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SREBP2-dependent lipid gene transcription enhances the infection of human dendritic cells by Zika virus.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33041-1
By:
- Branche, Emilie;
- Wang, Ying-Ting;
- Viramontes, Karla M.;
- Valls Cuevas, Joan M.;
- Xie, Jialei;
- Ana-Sosa-Batiz, Fernanda;
- Shafee, Norazizah;
- Duttke, Sascha H.;
- McMillan, Rachel E.;
- Clark, Alex E.;
- Nguyen, Michael N.;
- Garretson, Aaron F.;
- Crames, Jan J.;
- Spann, Nathan J.;
- Zhu, Zhe;
- Rich, Jeremy N.;
- Spector, Deborah H.;
- Benner, Christopher;
- Shresta, Sujan;
- Carlin, Aaron F.
Publication type:
Article
Author Correction: Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing.
Published in:
2022
By:
- Yuan, Baolei;
- Zhou, Xuan;
- Suzuki, Keiichiro;
- Ramos-Mandujano, Gerardo;
- Wang, Mengge;
- Tehseen, Muhammad;
- Cortés-Medina, Lorena V.;
- Moresco, James J.;
- Dunn, Sarah;
- Hernandez-Benitez, Reyna;
- Hishida, Tomoaki;
- Kim, Na Young;
- Andijani, Manal M.;
- Bi, Chongwei;
- Ku, Manching;
- Takahashi, Yuta;
- Xu, Jinna;
- Qiu, Jinsong;
- Huang, Ling;
- Benner, Christopher
Publication type:
Correction Notice
Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31220-8
By:
- Yuan, Baolei;
- Zhou, Xuan;
- Suzuki, Keiichiro;
- Ramos-Mandujano, Gerardo;
- Wang, Mengge;
- Tehseen, Muhammad;
- Cortés-Medina, Lorena V.;
- Moresco, James J.;
- Dunn, Sarah;
- Hernandez-Benitez, Reyna;
- Hishida, Tomoaki;
- Kim, Na Young;
- Andijani, Manal M.;
- Bi, Chongwei;
- Ku, Manching;
- Takahashi, Yuta;
- Xu, Jinna;
- Qiu, Jinsong;
- Huang, Ling;
- Benner, Christopher
Publication type:
Article
Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian hamsters.
Published in:
PLoS Pathogens, 2024, v. 20, n. 1, p. 1, doi. 10.1371/journal.ppat.1011805
By:
- Diego, Juan García-Bernalt;
- Singh, Gagandeep;
- Jangra, Sonia;
- Handrejk, Kim;
- Laporte, Manon;
- Chang, Lauren A.;
- El Zahed, Sara S.;
- Pache, Lars;
- Chang, Max W.;
- Warang, Prajakta;
- Aslam, Sadaf;
- Mena, Ignacio;
- Webb, Brett T.;
- Benner, Christopher;
- García-Sastre, Adolfo;
- Schotsaert, Michael
Publication type:
Article
A Day in the Life.
Published in:
JAAPA: Journal of the American Academy of Physician Assistants (Haymarket Media, Inc.), 2009, v. 22, n. 4, p. 16, doi. 10.1097/01720610-200904000-00006
By:
- Benner, D. Christopher
Publication type:
Article
MEPP: more transparent motif enrichment by profiling positional correlations.
Published in:
NAR Genomics & Bioinformatics, 2022, v. 4, n. 4, p. 1, doi. 10.1093/nargab/lqac075
By:
- Delos Santos, Nathaniel P;
- Duttke, Sascha;
- Heinz, Sven;
- Benner, Christopher
Publication type:
Article
A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells.
Published in:
NAR Genomics & Bioinformatics, 2021, v. 3, n. 3, p. 1, doi. 10.1093/nargab/lqab061
By:
- Shamie, Isaac;
- Duttke, Sascha H.;
- la Cour Karottki, Karen J.;
- Han, Claudia Z.;
- Hansen, Anders H.;
- Hefzi, Hooman;
- Kai Xiong;
- Shangzhong Li;
- Roth, Samuel J.;
- Jenhan Tao;
- Gyun Min Lee;
- Glass, Christopher K.;
- Kildegaard, Helene Faustrup;
- Benner, Christopher;
- Lewis, Nathan E.
Publication type:
Article
Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers.
Published in:
eLife, 2017, p. 1, doi. 10.7554/eLife.30506
By:
- Kelso, Timothy W. R.;
- Porter, Devin K.;
- Amaral, Maria Luisa;
- Shokhirev, Maxim N.;
- Benner, Christopher;
- Hargreaves, Diana C.
