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Reference EntriesFull Text
Weirauch, Matthew T
Journal title:American Men & Women of Science : A Biographical Directory of Today’s Leaders in Physical, Biological and Related Sciences: TRA-WID, 2022, p.12132-12132
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Weirauch, Matthew T
Journal title:American Men & Women of Science : A Biographical Directory of Today’s Leaders in Physical, Biological and Related Sciences: TRO-WIK, 2021, p.12100-12100
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ArticlesPeer ReviewedFull Text
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Author / Creator:Alipanahi, Babak ; Delong, Andrew ; Weirauch, Matthew T ; Frey, Brendan J
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2015-08, Vol.33 (8), p.831-838
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ArticlesPeer ReviewedFull Text
Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers
Author / Creator:Petrany, Michael J. ; Swoboda, Casey O. ; Sun, Chengyi ; Chetal, Kashish ; Chen, Xiaoting ; Weirauch, Matthew T. ; Salomonis, Nathan ; Millay, Douglas P.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-12, Vol.11 (1), p.6374-12, Article 6374
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ArticlesPeer ReviewedFull Text
Quantifying Inter-Laboratory Variability in Stable Isotope Analysis of Ancient Skeletal Remains
Author / Creator:Pestle, William J. ; Crowley, Brooke E. ; Weirauch, Matthew T.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2014-07, Vol.9 (7), p.e102844-e102844
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ArticlesPeer ReviewedFull Text
C2H2 zinc finger proteins greatly expand the human regulatory lexicon
Author / Creator:Najafabadi, Hamed S ; Mnaimneh, Sanie ; Schmitges, Frank W ; Garton, Michael ; Lam, Kathy N ; Yang, Ally ; Albu, Mihai ; Weirauch, Matthew T ; Radovani, Ernest ; Kim, Philip M ; Greenblatt, Jack ; Frey, Brendan J ; Hughes, Timothy R
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2015-05, Vol.33 (5), p.555-562
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ArticlesPeer ReviewedFull Text
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
Author / Creator:Fu, Hailu ; Zheng, Haizi ; Chen, Xiaoting ; Weirauch, Matthew T. ; Muglia, Louis J. ; Wang, Li ; Liu, Yaping
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2023-03, Vol.24 (1), p.50-50, Article 50
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ArticlesPeer ReviewedFull Text
Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets
Author / Creator:Hass, Matthew R. ; Brissette, Daniel ; Parameswaran, Sreeja ; Pujato, Mario ; Donmez, Omer ; Kottyan, Leah C. ; Weirauch, Matthew T. ; Kopan, Raphael
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2021-06, Vol.17 (6), p.e1009574-e1009574
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Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition
Author / Creator:Maezawa, So ; Sakashita, Akihiko ; Yukawa, Masashi ; Chen, Xiaoting ; Takahashi, Kazuki ; Alavattam, Kris G. ; Nakata, Ippo ; Weirauch, Matthew T. ; Barski, Artem ; Namekawa, Satoshi H.
Publisher:New York: Nature Publishing Group US
Journal title:Nature structural & molecular biology, 2020-10, Vol.27 (10), p.978-988
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ArticlesPeer ReviewedFull Text
SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression
Author / Creator:Hou, Guojun ; Harley, Isaac T. W. ; Lu, Xiaoming ; Zhou, Tian ; Xu, Ning ; Yao, Chao ; Qin, Yuting ; Ouyang, Ye ; Ma, Jianyang ; Zhu, Xinyi ; Yu, Xiang ; Xu, Hong ; Dai, Dai ; Ding, Huihua ; Yin, Zhihua ; Ye, Zhizhong ; Deng, Jun ; Zhou, Mi ; Tang, Yuanjia ; Namjou, Bahram ; Guo, Ya ; Weirauch, Matthew T. ; Kottyan, Leah C. ; Harley, John B. ; Shen, Nan
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-01, Vol.12 (1), p.135-135, Article 135
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ArticlesPeer ReviewedFull Text
Multiple layers of transcriptional regulation by PLZF in NKT-cell development
Author / Creator:Mao, Ai-Ping ; Constantinides, Michael G. ; Mathew, Rebecca ; Zuo, Zhixiang ; Chen, Xiaoting ; Weirauch, Matthew T. ; Bendelac, Albert
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2016-07, Vol.113 (27), p.7602-7607
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Lineage tracing of nuclei in skeletal myofibers uncovers distinct transcripts and interplay between myonuclear populations
Author / Creator:Sun, Chengyi ; Swoboda, Casey O. ; Morales, Fabian Montecino ; Calvo, Cristofer ; Petrany, Michael J. ; Parameswaran, Sreeja ; VonHandorf, Andrew ; Weirauch, Matthew T. ; Lepper, Christoph ; Millay, Douglas P.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-10, Vol.15 (1), p.9372-19, Article 9372
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ArticlesPeer ReviewedFull Text
Control of species-dependent cortico-motoneuronal connections underlying manual dexterity
Author / Creator:Gu, Zirong ; Kalamboglas, John ; Yoshioka, Shin ; Han, Wenqi ; Li, Zhuo ; Kawasawa, Yuka Imamura ; Pochareddy, Sirisha ; Li, Zhen ; Liu, Fuchen ; Xu, Xuming ; Wijeratne, Sagara ; Ueno, Masaki ; Blatz, Emily ; Salomone, Joseph ; Kumanogoh, Atsushi ; Rasin, Mladen-Roko ; Gebelein, Brian ; Weirauch, Matthew T. ; Sestan, Nenad ; Martin, John H. ; Yoshida, Yutaka
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2017-07, Vol.357 (6349), p.400-404
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ArticlesPeer ReviewedFull Text
MiR-125a targets effector programs to stabilize Treg-mediated immune homeostasis
