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Select item 103126741.

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor

Philipp Trepte, Christopher Secker, Simona Kostova, Sibusiso B. Maseko, Soon Gang Choi, Jeremy Blavier, Igor Minia, Eduardo Silva Ramos, Patricia Cassonnet, Sabrina Golusik, Martina Zenkner, Stephanie Beetz, Mara J. Liebich, Nadine Scharek, Anja Schütz, Marcel Sperling, Michael Lisurek, Yang Wang, Kerstin Spirohn, Tong Hao, Michael A. Calderwood, David E. Hill, Markus Landthaler, Julien Olivet, Jean-Claude Twizere, Marc Vidal, Erich E. Wanker

Version 1. bioRxiv. Preprint. 2023 Jun 14. doi: 10.1101/2023.06.14.544560

Published in:: Mol Syst Biol. 2024 Apr; 20(4): 428–457.

PMCID:: PMC10312674

Abstract Article PDF–9.6M

Select item 71699832.

A reference map of the human binary protein interactome

Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G. Coté, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amélie Dricot, Marinella Gebbia, Madeleine F. Hardy, Nishka Kishore, Jennifer J. Knapp, István A. Kovács, Irma Lemmens, Miles W. Mee, Joseph C. Mellor, Carl Pollis, Carles Pons, Aaron D. Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Christian Bowman-Colin, Suet-Feung Chin, Soon Gang Choi, Claudia Colabella, Georges Coppin, Cassandra D’Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Liana Goehring, Anjali Gopal, Ghazal Haddad, Elodie Hatchi, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Serena Landini, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N. Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San-Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M. Sheynkman, Eyal Simonovsky, Murat Taşan, Alexander Tejeda, Vincent Tropepe, Jean-Claude Twizere, Yang Wang, Robert J. Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger-Lotem, Quan Zhong, Patrick Aloy, Gary D. Bader, Javier De Las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, David E. Hill, Marc Vidal, Frederick P. Roth, Michael A. Calderwood

Nature. Author manuscript; available in PMC 2020 Oct 8.

Published in final edited form as: Nature. 2020 Apr; 580(7803): 402–408. Published online 2020 Apr 8. doi: 10.1038/s41586-020-2188-x

PMCID:: PMC7169983

Abstract Article PDF–5.4M

Select item 67776313.

Phenotypic spectrum associated with a CRADD founder variant underlying frontotemporal predominant pachygyria in the Finnish population

Daniel L. Polla, Elisa Rahikkala, Michaela K. Bode, Tuomo Määttä, Teppo Varilo, Thyrza Loman, Anju K. Philips, Mitja Kurki, Aarno Palotie, Jarmo Körkkö, Päivi Vieira, Kristiina Avela, Valérie Jacquemin, Isabelle Pirson, Marc Abramowicz, Arjan P. M. de Brouwer, Outi Kuismin, Hans van Bokhoven, Irma Järvelä

Eur J Hum Genet. 2019 Aug; 27(8): 1235–1243. Published online 2019 Mar 26. doi: 10.1038/s41431-019-0383-8

Correction in:: Eur J Hum Genet. 2020 Apr; 28(4): 532.

PMCID:: PMC6777631

Abstract Article PDF–927K

Select item 67426464.

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Robert Fragoza, Jishnu Das, Shayne D. Wierbowski, Jin Liang, Tina N. Tran, Siqi Liang, Juan F. Beltran, Christen A. Rivera-Erick, Kaixiong Ye, Ting-Yi Wang, Li Yao, Matthew Mort, Peter D. Stenson, David N. Cooper, Xiaomu Wei, Alon Keinan, John C. Schimenti, Andrew G. Clark, Haiyuan Yu

Nat Commun. 2019; 10: 4141. Published online 2019 Sep 12. doi: 10.1038/s41467-019-11959-3

PMCID:: PMC6742646

Abstract Article PDF–1.2M

Select item 67157255.