Publication type:
Article
Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 20, p. 12570, doi. 10.1093/nar/gku1036
By:
- Kaikkonen, Minna U.;
- Niskanen, Henri;
- Romanoski, Casey E.;
- Kansanen, Emilia;
- Kivelä, Annukka M.;
- Laitalainen, Jarkko;
- Heinz, Sven;
- Benner, Christopher;
- Glass, Christopher K.;
- Ylä-Herttuala, Seppo
Publication type:
Article
Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 13, p. 6391, doi. 10.1093/nar/gkt355
By:
- Pham, Thu-Hang;
- Minderjahn, Julia;
- Schmidl, Christian;
- Hoffmeister, Helen;
- Schmidhofer, Sandra;
- Chen, Wei;
- Längst, Gernot;
- Benner, Christopher;
- Rehli, Michael
Publication type:
Article
The selection and function of cell type-specific enhancers.
Published in:
Nature Reviews Molecular Cell Biology, 2015, v. 16, n. 3, p. 144, doi. 10.1038/nrm3949
By:
- Heinz, Sven;
- Romanoski, Casey E.;
- Benner, Christopher;
- Glass, Christopher K.
Publication type:
Article
Drug target prediction through deep learning functional representation of gene signatures.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46089-y
By:
- Hao Chen;
- King, Frederick J.;
- Bin Zhou;
- Yu Wang;
- Canedy, Carter J.;
- Hayashi, Joel;
- Yang Zhong;
- Chang, Max W.;
- Pache, Lars;
- Wong, Julian L.;
- Yong Jia;
- Joslin, John;
- Tao Jiang;
- Benner, Christopher;
- Chanda, Sumit K.;
- Yingyao Zhou
Publication type:
Article
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09234-6
By:
- Zhou, Yingyao;
- Zhou, Bin;
- Pache, Lars;
- Chang, Max;
- Khodabakhshi, Alireza Hadj;
- Tanaseichuk, Olga;
- Benner, Christopher;
- Chanda, Sumit K.
Publication type:
Article
Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08236-0
By:
- Fonseca, Gregory J.;
- Tao, Jenhan;
- Westin, Emma M.;
- Duttke, Sascha H.;
- Spann, Nathanael J.;
- Strid, Tobias;
- Shen, Zeyang;
- Stender, Joshua D.;
- Sakai, Mashito;
- Link, Verena M.;
- Benner, Christopher;
- Glass, Christopher K.
Publication type:
Article
A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela.
Published in:
PLoS Neglected Tropical Diseases, 2018, v. 12, n. 12, p. 1, doi. 10.1371/journal.pntd.0007053
By:
- Carlin, Aaron F.;
- Wen, Jinsheng;
- Vizcarra, Edward A.;
- McCauley, Melanie;
- Chaillon, Antoine;
- Akrami, Kevan;
- Kim, Cheryl;
- Ngono, Annie Elong;
- Lara-Marquez, Maria Luz;
- Smith, Davey M.;
- Glass, Christopher K.;
- Schooley, Robert T.;
- Benner, Christopher;
- Shresta, Sujan
Publication type:
Article
MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates.
Published in:
BMC Bioinformatics, 2020, v. 21, p. N.PAG, doi. 10.1186/s12859-020-03739-4
By:
- Delos Santos, Nathaniel P.;
- Texari, Lorane;
- Benner, Christopher
Publication type:
Article
ARTDeco: automatic readthrough transcription detection.
Published in:
BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-03551-0
By:
- Roth, Samuel J.;
- Heinz, Sven;
- Benner, Christopher
Publication type:
Article
Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate.
Published in:
Nature Immunology, 2012, v. 13, n. 12, p. 1196, doi. 10.1038/ni.2432
By:
- Lin, Yin C;
- Benner, Christopher;
- Mansson, Robert;
- Heinz, Sven;
- Miyazaki, Kazuko;
- Miyazaki, Masaki;
- Chandra, Vivek;
- Bossen, Claudia;
- Glass, Christopher K;
- Murre, Cornelis
Publication type:
Article
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.
Published in:
Nature Immunology, 2010, v. 11, n. 7, p. 635, doi. 10.1038/ni.1891
By:
- Lin, Yin C.;
- Jhunjhunwala, Suchit;
- Benner, Christopher;
- Heinz, Sven;
- Welinder, Eva;
- Mansson, Robert;
- Sigvardsson, Mikael;
- Hagman, James;
- Espinoza, Celso A.;
- Dutkowski, Janusz;
- Ideker, Trey;
- Glass, Christopher K.;
- Murre, Cornelis
Publication type:
Article
Effects of Early Life Oral Arsenic Exposure on Intestinal Tract Development and Lipid Homeostasis in Neonatal Mice: Implications for NAFLD Development.
Published in:
Environmental Health Perspectives, 2023, v. 131, n. 9, p. 097001-1, doi. 10.1289/EHP12381
By:
- Xiaojing Yang;
- Weber, André A.;
- Mennillo, Elvira;
- Secrest, Patrick;
- Chang, Max;
- Wong, Samantha;
- Le, Sabrina;
- Junlai Liu;
- Benner, Christopher W.;
- Karin, Michael;
- Gordts, Philip L. S. M.;
- Tukey, Robert H.;
- Shujuan Chen
Publication type:
Article
Yeast derlin Dfm1 employs a chaperone-like function to resolve misfolded membrane protein stress.
Published in:
PLoS Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1371/journal.pbio.3001950
By:
- Kandel, Rachel;
- Jung, Jasmine;
- Syau, Della;
- Kuo, Tiffany;
- Songster, Livia;
- Horn, Casey;
- Chapman, Claire;
- Aguayo, Analine;
- Duttke, Sascha;
- Benner, Christopher;
- Neal, Sonya E.
Publication type:
Article
The Wild West of spike-in normalization.
Published in:
Nature Biotechnology, 2024, v. 42, n. 9, p. 1343, doi. 10.1038/s41587-024-02377-y
By:
- Patel, Lauren A.;
- Cao, Yuwei;
- Mendenhall, Eric M.;
- Benner, Christopher;
- Goren, Alon
Publication type:
Article
Differential L1 regulation in pluripotent stem cells of humans and apes.
Published in:
Nature, 2013, v. 503, n. 7477, p. 525, doi. 10.1038/nature12686
By:
- Marchetto, Maria C. N.;
- Narvaiza, Iñigo;
- Denli, Ahmet M.;
- Benner, Christopher;
- Lazzarini, Thomas A.;
- Nathanson, Jason L.;
- Paquola, Apuã C. M.;
- Desai, Keval N.;
- Herai, Roberto H.;
- Weitzman, Matthew D.;
- Yeo, Gene W.;
- Muotri, Alysson R.;
- Gage, Fred H.
Publication type:
Article
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription.
Published in:
Nature, 2013, v. 498, n. 7455, p. 511, doi. 10.1038/nature12209
By:
- Lam, Michael T. Y.;
- Cho, Han;
- Lesch, Hanna P.;
- Gosselin, David;
- Heinz, Sven;
- Tanaka-Oishi, Yumiko;
- Benner, Christopher;
- Kaikkonen, Minna U.;
- Kim, Aneeza S.;
- Kosaka, Mika;
- Lee, Cindy Y.;
- Watt, Andy;
- Grossman, Tamar R.;
- Rosenfeld, Michael G.;
- Evans, Ronald M.;
- Glass, Christopher K.
Publication type:
Article
Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors.
Published in:
Nature Neuroscience, 2014, v. 17, n. 4, p. 513, doi. 10.1038/nn.3668
By:
- Crotti, Andrea;
- Benner, Christopher;
- Kerman, Bilal E;
- Gosselin, David;
- Lagier-Tourenne, Clotilde;
- Zuccato, Chiara;
- Cattaneo, Elena;
- Gage, Fred H;
- Cleveland, Don W;
- Glass, Christopher K
Publication type:
Article
Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.
Published in:
Nucleic Acids Research, 2023, v. 51, n. 15, p. e80, doi. 10.1093/nar/gkad562
By:
- Guzman, Carlos;
- Duttke, Sascha;
- Zhu, Yixin;
- De Arruda Saldanha, Camila;
- Downes, Nicholas L;
- Benner, Christopher;
- Heinz, Sven
Publication type:
Article
Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling.
Published in:
Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01117-y
By:
- Rahnamoun, Homa;
- Hanbin Lu;
- Duttke, Sascha H.;
- Benner, Christopher;
- Glass, Christopher K.;
- Lauberth, Shannon M.
Publication type:
Article
Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions.
Published in:
PLoS Genetics, 2013, v. 9, n. 11, p. 1, doi. 10.1371/journal.pgen.1003906
By:
- Benner, Christopher;
- Konovalov, Sergiy;
- Mackintosh, Carlos;
- Hutt, Kasey R.;
- Stunnenberg, Rieka;
- Garcia-Bassets, Ivan
Publication type:
Article
Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes.
Published in:
PLoS Genetics, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pgen.1002401
By:
- Escoubet-Lozach, Laure;
- Benner, Christopher;
- Kaikkonen, Minna U.;
- Lozach, Jean;
- Heinz, Sven;
- Spann, Nathan J.;
- Crotti, Andrea;
- Stender, Josh;
- Ghisletti, Serena;
- Reichart, Donna;
- Cheng, Christine S.;
- Luna, Rosa;
- Ludka, Colleen;
- Sasik, Roman;
- Garcia-Bassets, Ivan;
- Hoffmann, Alexander;
- Subramaniam, Shankar;
- Hardiman, Gary;
- Rosenfeld, Michael G.;
- Glass, Christopher K.
Publication type:
Article
Mutations in foregut SOX2<sup>+</sup> cells induce efficient proliferation via CXCR2 pathway.
