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Select item 87690721.

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Caroline Benz, Muhammad Ali, Izabella Krystkowiak, Leandro Simonetti, Ahmed Sayadi, Filip Mihalic, Johanna Kliche, Eva Andersson, Per Jemth, Norman E Davey, Ylva Ivarsson

Mol Syst Biol. 2022 Jan; 18(1): e10584. Published online 2022 Jan 19. doi: 10.15252/msb.202110584

PMCID:: PMC8769072

Abstract Article PDF–2.9M

Select item 83529642.

Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer

Athea Vichas, Amanda K. Riley, Naomi T. Nkinsi, Shriya Kamlapurkar, Phoebe C. R. Parrish, April Lo, Fujiko Duke, Jennifer Chen, Iris Fung, Jacqueline Watson, Matthew Rees, Austin M. Gabel, James D. Thomas, Robert K. Bradley, John K. Lee, Emily M. Hatch, Marina K. Baine, Natasha Rekhtman, Marc Ladanyi, Federica Piccioni, Alice H. Berger

Nat Commun. 2021; 12: 4789. Published online 2021 Aug 9. doi: 10.1038/s41467-021-24841-y

PMCID:: PMC8352964

Abstract Article PDF–4.5M

Select item 77376103.

Receptor‐mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy

Amelia E Ohnstad, Jose M Delgado, Brian J North, Isha Nasa, Arminja N Kettenbach, Sebastian W Schultz, Christopher J Shoemaker

EMBO J. 2020 Dec 15; 39(24): e104948. Published online 2020 Nov 23. doi: 10.15252/embj.2020104948

PMCID:: PMC7737610

Abstract Article PDF–3.7M

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 66009155.

TNF-α inhibits glucocorticoid receptor-induced gene expression by reshaping the GR nuclear cofactor profile

Karen Dendoncker, Steven Timmermans, Jolien Vandewalle, Melanie Eggermont, Joanna Lempiäinen, Evelien Van Hamme, Sylviane Dewaele, Sofie Vandevyver, Marlies Ballegeer, Jolien Souffriau, Lise Van Wyngene, Kelly Van Looveren, Tineke Vanderhaeghen, Rudi Beyaert, Karolien De Bosscher, Jorma J. Palvimo, Marc Van Montagu, Claude Libert

Proc Natl Acad Sci U S A. 2019 Jun 25; 116(26): 12942–12951. Published online 2019 Jun 10. doi: 10.1073/pnas.1821565116

Correction in:: Proc Natl Acad Sci U S A. 2019 Jul 30; 116(31): 15745.

PMCID:: PMC6600915

Abstract Article PDF–1.7M

Select item 63179946.

SNIP1 Recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response

Lei-Lei Chen, Huai-Peng Lin, Wen-Jie Zhou, Chen-Xi He, Zhi-Yong Zhang, Zhou-Li Cheng, Jun-Bin Song, Peng Liu, Xin-Yu Chen, Yu-Kun Xia, Xiu-Fei Chen, Ren-Qiang Sun, Jing-Ye Zhang, Yi-Ping Sun, Lei Song, Bing-Jie Liu, Rui-Kai Du, Chen Ding, Fei Lan, Sheng-Lin Huang, Feng Zhou, Suling Liu, Yue Xiong, Dan Ye, Kun-Liang Guan

Cell Rep. Author manuscript; available in PMC 2019 Jan 3.

Published in final edited form as: Cell Rep. 2018 Nov 6; 25(6): 1485–1500.e4. doi: 10.1016/j.celrep.2018.10.028

PMCID:: PMC6317994

Abstract Article PDF–1.4M

Select item 60736707.

Preliminary RNA-Seq Analysis of Long Non-Coding RNAs Expressed in Human Term Placenta

Marta Majewska, Aleksandra Lipka, Lukasz Paukszto, Jan Pawel Jastrzebski, Marek Gowkielewicz, Marcin Jozwik, Mariusz Krzysztof Majewski

Int J Mol Sci. 2018 Jul; 19(7): 1894. Published online 2018 Jun 27. doi: 10.3390/ijms19071894

PMCID:: PMC6073670

Abstract Article PDF–3.6M

Select item 58391588.

Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells

Giorgio Giurato, Giovanni Nassa, Annamaria Salvati, Elena Alexandrova, Francesca Rizzo, Tuula A. Nyman, Alessandro Weisz, Roberta Tarallo

Sci Data. 2018; 5: 180031. Published online 2018 Mar 6. doi: 10.1038/sdata.2018.31

PMCID:: PMC5839158

Abstract Article PDF–1.9M

Select item 58269269.

VIRMA mediates preferential m⁶A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation

Yanan Yue, Jun Liu, Xiaolong Cui, Jie Cao, Guanzheng Luo, Zezhou Zhang, Tao Cheng, Minsong Gao, Xiao Shu, Honghui Ma, Fengqin Wang, Xinxia Wang, Bin Shen, Yizhen Wang, Xinhua Feng, Chuan He, Jianzhao Liu

Cell Discov. 2018; 4: 10. Published online 2018 Feb 27. doi: 10.1038/s41421-018-0019-0

PMCID:: PMC5826926

Abstract Article PDF–2.3M

Select item 537173010.

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 436785711.

New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing

Fernanda Luisa Basei, Gabriela Vaz Meirelles, Germanna Lima Righetto, Deivid Lucas dos Santos Migueleti, Juliana Helena Costa Smetana, Jörg Kobarg

Proteome Sci. 2015; 13: 11. Published online 2015 Feb 26. doi: 10.1186/s12953-015-0065-6

PMCID:: PMC4367857

Abstract Article PDF–3.1M

Select item 401342812.

Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast

Rachael Natrajan, Paul M Wilkerson, Caterina Marchiò, Salvatore Piscuoglio, Charlotte KY Ng, Patty Wai, Maryou B Lambros, Eleftherios P Samartzis, Konstantin J Dedes, Jessica Frankum, Ilirjana Bajrami, Alicja Kopec, Alan Mackay, Roger A'hern, Kerry Fenwick, Iwanka Kozarewa, Jarle Hakas, Costas Mitsopoulos, David Hardisson, Christopher J Lord, Chandan Kumar-Sinha, Alan Ashworth, Britta Weigelt, Anna Sapino, Arul M Chinnaiyan, Christopher A Maher, Jorge S Reis-Filho

J Pathol. 2014 Apr; 232(5): 553–565. Published online 2014 Feb 5. doi: 10.1002/path.4325

PMCID:: PMC4013428

Abstract Article PDF–1.7M

Select item 357913813.

Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes?

James A Nathan, Hyoung Tae Kim, Lily Ting, Steven P Gygi, Alfred L Goldberg

EMBO J. 2013 Feb 20; 32(4): 552–565. Published online 2013 Jan 11. doi: 10.1038/emboj.2012.354

PMCID:: PMC3579138

Abstract Article PDF–1.5M

Select item 351199914.

DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution

Laura J. Dumas, Majesta S. O’Bleness, Jonathan M. Davis, C. Michael Dickens, Nathan Anderson, J.G. Keeney, Jay Jackson, Megan Sikela, Armin Raznahan, Jay Giedd, Judith Rapoport, Sandesh S.C. Nagamani, Ayelet Erez, Nicola Brunetti-Pierri, Rachel Sugalski, James R. Lupski, Tasha Fingerlin, Sau Wai Cheung, James M. Sikela

Am J Hum Genet. 2012 Sep 7; 91(3): 444–454. doi: 10.1016/j.ajhg.2012.07.016

PMCID:: PMC3511999

Abstract Article PDF–5.3M

Select item 342992815.

