experimental Allergy : Journal of the British Society For Allergy and Clinical Immunology. PMID 33382170 DOI: 10.1111/cea.13815  1
2020 Petrany MJ, Swoboda CO, Sun C, Chetal K, Chen X, Weirauch MT, Salomonis N, Millay DP. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 11: 6374. PMID 33311464 DOI: 10.1038/s41467-020-20063-w  1
2020 Yuin Ho JS, Wing-Yee Mok B, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, ... ... Weirauch MT, et al. Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models. Biorxiv : the Preprint Server For Biology. PMID 33299999 DOI: 10.1101/2020.12.01.404483  1
2020 Yin X, Kim K, Suetsugu H, Bang SY, Wen L, Koido M, Ha E, Liu L, Sakamoto Y, Jo S, Leng RX, Otomo N, Laurynenka V, Kwon YC, Sheng Y, ... ... Weirauch MT, et al. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Annals of the Rheumatic Diseases. PMID 33272962 DOI: 10.1136/annrheumdis-2020-219209  1
2020 Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, ... ... Weirauch MT, et al. Correction to: Genome-enabled insights into the biology of thrips as crop pests. Bmc Biology. 18: 169. PMID 33198778 DOI: 10.1186/s12915-020-00915-z  1
2020 Finch G, Nandyal S, Perretta C, Davies B, Rosendale AJ, Holmes CJ, Gantz JD, Spacht DE, Bailey ST, Chen X, Oyen K, Didion EM, Chakraborty S, Lee RE, Denlinger DL, ... ... Weirauch MT, et al. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Scientific Reports. 10: 19791. PMID 33188214 DOI: 10.1038/s41598-020-76139-6  1
2020 Zhu T, Zhang X, Chen X, Anthony BP, Weirauch MT, Guilbert TW, Khurana Hershey GK, Biagini JM, Ji H. Nasal DNA methylation differentiates severe from non-severe asthma in African-American children. Allergy. PMID 33175399 DOI: 10.1111/all.14655  1
2020 Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, ... ... Weirauch MT, et al. Genome-enabled insights into the biology of thrips as crop pests. Bmc Biology. 18: 142. PMID 33070780 DOI: 10.1186/s12915-020-00862-9  1
2020 Elliott KH, Chen X, Salomone J, Chaturvedi P, Schultz PA, Balchand SK, Servetas JD, Zuniga A, Zeller R, Gebelein B, Weirauch MT, Peterson KA, Brugmann SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. Elife. 9. PMID 33006313 DOI: 10.7554/eLife.56450  1
2020 Maezawa S, Sakashita A, Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nature Structural & Molecular Biology. PMID 32895557 DOI: 10.1038/S41594-020-0488-3  1
2020 Mukherjee S, Chatuverdi P, Rankin SA, Fish MB, Wlizla M, Paraiso KD, MacDonald M, Chen X, Weirauch MT, Blitz IL, Cho KW, Zorn AM. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. Elife. 9. PMID 32894225 DOI: 10.7554/Elife.58029  1
2020 Stevens ML, Zhang Z, Johansson E, Ray S, Jagpal A, Ruff BP, Kothari A, He H, Martin LJ, Ji H, Wikenheiser-Brokamp K, Weirauch MT, Supp DM, Biagini Myers JM, Khurana Hershey GK. Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk. Nature Communications. 11: 4092. PMID 32796837 DOI: 10.1038/S41467-020-17895-X  1
2020 Scott MJ, Benoit JB, Davis RJ, Bailey ST, Varga V, Martinson EO, Hickner PV, Syed Z, Cardoso GA, Torres TT, Weirauch MT, Scholl EH, Phillippy AM, Sagel A, Vasquez M, et al. Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. Communications Biology. 3: 424. PMID 32753684 DOI: 10.1038/s42003-020-01152-4  0.01
2020 Liu X, Hong T, Parameswaran S, Ernst K, Marazzi I, Weirauch MT, Fuxman Bass JI. Human Virus Transcriptional Regulators. Cell. 182: 24-37. PMID 32649876 DOI: 10.1016/J.Cell.2020.06.023  1
2020 Chan CC, Damen MSMA, Moreno-Fernandez ME, Stankiewicz TE, Cappelletti M, Alarcon PC, Oates JR, Doll JR, Mukherjee R, Chen X, Karns R, Weirauch MT, Helmrath MA, Inge TH, Divanovic S. Type I interferon sensing unlocks dormant adipocyte inflammatory potential. Nature Communications. 11: 2745. PMID 32488081 DOI: 10.1038/S41467-020-16571-4  1
2020 Bridges JP, Sudha P, Lipps D, Wagner A, Guo M, Du Y, Brown K, Filuta A, Kitzmiller JA, Stockman C, Chen X, Weirauch MT, Jobe AH, Whitsett JA, Xu Y. Glucocorticoid Regulates Mesenchymal Cell Differentiation Required for Perinatal Lung Morphogenesis and Function. American Journal of Physiology. Lung Cellular and Molecular Physiology. PMID 32460513 DOI: 10.1152/ajplung.00459.2019  1
2020 Rajaram S, Canaday LM, Ochayon DE, Rangel KM, Ali A, Gyurova IE, Krishnamurthy D, Fletcher JS, Reighard SD, Cox A, Weirauch MT, Kottyan LC, Deshmukh H, Zacharias WJ, Borchers MT, et al. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity. PMID 32405233 DOI: 10.1016/J.Immuni.2020.04.018  1
2020 Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni HV, Dugan S, Elpidina EN, Farrow DW, Friedrich M, Gibbs RA, ... ... Weirauch MT, et al. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. Bmc Genomics. 21: 227. PMID 32171258 DOI: 10.1186/S12864-020-6510-7  1
2020 Jennings EC, Korthauer MW, Hendershot JM, Bailey ST, Weirauch MT, Ribeiro JM, Benoit JB. Molecular mechanisms underlying milk production and viviparity in the cockroach, Diploptera punctata. Insect Biochemistry and Molecular Biology. 103333. PMID 32119906 DOI: 10.1016/J.Ibmb.2020.103333  0.01
2020 Sirvent S, Vallejo AF, Davies J, Clayton K, Wu Z, Woo J, Riddell J, Chaudhri VK, Stumpf P, Nazlamova LA, Wheway G, Rose-Zerilli M, West J, Pujato M, Chen X, ... ... Weirauch MT, et al. Genomic programming of IRF4-expressing human Langerhans cells. Nature Communications. 11: 313. PMID 31949143 DOI: 10.1038/S41467-019-14125-X  1
2020 Kottyan LC, Parameswaran S, Weirauch MT, Rothenberg ME, Martin LJ. The genetic etiology of eosinophilic esophagitis. The Journal of Allergy and Clinical Immunology. 145: 9-15. PMID 31910986 DOI: 10.1016/J.Jaci.2019.11.013  1
2020 Emadi B, Carter M, Eswar S, Chen X, Laurynenka V, Parameswaran S, Kaufman KM, Namjou B, Kottyan LC, Weirauch M, Harley J. P136 Epstein-Barr Virus Transcription Co-Factors Bind To Many Inflammatory Bowel Disease Risk Loci Gastroenterology. 158. DOI: 10.1053/J.Gastro.2019.11.142  1
2020 Johansson E, Myers JB, Martin L, He H, Weirauch M, Chen X, Hershey GK. NFE2L2 Interacts with Second Hand Smoke Exposure to Increase the Risk and Severity of Pediatric Asthma The Journal of Allergy and Clinical Immunology. 145. DOI: 10.1016/J.Jaci.2019.12.584  1
2020 Eapen A, Lu X, Forney C, Parameswaran S, Ray J, Weirauch M, Kottyan L. Massively Parallel Reporter Assays (MPRAs) Identify Allelic Transcriptional Dysregulation in Atopic Dermatitis The Journal of Allergy and Clinical Immunology. 145. DOI: 10.1016/J.Jaci.2019.12.289  1
2019 Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. PMID 31653690 DOI: 10.1084/Jem.20182009  1
2019 Liu X, Helenius D, Skotte L, Beaumont RN, Wielscher M, Geller F, Juodakis J, Mahajan A, Bradfield JP, Lin FTJ, Vogelezang S, Bustamante M, Ahluwalia TS, Pitkänen N, Wang CA, ... ... Weirauch MT, et al. Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Nature Communications. 10: 3927. PMID 31477735 DOI: 10.1038/S41467-019-11881-8  1
2019 Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, ... ... Weirauch MT, et al. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biology. 20: 187. PMID 31477173 DOI: 10.1186/S13059-019-1768-2  0.01
