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ArticlesPeer ReviewedFull Text
Lag penalized weighted correlation for time series clustering
Author / Creator:Chandereng, Thevaa ; Gitter, Anthony
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2020-01, Vol.21 (1), p.21-21, Article 21
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ArticlesPeer ReviewedFull Text
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package
Author / Creator:Tuncbag, Nurcan ; Gosline, Sara J. C. ; Kedaigle, Amanda ; Soltis, Anthony R. ; Gitter, Anthony ; Fraenkel, Ernest
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2016-04, Vol.12 (4), p.e1004879-e1004879
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ArticlesPeer ReviewedFull Text
Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus
Author / Creator:Baker, Steven F. ; Meistermann, Helene ; Tzouros, Manuel ; Baker, Aaron ; Golling, Sabrina ; Polster, Juliane Siebourg ; Ledwith, Mitchell P. ; Gitter, Anthony ; Augustin, Angelique ; Javanbakht, Hassan ; Mehle, Andrew
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2022-12, Vol.20 (12), p.e3001934
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ArticlesPeer ReviewedFull Text
Open collaborative writing with Manubot
Author / Creator:Himmelstein, Daniel S. ; Rubinetti, Vincent ; Slochower, David R. ; Hu, Dongbo ; Malladi, Venkat S. ; Greene, Casey S. ; Gitter, Anthony
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-06, Vol.15 (6), p.e1007128
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ArticlesPeer ReviewedFull Text
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism
Author / Creator:Sychev, Zoi E. ; Hu, Alex ; DiMaio, Terri A. ; Gitter, Anthony ; Camp, Nathan D. ; Noble, William S. ; Wolf-Yadlin, Alejandro ; Lagunoff, Michael
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2017-03, Vol.13 (3), p.e1006256-e1006256
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ArticlesPeer ReviewedFull Text
HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B
Author / Creator:Bruce, James W. ; Park, Eunju ; Magnano, Chris ; Horswill, Mark ; Richards, Alicia ; Potts, Gregory ; Hebert, Alexander ; Islam, Nafisah ; Coon, Joshua J. ; Gitter, Anthony ; Sherer, Nathan ; Ahlquist, Paul
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2023-07, Vol.19 (7), p.e1011492-e1011492
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ArticlesPeer ReviewedFull Text
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
Author / Creator:Schulz, Marcel H ; Devanny, William E ; Gitter, Anthony ; Zhong, Shan ; Ernst, Jason ; Bar-Joseph, Ziv
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2012-08, Vol.6 (1), p.104-104
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ArticlesPeer ReviewedFull Text
Automating parameter selection to avoid implausible biological pathway models
Author / Creator:Magnano, Chris S. ; Gitter, Anthony
Publisher:London: Nature Publishing Group UK
Journal title:NPJ systems biology and applications, 2021-02, Vol.7 (1), p.12-12, Article 12
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ArticlesPeer ReviewedFull Text
A Network-based Approach for Predicting Missing Pathway Interactions
Author / Creator:Navlakha, Saket ; Gitter, Anthony ; Bar-Joseph, Ziv
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2012-08, Vol.8 (8), p.e1002640-e1002640
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The Coming of Age of Nucleic Acid Vaccines during COVID-19
Author / Creator:Rando, Halie M. ; Lordan, Ronan ; Kolla, Likhitha ; Sell, Elizabeth ; Lee, Alexandra J. ; Wellhausen, Nils ; Naik, Amruta ; Kamil, Jeremy P. ; Gitter, Anthony ; Greene, Casey S. ; Barton, John P. ; Boca, Simina M. ; Boerckel, Joel D. ; Brueffer, Christian ; Byrd, James Brian ; Capone, Stephen ; Capone, Shikta ; Dattoli, Anna Ada ; Dziak, John J. ; Field, Jeffrey M. ; Ghosh, Soumita ; Gitter, Anthony ; Goel, Rishi Raj ; Greene, Casey S. ; Guebila, Marouen Ben ; Himmelstein, Daniel S. ; Hu, Fengling ; Jadavji, Nafisa M. ; Kamil, Jeremy P. ; Knyazev, Sergey ; Kolla, Likhitha ; Lee, Alexandra J. ; Lordan, Ronan ; Lubiana, Tiago ; Lukan, Temitayo ; MacLean, Adam L. ; Mai, David ; Mangul, Serghei ; Manheim, David ; McGowan, Lucy D’Agostino ; Meyer, Jesse G. ; Mundo, Ariel I. ; Naik, Amruta ; Park, YoSon ; Perrin, Dimitri ; Qi, Yanjun ; Rafizadeh, Diane N. ; Ramsundar, Bharath ; Rando, Halie M. ; Ray, Sandipan ; Robson, Michael P. ; Rubinetti, Vincent ; Sell, Elizabeth ; Shinholster, Lamonica ; Skelly, Ashwin N. ; Sun, Yuchen ; Sun, Yusha ; Szeto, Gregory L. ; Velazquez, Ryan ; Wang, Jinhui ; Wellhausen, Nils