Evolutionary History and Genome Organization of DUF1220 Protein Domains

Majesta S. O’Bleness, C. Michael Dickens, Laura J. Dumas, Hildegard Kehrer-Sawatzki, Gerald J. Wyckoff, James M. Sikela

G3 (Bethesda) 2012 Sep; 2(9): 977–986. Published online 2012 Sep 1. doi: 10.1534/g3.112.003061

PMCID:: PMC3429928

Abstract Article PDF–1.6M

Select item 320042716.

Systematic and quantitative assessment of the ubiquitin modified proteome

Woong Kim, Eric J. Bennett, Edward L. Huttlin, Ailan Guo, Jing Li, Anthony Possemato, Mathew E. Sowa, Ramin Rad, John Rush, Michael J. Comb, J. Wade Harper, Steven P. Gygi

Mol Cell. Author manuscript; available in PMC 2012 Oct 21.

Published in final edited form as: Mol Cell. 2011 Oct 21; 44(2): 325–340. Published online 2011 Sep 8. doi: 10.1016/j.molcel.2011.08.025

PMCID:: PMC3200427

Abstract Article PDF–3.1M

Select item 316943217.

Protein interactome reveals converging molecular pathways among autism disorders

Yasunari Sakai, Chad A. Shaw, Brian C. Dawson, Diana V. Dugas, Zaina Al-Mohtaseb, David E. Hill, Huda Y. Zoghbi

Sci Transl Med. Author manuscript; available in PMC 2011 Dec 8.

Published in final edited form as: Sci Transl Med. 2011 Jun 8; 3(86): 86ra49. doi: 10.1126/scitranslmed.3002166

PMCID:: PMC3169432

Abstract Article PDF–6.0M

Select item 308091018.

Genome-wide Association Study Implicates PARD3B-based AIDS Restriction

Jennifer L. Troyer, George W. Nelson, James A. Lautenberger, Leslie Chinn, Carl McIntosh, Randall C. Johnson, Efe Sezgin, Bailey Kessing, Michael Malasky, Sher L. Hendrickson, Guan Li, Joan Pontius, Minzhong Tang, Ping An, Cheryl A. Winkler, Sophie Limou, Sigrid Le Clerc, Olivier Delaneau, Jean-François Zagury, Hanneke Schuitemaker, Daniëlle van Manen, Jay H. Bream, Edward D. Gomperts, Susan Buchbinder, James J. Goedert, Gregory D. Kirk, Stephen J. O'Brien

J Infect Dis. 2011 May 15; 203(10): 1491–1502. doi: 10.1093/infdis/jir046

PMCID:: PMC3080910

Abstract Article PDF–870K

Select item 275525319.

Copy number variation at 1q21.1 associated with neuroblastoma

Sharon J. Diskin, Cuiping Hou, Joseph T. Glessner, Edward F. Attiyeh, Marci Laudenslager, Kristopher Bosse, Kristina Cole, Yael P. Mosse, Andrew Wood, Jill E. Lynch, Katlyn Pecor, Maura Diamond, Cynthia Winter, Kai Wang, Cecilia Kim, Elizabeth A. Geiger, Patrick W. McGrady, Alexandra I. F. Blakemore, Wendy B. London, Tamim H. Shaikh, Jonathan Bradfield, Struan F. A. Grant, Hongzhe Li, Marcella Devoto, Eric R. Rappaport, Hakon Hakonarson, John M. Maris

Nature. Author manuscript; available in PMC 2009 Oct 1.

Published in final edited form as: Nature. 2009 Jun 18; 459(7249): 987–991. doi: 10.1038/nature08035

PMCID:: PMC2755253

Abstract Article PDF–1.1M

Select item 189911120.

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Katsuki Tsuritani, Takuma Irie, Riu Yamashita, Yuta Sakakibara, Hiroyuki Wakaguri, Akinori Kanai, Junko Mizushima-Sugano, Sumio Sugano, Kenta Nakai, Yutaka Suzuki

Genome Res. 2007 Jul; 17(7): 1005–1014. doi: 10.1101/gr.6030107

PMCID:: PMC1899111

Abstract Article PDF–757K

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