Published in:
Protein & Cell, 2019, v. 10, n. 7, p. 485, doi. 10.1007/s13238-019-0630-3
By:
- Hishida, Tomoaki;
- Vazquez-Ferrer, Eric;
- Hishida-Nozaki, Yuriko;
- Sancho-Martinez, Ignacio;
- Takahashi, Yuta;
- Hatanaka, Fumiyuki;
- Wu, Jun;
- Ocampo, Alejandro;
- Reddy, Pradeep;
- Wu, Min-Zu;
- Gerken, Laurie;
- Shaw, Reuben J.;
- Rodriguez Esteban, Concepcion;
- Benner, Christopher;
- Nakagawa, Hiroshi;
- Guillen Garcia, Pedro;
- Nuñez Delicado, Estrella;
- Castells, Antoni;
- Campistol, Josep M.;
- Liu, Guang-Hui
Publication type:
Article
Mutations in foregut SOX2<sup>+</sup> cells induce efficient proliferation via CXCR2 pathway.
Published in:
Protein & Cell, 2019, p. 1, doi. 10.1007/s13238-019-0630-3
By:
- Hishida, Tomoaki;
- Vazquez-Ferrer, Eric;
- Hishida-Nozaki, Yuriko;
- Sancho-Martinez, Ignacio;
- Takahashi, Yuta;
- Hatanaka, Fumiyuki;
- Wu, Jun;
- Ocampo, Alejandro;
- Reddy, Pradeep;
- Wu, Min-Zu;
- Gerken, Laurie;
- Shaw, Reuben J.;
- Rodriguez Esteban, Concepcion;
- Benner, Christopher;
- Nakagawa, Hiroshi;
- Guillen Garcia, Pedro;
- Nuñez Delicado, Estrella;
- Castells, Antoni;
- Campistol, Josep M.;
- Liu, Guang-Hui
Publication type:
Article
Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes.
Published in:
Protein & Cell, 2014, v. 5, n. 1, p. 59, doi. 10.1007/s13238-013-0016-x
By:
- Gu, Ying;
- Liu, Guang-Hui;
- Plongthongkum, Nongluk;
- Benner, Christopher;
- Yi, Fei;
- Qu, Jing;
- Suzuki, Keiichiro;
- Yang, Jiping;
- Zhang, Weiqi;
- Li, Mo;
- Montserrat, Nuria;
- Crespo, Isaac;
- Sol, Antonio;
- Esteban, Concepcion;
- Zhang, Kun;
- Izpisua Belmonte, Juan
Publication type:
Article
The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 620, doi. 10.1186/1471-2164-15-620
By:
- Benner, Christopher;
- van der Meulen, Talitha;
- Cacéres, Elena;
- Tigyi, Kristof;
- Donaldson, Cynthia J;
- Huising, Mark O
Publication type:
Article
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function.
Published in:
Bioinformatics, 2020, v. 36, p. i84, doi. 10.1093/bioinformatics/btaa476
By:
- Shen, Zeyang;
- Hoeksema, Marten A;
- Ouyang, Zhengyu;
- Benner, Christopher;
- Glass, Christopher K
Publication type:
Article
LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16017-x
By:
- Vinckier, Nicholas K.;
- Patel, Nisha A.;
- Geusz, Ryan J.;
- Wang, Allen;
- Wang, Jinzhao;
- Matta, Ileana;
- Harrington, Austin R.;
- Wortham, Matthew;
- Wetton, Nichole;
- Wang, Jianxun;
- Jhala, Ulupi S.;
- Rosenfeld, Michael G.;
- Benner, Christopher W.;
- Shih, Hung-Ping;
- Sander, Maike
Publication type:
Article
Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction.
Published in:
Frontiers in Neuroscience, 2022, v. 16, p. 1, doi. 10.3389/fnins.2022.858427
By:
- Duttke, Sascha H.;
- Montilla-Perez, Patricia;
- Chang, Max W.;
- Li, Hairi;
- Chen, Hao;
- Carrette, Lieselot L. G.;
- Guglielmo, Giordano de;
- George, Olivier;
- Palmer, Abraham A.;
- Benner, Christopher;
- Telese, Francesca
Publication type:
Article
Ncor2/PPARα-Dependent Upregulation of MCUb in the Type 2 Diabetic Heart Impacts Cardiac Metabolic Flexibility and Function.
Published in:
2021
By:
- Cividini, Federico;
- Scott, Brian T.;
- Suarez, Jorge;
- Casteel, Darren E.;
- Heinz, Sven;
- Dai, Anzhi;
- Diemer, Tanja;
- Suarez, Jorge A.;
- Benner, Christopher W.;
- Ghassemian, Majid;
- Dillmann, Wolfgang H.
Publication type:
journal article

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