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2023-04, Vol.8 (2), p.e0092822-e0092822
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ArticlesPeer ReviewedFull Text
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Author / Creator:MacGilvray, Matthew E. ; Shishkova, Evgenia ; Chasman, Deborah ; Place, Michael ; Gitter, Anthony ; Coon, Joshua J. ; Gasch, Audrey P.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2018-05, Vol.13 (5), p.e1006088-e1006088
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ArticlesPeer ReviewedFull Text
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
Author / Creator:Jain, Siddhartha ; Gitter, Anthony ; Bar-Joseph, Ziv
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2014-12, Vol.10 (12), p.e1003943-e1003943
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ArticlesPeer ReviewedFull Text
Predicting kinase inhibitors using bioactivity matrix derived informer sets
Author / Creator:Zhang, Huikun ; Ericksen, Spencer S. ; Lee, Ching-pei ; Ananiev, Gene E. ; Wlodarchak, Nathan ; Yu, Peng ; Mitchell, Julie C. ; Gitter, Anthony ; Wright, Stephen J. ; Hoffmann, F. Michael ; Wildman, Scott A. ; Newton, Michael A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-08, Vol.15 (8), p.e1006813-e1006813
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ArticlesPeer ReviewedFull Text
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Author / Creator:Rando, Halie M. ; Lordan, Ronan ; Lee, Alexandra J. ; Naik, Amruta ; Wellhausen, Nils ; Sell, Elizabeth ; Kolla, Likhitha ; Gitter, Anthony ; Greene, Casey S. ; Bansal, Vikas ; Barton, John P. ; Boca, Simina M. ; Boerckel, Joel D. ; Brueffer, Christian ; Byrd, James Brian ; Capone, Stephen ; Das, Shikta ; Dattoli, Anna Ada ; Dziak, John J. ; Field, Jeffrey M. ; Ghosh, Soumita ; Gitter, Anthony ; Goel, Rishi Raj ; Greene, Casey S. ; Guebila, Marouen Ben ; Himmelstein, Daniel S. ; Hu, Fengling ; Jadavji, Nafisa M. ; Kamil, Jeremy P. ; Knyazev, Sergey ; Kolla, Likhitha ; Lee, Alexandra J. ; Lordan, Ronan ; Lubiana, Tiago ; Lukan, Temitayo ; MacLean, Adam L. ; Mai, David ; Mangul, Serghei ; Manheim, David ; McGowan, Lucy D’Agostino ; Meyer, Jesse G. ; Mundo, Ariel I. ; Naik, Amruta ; Park, YoSon ; Perrin, Dimitri ; Qi, Yanjun ; Rafizadeh, Diane N. ; Ramsundar, Bharath ; Rando, Halie M. ; Ray, Sandipan ; Robson, Michael P. ; Rubinetti, Vincent ; Sell, Elizabeth ; Shinholster, Lamonica ; Skelly, Ashwin N. ; Sun, Yuchen ; Sun, Yusha ; Szeto, Gregory L. ; Velazquez, Ryan ; Wang, Jinhui ; Wellhausen, Nils
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2023-04, Vol.8 (2), p.e0092722
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ArticlesPeer ReviewedFull Text
Backup in gene regulatory networks explains differences between binding and knockout results
Author / Creator:Gitter, Anthony ; Siegfried, Zehava ; Klutstein, Michael ; Fornes, Oriol ; Oliva, Baldo ; Simon, Itamar ; Bar‐Joseph, Ziv
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2009-06, Vol.5 (1), p.276-n/a
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Identification and Development of Therapeutics for COVID-19
Author / Creator:Rando, Halie M. ; Wellhausen, Nils ; Ghosh, Soumita ; Lee, Alexandra J. ; Dattoli, Anna Ada ; Hu, Fengling ; Byrd, James Brian ; Rafizadeh, Diane N. ; Lordan, Ronan ; Qi, Yanjun ; Sun, Yuchen ; Brueffer, Christian ; Field, Jeffrey M. ; Ben Guebila, Marouen ; Jadavji, Nafisa M. ; Skelly, Ashwin N. ; Ramsundar, Bharath ; Wang, Jinhui ; Goel, Rishi Raj ; Park, YoSon ; Boca, Simina M. ; Gitter, Anthony ; Greene, Casey S.
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2021-12, Vol.6 (6), p.e0023321-e0023321