2019 Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nature Genetics. PMID 31133749 DOI: 10.1038/S41588-019-0411-1  1
2019 Burleson JD, Siniard D, Yadagiri VK, Chen X, Weirauch MT, Ruff BP, Brandt EB, Hershey GKK, Ji H. TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells. Scientific Reports. 9: 7361. PMID 31089182 DOI: 10.1038/S41598-019-43767-6  1
2019 Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, et al. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biology. 20: 64. PMID 30935422 DOI: 10.1186/S13059-019-1660-0  1
2019 Chidambaran V, Zhang X, Geisler K, Stubbeman BL, Chen X, Weirauch MT, Meller J, Ji H. Enrichment of genomic pathways based on differential DNA methylation associated with chronic postsurgical pain and anxiety in children - a prospective, pilot study. The Journal of Pain : Official Journal of the American Pain Society. PMID 30639570 DOI: 10.1016/J.Jpain.2018.12.008  1
2019 Miller DE, Forney C, Rochman M, Cranert S, Habel J, Rymer J, Lynch A, Schroeder C, Lee J, Sauder A, Smith Q, Chawla M, Trimarchi MP, Lu X, Fjellman E, ... ... Weirauch MT, et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3 (Bethesda, Md.). PMID 30626591 DOI: 10.1534/G3.118.200901  1
2019 Oatman N, Dasgupta N, Dasgupta B, Choi K, Gawali M, Gupta N, Parameswaran S, Lawler S, Brennan C, Wu J, Sallans L, Desai P, Weirauch M, Komurov K. Cbmt-05. Genetic And Epigenetic Mechanisms Regulating Scd Inhibitor Sensitivity In Glioblastoma Neuro-Oncology. 21. DOI: 10.1093/Neuonc/Noz175.127  1
2018 Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, ... ... Weirauch MT, et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. PMID 30464347 DOI: 10.1038/S41586-018-0734-6  0.01
2018 Modur V, Singh N, Mohanty V, Chung E, Muhammad B, Choi K, Chen X, Chetal K, Ratner N, Salomonis N, Weirauch MT, Waltz S, Huang G, Privette-Vinnedge L, Park JS, et al. Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nature Communications. 9: 4410. PMID 30353012 DOI: 10.1038/S41467-018-06810-0  1
2018 Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell. 175: 598-599. PMID 30290144 DOI: 10.1016/j.cell.2018.09.045  1
2018 Valanejad L, Cast A, Wright M, Bissig KD, Karns R, Weirauch MT, Timchenko N. PARP1 activation increases expression of modified tumor suppressors and pathways underlying development of aggressive hepatoblastoma. Communications Biology. 1: 67. PMID 30271949 DOI: 10.1038/s42003-018-0077-8  0.01
2018 Muench DE, Ferchen K, Velu CS, Pradhan K, Chetal K, Chen X, Weirauch MT, Colmenares C, Verma A, Salomonis N, Grimes HL. controls MDS-associated chronic TGFβ signaling, aberrant splicing, and stem cell fitness. Blood. PMID 30249787 DOI: 10.1182/Blood-2018-06-860890  1
2018 Zhang C, Seo J, Murakami K, Salem ESB, Bernhard E, Borra VJ, Choi K, Yuan CL, Chan CC, Chen X, Huang T, Weirauch MT, Divanovic S, Qi NR, Thomas HE, et al. Hepatic Ago2-mediated RNA silencing controls energy metabolism linked to AMPK activation and obesity-associated pathophysiology. Nature Communications. 9: 3658. PMID 30201950 DOI: 10.1038/S41467-018-05870-6  1
2018 Chhipa RR, Fan Q, Anderson J, Muraleedharan R, Huang Y, Ciraolo G, Chen X, Waclaw R, Chow LM, Khuchua Z, Kofron M, Weirauch MT, Kendler A, McPherson C, Ratner N, et al. Author Correction: AMP kinase promotes glioblastoma bioenergetics and tumour growth. Nature Cell Biology. PMID 30190576 DOI: 10.1038/s41556-018-0203-3  1
2018 Chhipa RR, Fan Q, Anderson J, Muraleedharan R, Huang Y, Ciraolo G, Chen X, Waclaw R, Chow LM, Khuchua Z, Kofron M, Weirauch MT, Kendler A, McPherson C, Ratner N, et al. Publisher Correction: AMP kinase promotes glioblastoma bioenergetics and tumour growth. Nature Cell Biology. PMID 30089841 DOI: 10.1038/S41556-018-0185-1  1
2018 Bernstein DI, Lummus ZL, Kesavalu B, Yao J, Kottyan L, Miller D, Cartier A, Cruz MJ, Lemiere C, Muñoz X, Quirce S, Tarlo S, Sastre J, Boulet LP, Weirauch MT, et al. Genetic Variants with Gene Regulatory Effects are Associated with Diisocyanate Asthma. The Journal of Allergy and Clinical Immunology. PMID 29969634 DOI: 10.1016/J.Jaci.2018.06.022  1
2018 Chhipa RR, Fan Q, Anderson J, Muraleedharan R, Huang Y, Ciraolo G, Chen X, Waclaw R, Chow LM, Khuchua Z, Kofron M, Weirauch MT, Kendler A, McPherson C, Ratner N, et al. AMP kinase promotes glioblastoma bioenergetics and tumour growth. Nature Cell Biology. PMID 29915361 DOI: 10.1038/S41556-018-0126-Z  1
2018 Patel Z, Lu X, Miller D, Forney CR, Lee J, Lynch A, Schroeder C, Parks L, Magnusen AF, Chen X, Pujato M, Maddox A, Zoller EE, Namjou B, Brunner HI, ... ... Weirauch MT, et al. A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Human Molecular Genetics. PMID 29912393 DOI: 10.1093/Hmg/Ddy140  1
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  1
2018 Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H. Nasal DNA methylation is associated with childhood asthma. Epigenomics. PMID 29692198 DOI: 10.2217/Epi-2017-0127  1
2018 Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. PMID 29662164 DOI: 10.1038/S41588-018-0102-3  1
2018 Zandvakili A, Campbell I, Gutzwiller LM, Weirauch MT, Gebelein B. Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity. Plos Genetics. 14: e1007289. PMID 29617378 DOI: 10.1371/Journal.Pgen.1007289  0.01
2018 Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell. 172: 650-665. PMID 29425488 DOI: 10.1016/j.cell.2018.01.029  1
2018 Schoville SD, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, ... ... Weirauch MT, et al. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports. 8: 1931. PMID 29386578 DOI: 10.1038/S41598-018-20154-1  1
2018 Harley J, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen A, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman K, Kottyan L, Weirauch M. GG-09 A role for EBNA2 in mechanisms that are responsible for lupus and other autoimmune diseases Lupus Science & Medicine. 5. DOI: 10.1136/Lupus-2018-Lsm.96  1
2017 Tillo D, Ray S, Syed KS, Gaylor MR, He X, Wang J, Assad N, Durell S, Porollo A, Weirauch MT, Vinson C. The Epstein-Barr virus B-ZIP protein Zta recognizes specific DNA sequences containing 5-methylcytosine and 5-hydroxymethylcytosine. Biochemistry. PMID 29072898 DOI: 10.1021/Acs.Biochem.7B00741  1
2017 Zhang X, Biagini Myers JM, Yadagiri VK, Ulm A, Chen X, Weirauch MT, Khurana Hershey GK, Ji H. Nasal DNA methylation differentiates corticosteroid treatment response in pediatric asthma: A pilot study. Plos One. 12: e0186150. PMID 29028809 DOI: 10.1371/Journal.Pone.0186150  1
2017 Lander JM, Supp DM, He H, Martin LJ, Chen X, Weirauch MT, Boyce ST, Kopan R. Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. Plos One. 12: e0184500. PMID 28953906 DOI: 10.1371/Journal.Pone.0184500  1
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  1