Maximizing binary interactome mapping with a minimal number of assays

Soon Gang Choi, Julien Olivet, Patricia Cassonnet, Pierre-Olivier Vidalain, Katja Luck, Luke Lambourne, Kerstin Spirohn, Irma Lemmens, Mélanie Dos Santos, Caroline Demeret, Louis Jones, Sudharshan Rangarajan, Wenting Bian, Eloi P. Coutant, Yves L. Janin, Sylvie van der Werf, Philipp Trepte, Erich E. Wanker, Javier De Las Rivas, Jan Tavernier, Jean-Claude Twizere, Tong Hao, David E. Hill, Marc Vidal, Michael A. Calderwood, Yves Jacob

Nat Commun. 2019; 10: 3907. Published online 2019 Aug 29. doi: 10.1038/s41467-019-11809-2

PMCID:: PMC6715725

Abstract Article PDF–1.7M

Select item 60438506.

Dimer‐specific immunoprecipitation of active caspase‐2 identifies TRAF proteins as novel activators

Alexander C Robeson, Kelly R Lindblom, Jeffrey Wojton, Sally Kornbluth, Kenkyo Matsuura

EMBO J. 2018 Jul 13; 37(14): e97072. Published online 2018 Jun 6. doi: 10.15252/embj.201797072

PMCID:: PMC6043850

Abstract Article PDF–2.1M

Select item 54952257.

Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing

Teng Fei, Yiwen Chen, Tengfei Xiao, Wei Li, Laura Cato, Peng Zhang, Maura B. Cotter, Michaela Bowden, Rosina T. Lis, Shuang G. Zhao, Qiu Wu, Felix Y. Feng, Massimo Loda, Housheng Hansen He, X. Shirley Liu, Myles Brown

Proc Natl Acad Sci U S A. 2017 Jun 27; 114(26): E5207–E5215. Published online 2017 Jun 13. doi: 10.1073/pnas.1617467114

PMCID:: PMC5495225

Abstract Article PDF–1.3M

Select item 54610158.

NPM1 directs PIDDosome-dependent caspase-2 activation in the nucleolus

Kiyohiro Ando, Melissa J. Parsons, Richa B. Shah, Chloé I. Charendoff, Sheré L. Paris, Peter H. Liu, Sara R. Fassio, Brittany A. Rohrman, Ruth Thompson, Andrew Oberst, Samuel Sidi, Lisa Bouchier-Hayes

J Cell Biol. 2017 Jun 5; 216(6): 1795–1810. doi: 10.1083/jcb.201608095

PMCID:: PMC5461015

Abstract Article PDF–2.8M

Select item 53717309.

Systematic protein–protein interaction mapping for clinically relevant human GPCRs

Kate Sokolina, Saranya Kittanakom, Jamie Snider, Max Kotlyar, Pascal Maurice, Jorge Gandía, Abla Benleulmi‐Chaachoua, Kenjiro Tadagaki, Atsuro Oishi, Victoria Wong, Ramy H Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao, Xavier Morató, David Otasek, Hiroyuki Kobayashi, Javier Menendez, Daniel Auerbach, Stephane Angers, Natasa Pržulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica, Igor Stagljar

Mol Syst Biol. 2017 Mar; 13(3): 918. Published online 2017 Mar 15. doi: 10.15252/msb.20167430

PMCID:: PMC5371730

Abstract Article PDF–4.1M

Select item 509794510.

Mutations in CRADD Result in Reduced Caspase-2-Mediated Neuronal Apoptosis and Cause Megalencephaly with a Rare Lissencephaly Variant

Nataliya Di Donato, Ying Y. Jean, A. Murat Maga, Briana D. Krewson, Alison B. Shupp, Maria I. Avrutsky, Achira Roy, Sarah Collins, Carissa Olds, Rebecca A. Willert, Agnieszka M. Czaja, Rachel Johnson, Jessi A. Stover, Steven Gottlieb, Deborah Bartholdi, Anita Rauch, Amy Goldstein, Victoria Boyd-Kyle, Kimberly A. Aldinger, Ghayda M. Mirzaa, Anke Nissen, Karlla W. Brigatti, Erik G. Puffenberger, Kathleen J. Millen, Kevin A. Strauss, William B. Dobyns, Carol M. Troy, Robert N. Jinks

Am J Hum Genet. 2016 Nov 3; 99(5): 1117–1129. Published online 2016 Oct 20. doi: 10.1016/j.ajhg.2016.09.010

PMCID:: PMC5097945

Abstract Article PDF–1.3M

Select item 484876211.

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

Nozomu Yachie, Evangelia Petsalaki, Joseph C Mellor, Jochen Weile, Yves Jacob, Marta Verby, Sedide B Ozturk, Siyang Li, Atina G Cote, Roberto Mosca, Jennifer J Knapp, Minjeong Ko, Analyn Yu, Marinella Gebbia, Nidhi Sahni, Song Yi, Tanya Tyagi, Dayag Sheykhkarimli, Jonathan F Roth, Cassandra Wong, Louai Musa, Jamie Snider, Yi‐Chun Liu, Haiyuan Yu, Pascal Braun, Igor Stagljar, Tong Hao, Michael A Calderwood, Laurence Pelletier, Patrick Aloy, David E Hill, Marc Vidal, Frederick P Roth

Mol Syst Biol. 2016 Apr; 12(4): 863. Published online 2016 Apr 23. doi: 10.15252/msb.20156660

PMCID:: PMC4848762

Abstract Article PDF–2.8M

Select item 461928812.

PIDDosome Expression and the Role of Caspase-2 Activation for Chemotherapy-Induced Apoptosis in RCCs

Sebastian Heikaus, Igor Pejin, Helmut Erich Gabbert, Uwe Ramp, Csaba Mahotka

Cell Oncol. 2010; 32(1-2): 29–42. Published online 2010 Feb 4. doi: 10.3233/CLO-2009-0492

PMCID:: PMC4619288

Abstract PDF–543K

Select item 445819313.

An Inhibitor of PIDDosome Formation

Ruth Thompson, Richa B. Shah, Peter H. Liu, Yogesh Gupta, Kiyohiro Ando, Aneel K. Aggarwal, Samuel Sidi

Mol Cell. Author manuscript; available in PMC 2016 Jun 4.

Published in final edited form as: Mol Cell. 2015 Jun 4; 58(5): 767–779. Published online 2015 Apr 30. doi: 10.1016/j.molcel.2015.03.034

PMCID:: PMC4458193

Abstract Article PDF–2.5M

Select item 444121514.

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

Nidhi Sahni, Song Yi, Mikko Taipale, Juan I. Fuxman Bass, Jasmin Coulombe-Huntington, Fan Yang, Jian Peng, Jochen Weile, Georgios I. Karras, Yang Wang, István A. Kovács, Atanas Kamburov, Irina Krykbaeva, Mandy H. Lam, George Tucker, Vikram Khurana, Amitabh Sharma, Yang-Yu Liu, Nozomu Yachie, Quan Zhong, Yun Shen, Alexandre Palagi, Adriana San-Miguel, Changyu Fan, Dawit Balcha, Amelie Dricot, Daniel M. Jordan, Jennifer M. Walsh, Akash A. Shah, Xinping Yang, Ani Stoyanova, Alex Leighton, Michael A. Calderwood, Yves Jacob, Michael E. Cusick, Kourosh Salehi-Ashtiani, Luke J. Whitesell, Shamil Sunyaev, Bonnie Berger, Albert-László Barabási, Benoit Charloteaux, David E. Hill, Tong Hao, Frederick P. Roth, Yu Xia, Albertha J.M. Walhout, Susan Lindquist, Marc Vidal

Cell. Author manuscript; available in PMC 2016 Apr 23.

Published in final edited form as: Cell. 2015 Apr 23; 161(3): 647–660. doi: 10.1016/j.cell.2015.04.013

PMCID:: PMC4441215

Abstract Article PDF–1.2M

Select item 426658815.

A proteome-scale map of the human interactome network

Thomas Rolland, Murat Taşan, Benoit Charloteaux, Samuel J. Pevzner, Quan Zhong, Nidhi Sahni, Song Yi, Irma Lemmens, Celia Fontanillo, Roberto Mosca, Atanas Kamburov, Susan D. Ghiassian, Xinping Yang, Lila Ghamsari, Dawit Balcha, Bridget E. Begg, Pascal Braun, Marc Brehme, Martin P. Broly, Anne-Ruxandra Carvunis, Dan Convery-Zupan, Roser Corominas, Jasmin Coulombe-Huntington, Elizabeth Dann, Matija Dreze, Amélie Dricot, Changyu Fan, Eric Franzosa, Fana Gebreab, Bryan J. Gutierrez, Madeleine F. Hardy, Mike Jin, Shuli Kang, Ruth Kiros, Guan Ning Lin, Katja Luck, Andrew MacWilliams, Jörg Menche, Ryan R. Murray, Alexandre Palagi, Matthew M. Poulin, Xavier Rambout, John Rasla, Patrick Reichert, Viviana Romero, Elien Ruyssinck, Julie M. Sahalie, Annemarie Scholz, Akash A. Shah, Amitabh Sharma, Yun Shen, Kerstin Spirohn, Stanley Tam, Alexander O. Tejeda, Shelly A. Wanamaker, Jean-Claude Twizere, Kerwin Vega, Jennifer Walsh, Michael E. Cusick, Yu Xia, Albert-László Barabási, Lilia M. Iakoucheva, Patrick Aloy, Javier De Las Rivas, Jan Tavernier, Michael A. Calderwood, David E. Hill, Tong Hao, Frederick P. Roth, Marc Vidal

Cell. Author manuscript; available in PMC 2015 Nov 20.

Published in final edited form as: Cell. 2014 Nov 20; 159(5): 1212–1226. doi: 10.1016/j.cell.2014.10.050

PMCID:: PMC4266588

Abstract Article PDF–3.1M

Select item 413921416.

The Adaptor CRADD/RAIDD Controls Activation of Endothelial Cells by Proinflammatory Stimuli

Huan Qiao, Yan Liu, Ruth A. Veach, Lukasz Wylezinski, Jacek Hawiger

J Biol Chem. 2014 Aug 8; 289(32): 21973–21983. Published online 2014 Jun 23. doi: 10.1074/jbc.M114.588723

PMCID:: PMC4139214

Abstract Article PDF–2.1M

Select item 376099517.

Genome Wide Association Study of the Rate of Cognitive Decline in Alzheimer’s Disease

Richard Sherva, Yorghos Tripodis, David Bennett, Lori B. Chibnik, Paul K. Crane, Philip de Jager, Lindsay A. Farrer, Andrew J. Saykin, Joshua Shulman, Robert C. Green, the Alzheimer’s Disease Neuroimaging Initiative

Alzheimers Dement. Author manuscript; available in PMC 2015 Jan 1.

Published in final edited form as: Alzheimers Dement. 2014 Jan; 10(1): 10.1016/j.jalz.2013.01.008. Published online 2013 Mar 25. doi: 10.1016/j.jalz.2013.01.008

PMCID:: PMC3760995

Abstract Article PDF–589K

Select item 345893018.

Cytoplasmic and Nuclear Anti-Apoptotic Roles of αB-Crystallin in Retinal Pigment Epithelial Cells

Woo Jin Jeong, Jee Hyun Rho, Young Geol Yoon, Seung Hee Yoo, Na Young Jeong, Won Yeol Ryu, Hee Bae Ahn, Woo Chan Park, Sae Heun Rho, Hee Seong Yoon, Yung Hyun Choi, Young Hyun Yoo

PLoS One. 2012; 7(9): e45754. Published online 2012 Sep 26. doi: 10.1371/journal.pone.0045754

PMCID:: PMC3458930

Abstract Article PDF–4.7M

Select item 344462019.

PIDD Death-Domain Phosphorylation by ATM Controls Prodeath Versus Prosurvival PIDDosome Signaling

Kiyohiro Ando, Jennifer L. Kernan, Peter H. Liu, Takaomi Sanda, Emmanuelle Logette, Jurg Tschopp, A. Thomas Look, Jianlong Wang, Lisa Bouchier-Hayes, Samuel Sidi

Mol Cell. Author manuscript; available in PMC 2013 Sep 14.

Published in final edited form as: Mol Cell. 2012 Sep 14; 47(5): 681–693. Published online 2012 Jul 30. doi: 10.1016/j.molcel.2012.06.024

PMCID:: PMC3444620

Abstract Article PDF–2.3M

Select item 338606920.

Functional genomics identifies therapeutic targets for MYC-driven cancer

Masafumi Toyoshima, Heather L. Howie, Maki Imakura, Ryan M. Walsh, James E. Annis, Aaron N. Chang, Jason Frazier, B. Nelson Chau, Andrey Loboda, Peter S. Linsley, Michele A. Cleary, Julie R. Park, Carla Grandori

Proc Natl Acad Sci U S A. 2012 Jun 12; 109(24): 9545–9550. Published online 2012 May 23. doi: 10.1073/pnas.1121119109