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Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Author / Creator:Rando, Halie M. ; MacLean, Adam L. ; Lee, Alexandra J. ; Lordan, Ronan ; Ray, Sandipan ; Bansal, Vikas ; Skelly, Ashwin N. ; Sell, Elizabeth ; Dziak, John J. ; Shinholster, Lamonica ; D’Agostino McGowan, Lucy ; Ben Guebila, Marouen ; Wellhausen, Nils ; Knyazev, Sergey ; Boca, Simina M. ; Capone, Stephen ; Qi, Yanjun ; Park, YoSon ; Mai, David ; Sun, Yuchen ; Boerckel, Joel D. ; Brueffer, Christian ; Byrd, James Brian ; Kamil, Jeremy P. ; Wang, Jinhui ; Velazquez, Ryan ; Szeto, Gregory L. ; Barton, John P. ; Goel, Rishi Raj ; Mangul, Serghei ; Lubiana, Tiago ; Gitter, Anthony ; Greene, Casey S.
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2021-10, Vol.6 (5)
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ArticlesPeer ReviewedFull Text
Studying and modelling dynamic biological processes using time-series gene expression data
Author / Creator:Bar-Joseph, Ziv ; Gitter, Anthony ; Simon, Itamar
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2012-08, Vol.13 (8), p.552-564
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Neural networks to learn protein sequence–function relationships from deep mutational scanning data
Author / Creator:Gelman, Sam ; Fahlberg, Sarah A. ; Heinzelman, Pete ; Romero, Philip A. ; Gitter, Anthony
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2021-11, Vol.118 (48), p.1-12
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Assessment of network module identification across complex diseases
Author / Creator:Choobdar, Sarvenaz ; Ahsen, Mehmet E. ; Crawford, Jake ; Tomasoni, Mattia ; Fang, Tao ; Lamparter, David ; Lin, Junyuan ; Hescott, Benjamin ; Hu, Xiaozhe ; Mercer, Johnathan ; Natoli, Ted ; Narayan, Rajiv ; Subramanian, Aravind ; Zhang, Jitao D. ; Stolovitzky, Gustavo ; Kutalik, Zoltán ; Lage, Kasper ; Slonim, Donna K. ; Saez-Rodriguez, Julio ; Cowen, Lenore J. ; Bergmann, Sven ; Marbach, Daniel
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-09, Vol.16 (9), p.843-852
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Showing 1 to 20 of 58 results

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Lag penalized weighted correlation for time series clustering

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

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Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus

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Open collaborative writing with Manubot

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Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism

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HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B

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DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

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Automating parameter selection to avoid implausible biological pathway models

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A Network-based Approach for Predicting Missing Pathway Interactions

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The Coming of Age of Nucleic Acid Vaccines during COVID-19

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Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

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Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu

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Predicting kinase inhibitors using bioactivity matrix derived informer sets

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Application of Traditional Vaccine Development Strategies to SARS-CoV-2

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Backup in gene regulatory networks explains differences between binding and knockout results

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Identification and Development of Therapeutics for COVID-19

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Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

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Studying and modelling dynamic biological processes using time-series gene expression data

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Neural networks to learn protein sequence–function relationships from deep mutational scanning data

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Assessment of network module identification across complex diseases

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