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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 80090482.

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yimeng Yin, Ekaterina Morgunova, Arttu Jolma, Eevi Kaasinen, Biswajyoti Sahu, Syed Khund-Sayeed, Pratyush K. Das, Teemu Kivioja, Kashyap Dave, Fan Zhong, Kazuhiro R. Nitta, Minna Taipale, Alexander Popov, Paul A. Ginno, Silvia Domcke, Jian Yan, Dirk Schübeler, Charles Vinson, Jussi Taipale

Science. Author manuscript; available in PMC 2021 Mar 30.

Published in final edited form as: Science. 2017 May 5; 356(6337): eaaj2239. doi: 10.1126/science.aaj2239

PMCID:: PMC8009048

Abstract Article PDF–2.6M

Select item 79050403.

Molecular Characterization of the Oncogene BTF3 and Its Targets in Colorectal Cancer

Hantao Wang, Junjie Xing, Wei Wang, Guifen Lv, Haiyan He, Yeqing Lu, Mei Sun, Haiyan Chen, Xu Li

Front Cell Dev Biol. 2020; 8: 601502. Published online 2021 Feb 11. doi: 10.3389/fcell.2020.601502

PMCID:: PMC7905040

Abstract Article PDF–3.2M

Select item 64684594.

N-Glycomic and Transcriptomic Changes Associated with CDX1 mRNA Expression in Colorectal Cancer Cell Lines

Stephanie Holst, Jennifer L. Wilding, Kamila Koprowska, Yoann Rombouts, Manfred Wuhrer

Cells. 2019 Mar; 8(3): 273. Published online 2019 Mar 22. doi: 10.3390/cells8030273

PMCID:: PMC6468459

Abstract Article PDF–3.3M

Select item 63183915.

Campylobacter Concisus and Its Effect on the Expression of CDX1 and COX2

Behrooz Mozaffari Namin, Mohammad Mehdi Soltan Dallal

Asian Pac J Cancer Prev. 2018; 19(11): 3211–3216. doi: 10.31557/APJCP.2018.19.11.3211

PMCID:: PMC6318391

Abstract Article PDF–437K

Select item 61666826.

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei

Domenico Fasci, Hugo van Ingen, Richard A. Scheltema, Albert J. R. Heck

Mol Cell Proteomics. 2018 Oct; 17(10): 2018–2033. Published online 2018 Jul 18. doi: 10.1074/mcp.RA118.000924

PMCID:: PMC6166682

Abstract Article PDF–3.8M

Select item 55316117.

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 52703498.

Combining omics data to identify genes associated with allergic rhinitis

Andréanne Morin, Michel Laviolette, Tomi Pastinen, Louis-Philippe Boulet, Catherine Laprise

Clin Epigenetics. 2017; 9: 3. Published online 2017 Jan 18. doi: 10.1186/s13148-017-0310-1

PMCID:: PMC5270349

Abstract Article PDF–514K

Select item 47625319.

N-glycosylation Profiling of Colorectal Cancer Cell Lines Reveals Association of Fucosylation with Differentiation and Caudal Type Homebox 1 (CDX1)/Villin mRNA Expression

Stephanie Holst, Anna J. M. Deuss, Gabi W. van Pelt, Sandra J. van Vliet, Juan J. Garcia-Vallejo, Carolien A. M. Koeleman, André M. Deelder, Wilma E. Mesker, Rob A. Tollenaar, Yoann Rombouts, Manfred Wuhrer

Mol Cell Proteomics. 2016 Jan; 15(1): 124–140. doi: 10.1074/mcp.M115.051235

PMCID:: PMC4762531

Abstract Article PDF–3.2M

Select item 458409410.

Comprehensive comparative homeobox gene annotation in human and mouse

Laurens G. Wilming, Veronika Boychenko, Jennifer L. Harrow

Database (Oxford) 2015; 2015: bav091. Published online 2015 Sep 25. doi: 10.1093/database/bav091

PMCID:: PMC4584094

Abstract Article PDF–2.1M

Select item 438639311.

The CDX1–microRNA-215 axis regulates colorectal cancer stem cell differentiation

Matthew F. Jones, Toshifumi Hara, Princy Francis, Xiao Ling Li, Sven Bilke, Yuelin Zhu, Marbin Pineda, Murugan Subramanian, Walter F. Bodmer, Ashish Lal

Proc Natl Acad Sci U S A. 2015 Mar 31; 112(13): E1550–E1558. Published online 2015 Mar 16. doi: 10.1073/pnas.1503370112

PMCID:: PMC4386393

Abstract Article PDF–1.3M

Select item 397730512.

