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---
layout: page
title: Publications
layout: about
---

Basically Basic is a [Jekyll theme](https://jekyllrb.com/docs/themes/) meant as a substitute for the default --- [Minima](https://github.com/jekyll/minima). Conventions and features found there are fully supported by **Basically Basic**, with a few enhancements thrown in for good measure:
[//]:# Selected Publications
[//]:# ---

### 2021

{:.paper}
<span>Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis</span>{:.papertitle}
<span>Roarke A Kamber, Yoko Nishiga, Bhek Morton, Allison M Banuelos, Amira A Barkal, Felipe Vences-Catalán, Mingxin Gu, Daniel Fernandez, **Jose A Seoane**, David Yao, Katherine Liu, Sijie Lin, Kaitlyn Spees, Christina Curtis, Livnat Jerby-Arnon, Irving L Weissman, Julien Sage, Michael C Bassik</span>{:.authors}<br>
<span>_Nature_, 597:549-554 ,, Sep. 2021</span>{:.journal}
<span>**URL:**[https://www.nature.com/articles/s41586-021-03879-4](https://www.nature.com/articles/s41586-021-03879-4)</span>{:.doi}

{:.paper}
<span>The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D</span>{:.papertitle}
<span>Andrea C Chaikovsky, Chuan Li, Edwin E Jeng, Samuel Loebell, Myung Chang Lee, Christopher W Murray, Ran Cheng, Janos Demeter, Danielle L Swaney, Si-Han Chen, Billy W Newton, Jeffrey R Johnson, Alexandros P Drainas, Yan Ting Shue, **Jose A Seoane**, Preethi Srinivasan, Andy He, Akihiro Yoshida, Susan Q Hipkins, Edel McCrea, Carson D Poltorack, Nevan J Krogan, J Alan Diehl, Christina Kong, Peter K Jackson, Christina Curtis, Dmitri A Petrov, Michael C Bassik, Monte M Winslow, Julien Sage</span>{:.authors}<br>
<span>_Nature_, 592:794-798 ,, Apr. 2021</span>{:.journal}
<span>**URL:**[https://www.nature.com/articles/s41586-021-03474-7](https://www.nature.com/articles/s41586-021-03474-7)</span>{:.doi}

{:.paper}
<span>Cell of Origin Influences Pancreatic Cancer Subtype</span>{:.papertitle}
<span>Brittany M Flowers, Hang Xu, Abigail S Mulligan, Kathryn J Hanson, **Jose A Seoane**, Hannes Vogel, Christina Curtis, Laura D Wood, Laura D Attardi</span>{:.authors}<br>
<span>_Cancer Discovery_, 11(3):660-677 ,, March. 2021</span>{:.journal}
<span>**URL:**[https://cancerdiscovery.aacrjournals.org/content/11/3/660.abstract](https://cancerdiscovery.aacrjournals.org/content/11/3/660.abstract)</span>{:.doi}

{:.paper}
<span>A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation</span>{:.papertitle}
<span>Yuan-Hung Lo, Kevin S Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D Sobba, Kasper Karlsson, Sunny J Jones, Teri A Longacre, Amanda T Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, **Jose A Seoane**, Jin Chen, Ilya Shmulevich, Jonathan S Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald R Crabtree, Calvin J Kuo</span>{:.authors}<br>
<span>_Cancer Discovery_, Jan. 2021</span>{:.journal}
<span>**URL:**[https://cancerdiscovery.aacrjournals.org/content/early/2021/01/14/2159-8290.CD-20-1109](https://cancerdiscovery.aacrjournals.org/content/early/2021/01/14/2159-8290.CD-20-1109)</span>{:.doi}



### 2020

{:.paper}
<span>Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program</span>{:.papertitle}
<span>Kathryn T Bieging-Rolett, Alyssa M Kaiser, David W Morgens, Anthony M Boutelle, **Jose A Seoane**, Eric L Van Nostrand, Changyu Zhu, Shauna L Houlihan, Stephano S Mello, Brian A Yee, Jacob McClendon, Sarah E Pierce, Ian P Winters, Mengxiong Wang, Andrew J Connolly, Scott W Lowe, Christina Curtis, Gene W Yeo, Monte M Winslow, Michael C Bassik, Laura D Attardi</span>{:.authors}<br>
<span>_Molecular Cell_, 80(3):452-469.e9 ,, Nov. 2020</span>{:.journal}
<span>**URL:**[www.sciencedirect.com/science/article/pii/S1097276520307292](https://www.sciencedirect.com/science/article/pii/S1097276520307292)</span>{:.doi}

{:.paper}
<span>The m6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor</span>{:.papertitle}
<span>Yiren Xiao, Kaushik N Thakkar, Hongjuan Zhao, James Broughton, Yang Li, **Jose A Seoane**, Anh N Diep, Thomas J Metzner, Rie von Eyben, David L Dill, James D Brooks, Christina Curtis, John T Leppert, Jiangbin Ye, Donna M Peehl, Amato J Giaccia, Subarna Sinha, Erinn B Rankin</span>{:.authors}<br>
<span>_Proceedings of the National Academy of Sciences_, 117(35):21441-21449, Sep. 2020</span>{:.journal}
<span>**URL:**[www.pnas.org/content/117/35/21441.short](https://www.pnas.org/content/117/35/21441.short)</span>{:.doi}

{:.paper}
<span>CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities</span>{:.papertitle}
<span>Kyuho Han, Sarah E Pierce, Amy Li, Kaitlyn Spees, Grace R Anderson, **Jose A Seoane**, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R Kelly, Maryam Yousefi, Scott W Simpkins, David Yao, Keonil Lee, Calvin J Kuo, Peter K Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J Gentles, Christina Curtis, Monte M Winslow, Michael C Bassik</span>{:.authors}<br>
<span>_Nature_, 580(7801):136-141, April. 2020</span>{:.journal}
<span>**URL:**[www.nature.com/articles/s41586-020-2099-x](https://www.nature.com/articles/s41586-020-2099-x)</span>{:.doi}

{:.paper}
<span>Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism</span>{:.papertitle}
<span>Albert M Li, Gregory S Ducker, Yang Li, **Jose A Seoane**, Yiren Xiao, Stavros Melemenidis, Yiren Zhou, Ling Liu, Sakari Vanharanta, Edward E Graves, Erinn B Rankin, Christina Curtis, Joan Massagué, Joshua D Rabinowitz, Craig B Thompson, Jiangbin Ye</span>{:.authors}<br>
<span>_Molecular Cancer Research_, 18(4):599-611, April. 2020</span>{:.journal}
<span>**URL:**[mcr.aacrjournals.org/content/18/4/599.abstract](https://mcr.aacrjournals.org/content/18/4/599.abstract)</span>{:.doi}

{:.paper}
<span>Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers</span>{:.papertitle}
<span>Nasa Sinnott-Armstrong, **Jose A Seoane**, Jonathan K Pritchard, Christina Curtis, Michael P Snyder</span>{:.authors}<br>
<span>_BioRxiv_, Nov. 2020</span>{:.journal}
<span>**URL:**[https://www.biorxiv.org/content/10.1101/2020.08.21.239954v1.abstract](https://www.biorxiv.org/content/10.1101/2020.08.21.239954v1.abstract)</span>{:.doi}

### 2019

{:.paper}
<span>Chromatin regulators mediate anthracycline sensitivity in breast cancer</span>{:.papertitle}
<span>**Jose A Seoane**, Jacob G Kirkland, Jennifer L Caswell-Jin, Gerald R Crabtree, Christina Curtis</span>{:.authors}<br>
<span>_Nature medicine_, 25(11):1721-1727, Nov. 2019</span>{:.journal}
<span>**URL:**[www.nature.com/articles/s41591-019-0638-5](https://www.nature.com/articles/s41591-019-0638-5)</span>{:.doi}

{:.paper}
<span>Quantitative evidence for early metastatic seeding in colorectal cancer</span>{:.papertitle}
<span>Zheng Hu, Jie Ding, Zhicheng Ma, Ruping Sun, **Jose A Seoane**, J Scott Shaffer, Carlos J Suarez, Anna S Berghoff, Chiara Cremolini, Alfredo Falcone, Fotios Loupakis, Peter Birner, Matthias Preusser, Heinz-Josef Lenz, Christina Curtis</span>{:.authors}<br>
<span>_Nature genetics_, 51(7):1113-1122, Jul. 2019</span>{:.journal}
<span>**URL:**[www.nature.com/articles/s41588-019-0423-x](https://www.nature.com/articles/s41588-019-0423-x)</span>{:.doi}

{:.paper}
<span>Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups</span>{:.papertitle}
<span>Oscar M Rueda, Stephen-John Sammut, **Jose A Seoane**, Suet-Feung Chin, Jennifer L Caswell-Jin, Maurizio Callari, Rajbir Batra, Bernard Pereira, Alejandra Bruna, H Raza Ali, Elena Provenzano, Bin Liu, Michelle Parisien, Cheryl Gillett, Steven McKinney, Andrew R Green, Leigh Murphy, Arnie Purushotham, Ian O Ellis, Paul D Pharoah, Cristina Rueda, Samuel Aparicio, Carlos Caldas, Christina Curtis</span>{:.authors}<br>
<span>_Nature_, 567(7748):399-404, Mar. 2019</span>{:.journal}
<span>**URL:**[www.nature.com/articles/s41586-019-1007-8](https://www.nature.com/articles/s41586-019-1007-8)</span>{:.doi}

{:.paper}
<span>Assessment of ERBB2/HER2 status in HER2-equivocal breast cancers by FISH and 2013/2014 ASCO-CAP guidelines</span>{:.papertitle}
<span>Michael F Press, **Jose A Seoane**, Christina Curtis, Emmanuel Quinaux, Roberta Guzman, Guido Sauter, Wolfgang Eiermann, John R Mackey, Nicholas Robert, Tadeusz Pienkowski, John Crown, Miguel Martin, Vicente Valero, Valerie Bee, Yanling Ma, Ivonne Villalobos, Dennis J Slamon</span>{:.authors}<br>
<span>_JAMA oncology_, 5(3):366-375, Mar. 2019</span>{:.journal}
<span>**URL:**[jamanetwork.com/journals/jamaoncology/article-abstract/2718266](https://jamanetwork.com/journals/jamaoncology/article-abstract/2718266)</span>{:.doi}

### 2018

{:.paper}
<span>The chromatin accessibility landscape of primary human cancers</span>{:.papertitle}
<span>M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, **Jose A Seoane**, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho, Ansuman T Satpathy, Maxwell R Mumbach, Katherine A Hoadley, A Gordon Robertson, Nathan C Sheffield, Ina Felau, Mauro AA Castro, Benjamin P Berman, Louis M Staudt, Jean C Zenklusen, Peter W Laird, Christina Curtis, William J Greenleaf, Howard Y Chang</span>{:.authors}<br>
<span>_Science_, 362(6413), Oct. 2018</span>{:.journal}
<span>**URL:**[https://science.sciencemag.org/content/362/6413/eaav1898.abstract](https://science.sciencemag.org/content/362/6413/eaav1898.abstract)</span>{:.doi}

{:.paper}
<span>Comparative molecular analysis of gastrointestinal adenocarcinomas</span>{:.papertitle}
<span>Yang Liu, Nilay S Sethi, Toshinori Hinoue, Barbara G Schneider, Andrew D Cherniack, Francisco Sanchez-Vega, **Jose A Seoane**, Farshad Farshidfar, Reanne Bowlby, Mirazul Islam, Jaegil Kim, Walid Chatila, