PMC Links for GEO Profiles (Select 88257612) - PMC

Select item 100339371.

Assessment of community efforts to advance network-based prediction of protein–protein interactions

Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P. Wytock, István A. Kovács, Olivér M. Balogh, Bettina Benczik, Mátyás Pétervári, Bence Ágg, Péter Ferdinandy, Loan Vulliard, Jörg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A. Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K. Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu

Nat Commun. 2023; 14: 1582. Published online 2023 Mar 22. doi: 10.1038/s41467-023-37079-7

PMCID:: PMC10033937

Abstract Article PDF–1.5M

Select item 98491412.

A proteome-scale map of the SARS-CoV-2–human contactome

Dae-Kyum Kim, Benjamin Weller, Chung-Wen Lin, Dayag Sheykhkarimli, Jennifer J. Knapp, Guillaume Dugied, Andreas Zanzoni, Carles Pons, Marie J. Tofaute, Sibusiso B. Maseko, Kerstin Spirohn, Florent Laval, Luke Lambourne, Nishka Kishore, Ashyad Rayhan, Mayra Sauer, Veronika Young, Hridi Halder, Nora Marín-de la Rosa, Oxana Pogoutse, Alexandra Strobel, Patrick Schwehn, Roujia Li, Simin T. Rothballer, Melina Altmann, Patricia Cassonnet, Atina G. Coté, Lena Elorduy Vergara, Isaiah Hazelwood, Betty B. Liu, Maria Nguyen, Ramakrishnan Pandiarajan, Bushra Dohai, Patricia A. Rodriguez Coloma, Juline Poirson, Paolo Giuliana, Luc Willems, Mikko Taipale, Yves Jacob, Tong Hao, David E. Hill, Christine Brun, Jean-Claude Twizere, Daniel Krappmann, Matthias Heinig, Claudia Falter, Patrick Aloy, Caroline Demeret, Marc Vidal, Michael A. Calderwood, Frederick P. Roth, Pascal Falter-Braun

Nat Biotechnol. 2023; 41(1): 140–149. Published online 2022 Oct 10. doi: 10.1038/s41587-022-01475-z

PMCID:: PMC9849141

Abstract Article PDF–7.1M

Select item 81650303.

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Edward L. Huttlin, Raphael J. Bruckner, Jose Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab, Melanie P. Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam, John Szpyt, Brandon M. Gassaway, Alexandra Panov, Hannah Parzen, Sipei Fu, Arvene Golbazi, Eila Maenpaa, Keegan Stricker, Sanjukta Guha Thakurta, Tian Zhang, Ramin Rad, Joshua Pan, David P. Nusinow, Joao A. Paulo, Devin K. Schweppe, Laura Pontano Vaites, J. Wade Harper, Steven P. Gygi

Cell. Author manuscript; available in PMC 2022 May 27.

Published in final edited form as: Cell. 2021 May 27; 184(11): 3022–3040.e28. Published online 2021 May 6. doi: 10.1016/j.cell.2021.04.011

PMCID:: PMC8165030

Abstract Article PDF–2.2M

Select item 71699834.

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 69812065.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS^G13D

Susan A. Kennedy, Mohamed-Ali Jarboui, Sriganesh Srihari, Cinzia Raso, Kenneth Bryan, Layal Dernayka, Theodosia Charitou, Manuel Bernal-Llinares, Carlos Herrera-Montavez, Aleksandar Krstic, David Matallanas, Max Kotlyar, Igor Jurisica, Jasna Curak, Victoria Wong, Igor Stagljar, Thierry LeBihan, Lisa Imrie, Priyanka Pillai, Miriam A. Lynn, Erik Fasterius, Cristina Al-Khalili Szigyarto, James Breen, Christina Kiel, Luis Serrano, Nora Rauch, Oleksii Rukhlenko, Boris N. Kholodenko, Luis F. Iglesias-Martinez, Colm J. Ryan, Ruth Pilkington, Patrizia Cammareri, Owen Sansom, Steven Shave, Manfred Auer, Nicola Horn, Franziska Klose, Marius Ueffing, Karsten Boldt, David J. Lynn, Walter Kolch

Nat Commun. 2020; 11: 499. Published online 2020 Jan 24. doi: 10.1038/s41467-019-14224-9

PMCID:: PMC6981206

Abstract Article PDF–3.7M

Select item 60777226.

Estrogen-regulated feedback loop limits the efficacy of estrogen receptor–targeted breast cancer therapy

Tengfei Xiao, Wei Li, Xiaoqing Wang, Han Xu, Jixin Yang, Qiu Wu, Ying Huang, Joseph Geradts, Peng Jiang, Teng Fei, David Chi, Chongzhi Zang, Qi Liao, Jonathan Rennhack, Eran Andrechek, Nanlin Li, Simone Detre, Mitchell Dowsett, Rinath M. Jeselsohn, X. Shirley Liu, Myles Brown

Proc Natl Acad Sci U S A. 2018 Jul 31; 115(31): 7869–7878. Published online 2018 Jul 9. doi: 10.1073/pnas.1722617115

PMCID:: PMC6077722

Abstract Article PDF–2.4M

Select item 56785817.

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello, Gracjan Michlewski

BMC Biol. 2017; 15: 105. Published online 2017 Nov 8. doi: 10.1186/s12915-017-0444-9

PMCID:: PMC5678581

Abstract Article PDF–3.2M

Select item 46479418.

hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes

Philippe Lamesch, Ning Li, Stuart Milstein, Changyu Fan, Tong Hao, Gabor Szabo, Zhenjun Hu, Kavitha Venkatesan, Graeme Bethel, Paul Martin, Jane Rogers, Stephanie Lawlor, Stuart McLaren, Amélie Dricot, Heather Borick, Michael E. Cusick, Jean Vandenhaute, Ian Dunham, David E. Hill, Marc Vidal

Genomics. 2007 Mar; 89(3): 307–315. doi: 10.1016/j.ygeno.2006.11.012

PMCID:: PMC4647941

Abstract Article

Select item 40045989.

Systematic identification of pathological lamin A interactors

Travis A. Dittmer, Nidhi Sahni, Nard Kubben, David E. Hill, Marc Vidal, Rebecca C. Burgess, Vassilis Roukos, Tom Misteli

Mol Biol Cell. 2014 May 1; 25(9): 1493–1510. doi: 10.1091/mbc.E14-02-0733

PMCID:: PMC4004598

Abstract Article PDF–3.5M

Select item 347780410.

A Census of Human Soluble Protein Complexes

Pierre C. Havugimana, G. Traver Hart, Tamás Nepusz, Haixuan Yang, Andrei L. Turinsky, Zhihua Li, Peggy I. Wang, Daniel R. Boutz, Vincent Fong, Sadhna Phanse, Mohan Babu, Stephanie A. Craig, Pingzhao Hu, Cuihong Wan, James Vlasblom, Vaqaarun-Nisa Dar, Alexander Bezginov, Gregory W. Clark, Gabriel C. Wu, Shoshana J. Wodak, Elisabeth R.M. Tillier, Alberto Paccanaro, Edward M. Marcotte, Andrew Emili

Cell. Author manuscript; available in PMC 2013 Aug 31.

Published in final edited form as: Cell. 2012 Aug 31; 150(5): 1068–1081. doi: 10.1016/j.cell.2012.08.011

PMCID:: PMC3477804

Abstract Article PDF–7.7M

Select item 318838811.

Leveraging the power of next-generation sequencing to generate interactome datasets

Haiyuan Yu, Leah Tardivo, Stanley Tam, Evan Weiner, Fana Gebreab, Changyu Fan, Nenad Svrzikapa, Tomoko Hirozane-Kishikawa, Edward Rietman, Xinping Yang, Julie Sahalie, Kourosh Salehi-Ashtiani, Tong Hao, Michael E. Cusick, David E. Hill, Frederick P. Roth, Pascal Braun, Marc Vidal

Nat Methods. Author manuscript; available in PMC 2011 Dec 1.

Published in final edited form as: Nat Methods. 2011 Jun; 8(6): 478–480. Published online 2011 Apr 24. doi: 10.1038/nmeth.1597

PMCID:: PMC3188388

Abstract Article PDF–932K

Select item 317805912.

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

Pascale Gaudet, Michael S. Livstone, Suzanna E. Lewis, Paul D. Thomas

Brief Bioinform. 2011 Sep; 12(5): 449–462. Published online 2011 Aug 27. doi: 10.1093/bib/bbr042

PMCID:: PMC3178059

Abstract Article PDF–1.0M

Select item 135612913.

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

Kouichi Kimura, Ai Wakamatsu, Yutaka Suzuki, Toshio Ota, Tetsuo Nishikawa, Riu Yamashita, Jun-ichi Yamamoto, Mitsuo Sekine, Katsuki Tsuritani, Hiroyuki Wakaguri, Shizuko Ishii, Tomoyasu Sugiyama, Kaoru Saito, Yuko Isono, Ryotaro Irie, Norihiro Kushida, Takahiro Yoneyama, Rie Otsuka, Katsuhiro Kanda, Takahide Yokoi, Hiroshi Kondo, Masako Wagatsuma, Katsuji Murakawa, Shinichi Ishida, Tadashi Ishibashi, Asako Takahashi-Fujii, Tomoo Tanase, Keiichi Nagai, Hisashi Kikuchi, Kenta Nakai, Takao Isogai, Sumio Sugano

Genome Res. 2006 Jan; 16(1): 55–65. doi: 10.1101/gr.4039406