RSPO–LGR4 functions via IQGAP1 to potentiate Wnt signaling

Kendra S. Carmon, Xing Gong, Jing Yi, Anthony Thomas, Qingyun Liu

Proc Natl Acad Sci U S A. 2014 Apr 1; 111(13): E1221–E1229. Published online 2014 Mar 17. doi: 10.1073/pnas.1323106111

PMCID:: PMC3977305

Abstract Article PDF–1.7M

Select item 394941613.

A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype

Ryan W Serra, Minggang Fang, Sung Mi Park, Lloyd Hutchinson, Michael R Green

eLife. 2014; 3: e02313. Published online 2014 Mar 12. doi: 10.7554/eLife.02313

PMCID:: PMC3949416

Abstract Article PDF–5.2M

Select item 394721014.

Single nucleotide polymorphisms of Caudal type homeobox 1 and 2 are associated with Barrett’s esophagus

Dongren Ren, Gaolin Zheng, Susan Bream, Whitney Tevebaugh, Nicholas J. Shaheen, Xiaoxin Chen

Dig Dis Sci. Author manuscript; available in PMC 2015 Jan 1.

Published in final edited form as: Dig Dis Sci. 2014 Jan; 59(1): 57–63. Published online 2013 Aug 6. doi: 10.1007/s10620-013-2804-9

PMCID:: PMC3947210

Abstract Article PDF–99K

Select item 381101015.

Differential Gene Expression in Normal Esophagus and Barrett’s Esophagus

Jacob Wang, Rong Qin, Yan Ma, Huiyun Wu, Heiko Peters, Matthew Tyska, Nicholas J. Shaheen, Xiaoxin Chen

J Gastroenterol. Author manuscript; available in PMC 2013 Oct 29.

Published in final edited form as: J Gastroenterol. 2009; 44(9): 10.1007/s00535-009-0082-2. Published online 2009 May 27. doi: 10.1007/s00535-009-0082-2

PMCID:: PMC3811010

Abstract Article PDF–2.6M

Select item 354721816.

Mutations and Down-Regulation of CDX1 in Children with Anorectal Malformations

Tao Zhang, Xiao Bing Tang, Li Li Wang, Yu Zuo Bai, Guang Rong Qiu, Zheng Wei Yuan, Wei Lin Wang

Int J Med Sci. 2013; 10(2): 191–197. Published online 2013 Jan 9. doi: 10.7150/ijms.4929

PMCID:: PMC3547218

Abstract Article PDF–441K

Select item 352849317.

CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5

Yumiko Fujii, Kyoko Yoshihashi, Hidekazu Suzuki, Shuichi Tsutsumi, Hiroyuki Mutoh, Shin Maeda, Yukinori Yamagata, Yasuyuki Seto, Hiroyuki Aburatani, Masanori Hatakeyama

Proc Natl Acad Sci U S A. 2012 Dec 11; 109(50): 20584–20589. Published online 2012 Oct 29. doi: 10.1073/pnas.1208651109

PMCID:: PMC3528493

Abstract Article PDF–1.2M

Select item 350415118.

Whole-Transcriptome Sequencing Identifies Novel IRF2BP2-CDX1 Fusion Gene Brought about by Translocation t(1;5)(q42;q32) in Mesenchymal Chondrosarcoma

Kaja B. Nyquist, Ioannis Panagopoulos, Jim Thorsen, Lisbeth Haugom, Ludmila Gorunova, Bodil Bjerkehagen, Alexander Fosså, Marianne Guriby, Torfinn Nome, Ragnhild A. Lothe, Rolf I. Skotheim, Sverre Heim, Francesca Micci

PLoS One. 2012; 7(11): e49705. Published online 2012 Nov 21. doi: 10.1371/journal.pone.0049705

PMCID:: PMC3504151

Abstract Article PDF–1.8M

Select item 340944319.

Methylation-Dependent Activation of CDX1 through NF-κB: A Link from Inflammation to Intestinal Metaplasia in the Human Stomach

Tilman T. Rau, Anja Rogler, Myrjam Frischauf, Andreas Jung, Peter C. Konturek, Arno Dimmler, Gerhard Faller, Bettina Sehnert, Wael El-Rifai, Arndt Hartmann, Reinhard E. Voll, Regine Schneider-Stock

Am J Pathol. 2012 Aug; 181(2): 487–498. doi: 10.1016/j.ajpath.2012.04.028

PMCID:: PMC3409443

Abstract Article PDF–2.9M

Select item 317805920.

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

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