2017 Zhang G, Feenstra B, Bacelis J, Liu X, Muglia LM, Juodakis J, Miller DE, Litterman N, Jiang PP, Russell L, Hinds DA, Hu Y, Weirauch MT, Chen X, Chavan AR, et al. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. The New England Journal of Medicine. PMID 28877031 DOI: 10.1056/Nejmoa1612665  1
2017 Gu Z, Kalamboglas J, Yoshioka S, Han W, Li Z, Kawasawa YI, Pochareddy S, Li Z, Liu F, Xu X, Wijeratne S, Ueno M, Blatz E, Salomone J, Kumanogoh A, ... ... Weirauch MT, et al. Control of species-dependent cortico-motoneuronal connections underlying manual dexterity. Science (New York, N.Y.). 357: 400-404. PMID 28751609 DOI: 10.1126/Science.Aan3721  0.01
2017 Lin S, Ptasinska A, Chen X, Shrestha M, Assi SA, Chin PS, Imperato MR, Aronow B, Zhang J, Weirauch MT, Bonifer C, Mulloy JC. A FOXO1-induced oncogenic network defines the AML1-ETO pre-leukemic program. Blood. PMID 28710059 DOI: 10.1182/Blood-2016-11-750976  1
2017 Endale M, Ahlfeld S, Bao E, Chen X, Green J, Bess Z, Weirauch M, Xu Y, Perl AK. Dataset on transcriptional profiles and the developmental characteristics of PDGFRα expressing lung fibroblasts. Data in Brief. 13: 415-431. PMID 28702480 DOI: 10.1016/j.dib.2017.06.001  1
2017 Chidambaran V, Zhang X, Martin LJ, Ding L, Weirauch MT, Geisler K, Stubbeman BL, Sadhasivam S, Ji H. DNA methylation at the mu-1 opioid receptor gene (OPRM1) promoter predicts preoperative, acute, and chronic postsurgical pain after spine fusion. Pharmacogenomics and Personalized Medicine. 10: 157-168. PMID 28533693 DOI: 10.2147/Pgpm.S132691  1
2017 Endale M, Ahlfeld S, Bao E, Chen X, Green J, Bess Z, Weirauch MT, Xu Y, Perl AK. Temporal, Spatial, and Phenotypical Changes of PDGFRα Expressing Fibroblasts during Late Lung Development. Developmental Biology. PMID 28408205 DOI: 10.1016/j.ydbio.2017.03.020  1
2017 Dauber A, Cunha-Silva M, Macedo DB, Brito VN, Abreu AP, Roberts SA, Montenegro LR, Andrew M, Kirby A, Weirauch MT, Labilloy G, Bessa DS, Carroll RS, Jacobs DC, Chappell PE, et al. Paternally Inherited DLK1 Deletion Associated with Familial Central Precocious Puberty. The Journal of Clinical Endocrinology and Metabolism. PMID 28324015 DOI: 10.1210/Jc.2016-3677  0.01
2017 Fang J, Bolanos LC, Choi K, Liu X, Christie S, Akunuru S, Kumar R, Wang D, Chen X, Greis KD, Stoilov P, Filippi MD, Maciejewski JP, Garcia-Manero G, Weirauch MT, et al. Corrigendum: Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nature Immunology. 18: 474. PMID 28323261 DOI: 10.1038/Ni0417-474A  1
2017 Johansson E, Biagini Myers JM, Martin LJ, He H, Pilipenko V, Mersha T, Weirauch M, Salomonis N, Ryan P, LeMasters GK, Bernstein DI, Lockey J, Khurana Hershey GK. KIF3A genetic variation is associated with pediatric asthma in the presence of eczema independent of allergic rhinitis. The Journal of Allergy and Clinical Immunology. PMID 28238750 DOI: 10.1016/J.Jaci.2017.02.003  1
2017 Vander Lugt B, Riddell J, Khan AA, Hackney JA, Lesch J, DeVoss J, Weirauch MT, Singh H, Mellman I. Transcriptional determinants of tolerogenic and immunogenic states during dendritic cell maturation. The Journal of Cell Biology. PMID 28130292 DOI: 10.1083/Jcb.201512012  0.01
2016 Fang J, Bolanos LC, Choi K, Liu X, Christie S, Akunuru S, Kumar R, Wang D, Chen X, Greis KD, Stoilov P, Filippi MD, Maciejewski JP, Garcia-Manero G, Weirauch MT, et al. Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nature Immunology. PMID 28024152 DOI: 10.1038/Ni.3654  1
2016 Imai F, Chen X, Weirauch MT, Yoshida Y. Requirement for Dicer in Maintenance of Monosynaptic Sensory-Motor Circuits in the Spinal Cord. Cell Reports. 17: 2163-2172. PMID 27880894 DOI: 10.1016/J.Celrep.2016.10.083  1
2016 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. 64: 213. PMID 27716485 DOI: 10.1016/j.molcel.2016.09.035  1
2016 Miller DE, Patel ZH, Lu X, Lynch AT, Weirauch MT, Kottyan LC. Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). Journal of Visualized Experiments : Jove. PMID 27585267 DOI: 10.3791/54093  1
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  1
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  1
2016 Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JS, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, ... ... Weirauch M, et al. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science (New York, N.Y.). PMID 27127234 DOI: 10.1126/Science.Aad7993  1
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  1
2016 Patel Z, Weirauch M, Kottyan LC, Harley JB. GG-03 STAT1-STAT4 association with systemic lupus erythematosus (SLE) Lupus Science & Medicine. 3. DOI: 10.1136/Lupus-2016-000179.55  1
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.7118.2  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Fowler T, Garruss AS, Ghosh A, De S, Becker KG, Wood WH, Weirauch MT, Smale ST, Aronow B, Sen R, Roy AL. Divergence of transcriptional landscape occurs early in B cell activation. Epigenetics & Chromatin. 8: 20. PMID 25987903 DOI: 10.1186/S13072-015-0012-X  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Moncrieffe H, Lele A, Shams KA, Levy BE, Marion M, Sudman M, Brungs L, Cobb J, Hinks A, Bohnsack J, Wedderburn LR, Haas J-, Videm V, Rygg M, Nordal E, ... ... Weirauch MT, et al. OP0122 Fine Mapping of the CHR 22Q13.1 Juvenile Idiopathic Arthritis Risk Locus Annals of the Rheumatic Diseases. 74: 114-114. DOI: 10.1136/Annrheumdis-2015-Eular.5296  1
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  1
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  1
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  1
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  1
2014 Zhang X, Ulm A, Somineni HK, Oh S, Weirauch MT, Zhang HX, Chen X, Lehn MA, Janssen EM, Ji H. DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells. Epigenetics & Chromatin. 7: 21. PMID 25161698 DOI: 10.1186/1756-8935-7-21  1
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  1
2014 Pestle WJ, Crowley BE, Weirauch MT. Quantifying inter-laboratory variability in stable isotope analysis of ancient skeletal remains. Plos One. 9: e102844. PMID 25061843 DOI: 10.1371/Journal.Pone.0102844  1
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  1
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  1
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  1
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. Author response: Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways Elife. DOI: 10.7554/Elife.02626.031  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Weirauch MT, Wong CK, Byrne AB, Stuart JM. Information-based methods for predicting gene function from systematic gene knock-downs. Bmc Bioinformatics. 9: 463. PMID 18959798 DOI: 10.1186/1471-2105-9-463  1
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  1
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  1
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  1
2005 Elnitski L, Giardine B, Shah P, Zhang Y, Riemer C, Weirauch M, Burhans R, Miller W, Hardison RC. Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Research. 33: D466-70. PMID 15608239 DOI: 10.1093/Nar/Gki045  1
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