Author / Creator:Pan, Wen ; Zhu, Shu ; Dai, Dai ; Liu, Zheng ; Li, Dan ; Li, Bin ; Gagliani, Nicola ; Zheng, Yunjiang ; Tang, Yuanjia ; Weirauch, Matthew T. ; Chen, Xiaoting ; Zhu, Wei ; Wang, Yue ; Chen, Bo ; Qian, Youcun ; Chen, Yingxuan ; Fang, Jingyuan ; Herbst, Ronald ; Richman, Laura ; Jallal, Bahija ; Harley, John B. ; Flavell, Richard A. ; Yao, Yihong ; Shen, Nan
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2015-05, Vol.6 (1), p.7096-7096, Article 7096
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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Author / Creator:Cazares, Tareian A. ; Rizvi, Faiz W. ; Iyer, Balaji ; Chen, Xiaoting ; Kotliar, Michael ; Bejjani, Anthony T. ; Wayman, Joseph A. ; Donmez, Omer ; Wronowski, Benjamin ; Parameswaran, Sreeja ; Kottyan, Leah C. ; Barski, Artem ; Weirauch, Matthew T. ; Prasath, V. B. Surya ; Miraldi, Emily R.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2023-01, Vol.19 (1), p.e1010863
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ArticlesPeer ReviewedFull Text
Global discovery of lupus genetic risk variant allelic enhancer activity
Author / Creator:Lu, Xiaoming ; Chen, Xiaoting ; Forney, Carmy ; Donmez, Omer ; Miller, Daniel ; Parameswaran, Sreeja ; Hong, Ted ; Huang, Yongbo ; Pujato, Mario ; Cazares, Tareian ; Miraldi, Emily R. ; Ray, John P. ; de Boer, Carl G. ; Harley, John B. ; Weirauch, Matthew T. ; Kottyan, Leah C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-03, Vol.12 (1), p.1611-1611, Article 1611
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ArticlesPeer ReviewedFull Text
Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins
Author / Creator:Gordon, Blair R.G ; Li, Yifei ; Cote, Atina ; Weirauch, Matthew T ; Ding, Pengfei ; Hughes, Timothy R ; Navarre, William Wiley ; Xia, Bin ; Liu, Jun
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (26), p.10690-10695
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Type I interferon sensing unlocks dormant adipocyte inflammatory potential
Author / Creator:Chan, Calvin C. ; Damen, Michelle S. M. A. ; Moreno-Fernandez, Maria E. ; Stankiewicz, Traci E. ; Cappelletti, Monica ; Alarcon, Pablo C. ; Oates, Jarren R. ; Doll, Jessica R. ; Mukherjee, Rajib ; Chen, Xiaoting ; Karns, Rebekah ; Weirauch, Matthew T. ; Helmrath, Michael A. ; Inge, Thomas H. ; Divanovic, Senad
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-06, Vol.11 (1), p.2745-2745, Article 2745
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Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor
Author / Creator:Kuang, Yi ; Pyo, Anna ; Eafergan, Natanel ; Cain, Brittany ; Gutzwiller, Lisa M. ; Axelrod, Ofri ; Gagliani, Ellen K. ; Weirauch, Matthew T. ; Kopan, Raphael ; Kovall, Rhett A. ; Sprinzak, David ; Gebelein, Brian
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2021-09, Vol.17 (9), p.e1009039-e1009039
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ArticlesPeer ReviewedFull Text
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
Author / Creator:Chang, Katherine Noelani ; Zhong, Shan ; Weirauch, Matthew T ; Hon, Gary ; Pelizzola, Mattia ; Li, Hai ; Huang, Shao-shan Carol ; Schmitz, Robert J ; Urich, Mark A ; Kuo, Dwight ; Nery, Joseph R ; Qiao, Hong ; Yang, Ally ; Jamali, Abdullah ; Chen, Huaming ; Ideker, Trey ; Ren, Bing ; Bar-Joseph, Ziv ; Hughes, Timothy R ; Ecker, Joseph R
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2013-06, Vol.2, p.e00675-e00675
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Weirauch, Matthew T

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Weirauch, Matthew T

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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

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Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers

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Quantifying Inter-Laboratory Variability in Stable Isotope Analysis of Ancient Skeletal Remains

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C2H2 zinc finger proteins greatly expand the human regulatory lexicon

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NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

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Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets

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Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition

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SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

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Multiple layers of transcriptional regulation by PLZF in NKT-cell development

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Lineage tracing of nuclei in skeletal myofibers uncovers distinct transcripts and interplay between myonuclear populations

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Control of species-dependent cortico-motoneuronal connections underlying manual dexterity

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MiR-125a targets effector programs to stabilize Treg-mediated immune homeostasis

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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

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Global discovery of lupus genetic risk variant allelic enhancer activity

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Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

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Type I interferon sensing unlocks dormant adipocyte inflammatory potential

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Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor

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Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

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