PMC Links for GEO Profiles (Select 56873607) - PMC

Select item 81650301.

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 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 64637033.

Identification of residues critical for topology inversion of the transmembrane protein TM4SF20 through regulated alternative translocation

Jingcheng Wang, Lisa N. Kinch, Bray Denard, Ching-En Lee, Elina Esmaeilzadeh Gharehdaghi, Nick Grishin, Jin Ye

J Biol Chem. 2019 Apr 12; 294(15): 6054–6061. Published online 2019 Feb 26. doi: 10.1074/jbc.RA119.007681

PMCID:: PMC6463703

Abstract Article PDF–942K

Select item 55316114.

Architecture of the human interactome defines protein communities and disease networks

Edward L. Huttlin, Raphael J. Bruckner, Joao A. Paulo, Joe R. Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P. Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E. White, Devin K. Schweppe, Ramin Rad, Brian K. Erickson, Robert A. Obar, K.G. Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P. Gygi, J. Wade Harper

Nature. Author manuscript; available in PMC 2017 Nov 17.

Published in final edited form as: Nature. 2017 May 25; 545(7655): 505–509. Published online 2017 May 17. doi: 10.1038/nature22366

PMCID:: PMC5531611

Abstract Article PDF–2.7M

Select item 49924485.

Inverting the Topology of a Transmembrane Protein by Regulating the Translocation of the First Transmembrane Helix

Qiuyue Chen, Bray Denard, Ching-En Lee, Sungwon Han, James S. Ye, Jin Ye

Mol Cell. Author manuscript; available in PMC 2017 Aug 18.

Published in final edited form as: Mol Cell. 2016 Aug 18; 63(4): 567–578. Published online 2016 Aug 4. doi: 10.1016/j.molcel.2016.06.032

PMCID:: PMC4992448

Abstract Article PDF–2.1M

Select item 46172116.

The BioPlex Network: A Systematic Exploration of the Human Interactome

Edward L. Huttlin, Lily Ting, Raphael J. Bruckner, Fana Gebreab, Melanie P. Gygi, John Szpyt, Stanley Tam, Gabriela Zarraga, Greg Colby, Kurt Baltier, Rui Dong, Virginia Guarani, Laura Pontano Vaites, Alban Ordureau, Ramin Rad, Brian K. Erickson, Martin Wühr, Joel Chick, Bo Zhai, Deepak Kolippakkam, Julian Mintseris, Robert A. Obar, Tim Harris, Spyros Artavanis-Tsakonas, Mathew E. Sowa, Pietro DeCamilli, Joao A. Paulo, J. Wade Harper, Steven P. Gygi

Cell. Author manuscript; available in PMC 2016 Jul 16.

Published in final edited form as: Cell. 2015 Jul 16; 162(2): 425–440. doi: 10.1016/j.cell.2015.06.043

PMCID:: PMC4617211

Abstract Article PDF–2.2M

Select item 41955867.

Sustained Induction of Collagen Synthesis by TGF-β Requires Regulated Intramembrane Proteolysis of CREB3L1

Qiuyue Chen, Ching-En Lee, Bray Denard, Jin Ye

PLoS One. 2014; 9(10): e108528. Published online 2014 Oct 13. doi: 10.1371/journal.pone.0108528

PMCID:: PMC4195586

Abstract Article PDF–1.6M

Select item 40045988.

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 37388329.

TM4SF20 Ancestral Deletion and Susceptibility to a Pediatric Disorder of Early Language Delay and Cerebral White Matter Hyperintensities

Wojciech Wiszniewski, Jill V. Hunter, Neil A. Hanchard, Jason R. Willer, Chad Shaw, Qi Tian, Anna Illner, Xueqing Wang, Sau W. Cheung, Ankita Patel, Ian M. Campbell, Violet Gelowani, Patricia Hixson, Audrey R. Ester, Mahshid S. Azamian, Lorraine Potocki, Gladys Zapata, Patricia P. Hernandez, Melissa B. Ramocki, Regie L.P. Santos-Cortez, Gao Wang, Michele K. York, Monica J. Justice, Zili D. Chu, Patricia I. Bader, Lisa Omo-Griffith, Nirupama S. Madduri, Gunter Scharer, Heather P. Crawford, Pattamawadee Yanatatsaneejit, Anna Eifert, Jeffery Kerr, Carlos A. Bacino, Adiaha I.A. Franklin, Robin P. Goin-Kochel, Gayle Simpson, Ladonna Immken, Muhammad E. Haque, Marija Stosic, Misti D. Williams, Thomas M. Morgan, Sumit Pruthi, Reed Omary, Simeon A. Boyadjiev, Kay K. Win, Aye Thida, Matthew Hurles, Martin Lloyd Hibberd, Chiea Chuen Khor, Nguyen Van Vinh Chau, Thomas E. Gallagher, Apiwat Mutirangura, Pawel Stankiewicz, Arthur L. Beaudet, Mirjana Maletic-Savatic, Jill A. Rosenfeld, Lisa G. Shaffer, Erica E. Davis, John W. Belmont, Sarah Dunstan, Cameron P. Simmons, Penelope E. Bonnen, Suzanne M. Leal, Nicholas Katsanis, James R. Lupski, Seema R. Lalani

Am J Hum Genet. 2013 Aug 8; 93(2): 197–210. doi: 10.1016/j.ajhg.2013.05.027

Correction in:: Am J Hum Genet. 2013 Aug 8; 93(2): 405.

PMCID:: PMC3738832

Abstract Article PDF–2.1M

Select item 328913910.

Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia

A Piton, J Gauthier, FF Hamdan, RG Lafrenière, Y Yang, E Henrion, S Laurent, A Noreau, P Thibodeau, L Karemera, D Spiegelman, F Kuku, J Duguay, L Destroismaisons, P Jolivet, M Côté, K Lachapelle, O Diallo, A Raymond, C Marineau, N Champagne, L Xiong, C Gaspar, J-B Rivière, J Tarabeux, P Cossette, M-O Krebs, JL Rapoport, A Addington, LE DeLisi, L Mottron, R Joober, E Fombonne, P Drapeau, GA Rouleau

Mol Psychiatry. Author manuscript; available in PMC 2012 Feb 28.

Published in final edited form as: Mol Psychiatry. 2011 Aug; 16(8): 867–880. Published online 2010 May 18. doi: 10.1038/mp.2010.54

PMCID:: PMC3289139

Abstract Article PDF–1.2M

Select item 317805911.

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 135612912.

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

PMCID:: PMC1356129

Abstract Article PDF–438K

Select item 52892813.

The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

Genome Res. 2004 Oct; 14(10b): 2121–2127. doi: 10.1101/gr.2596504

Correction in:: Genome Res. 2006 Jun; 16(6): 804.

PMCID:: PMC528928

Abstract Article PDF–140K

Select item 51531614.

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Kenta Nakai, Sumio Sugano

Genome Res. 2004 Sep; 14(9): 1711–1718. doi: 10.1101/gr.2435604

PMCID:: PMC515316

Abstract Article PDF–181K

Select item 40369715.

The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment

Hilary F. Clark, Austin L. Gurney, Evangeline Abaya, Kevin Baker, Daryl Baldwin, Jennifer Brush, Jian Chen, Bernard Chow, Clarissa Chui, Craig Crowley, Bridget Currell, Bethanne Deuel, Patrick Dowd, Dan Eaton, Jessica Foster, Christopher Grimaldi, Qimin Gu, Philip E. Hass, Sherry Heldens, Arthur Huang, Hok Seon Kim, Laura Klimowski, Yisheng Jin, Stephanie Johnson, James Lee, Lhney Lewis, Dongzhou Liao, Melanie Mark, Edward Robbie, Celina Sanchez, Jill Schoenfeld, Somasekar Seshagiri, Laura Simmons, Jennifer Singh, Victoria Smith, Jeremy Stinson, Alicia Vagts, Richard Vandlen, Colin Watanabe, David Wieand, Kathryn Woods, Ming-Hong Xie, Daniel Yansura, Sothy Yi, Guoying Yu, Jean Yuan, Min Zhang, Zemin Zhang, Audrey Goddard, William I. Wood, Paul Godowski

Genome Res. 2003 Oct; 13(10): 2265–2270. doi: 10.1101/gr.1293003

Correction in:: Genome Res. 2003 Dec; 13(12): 2759.

PMCID:: PMC403697

Abstract Article PDF–120K

Select item 13924116.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

Mammalian Gene Collection (MGC) Program Team

Proc Natl Acad Sci U S A. 2002 Dec 24; 99(26): 16899–16903. Published online 2002 Dec 11. doi: 10.1073/pnas.242603899

PMCID:: PMC139241

Abstract Article PDF–118K

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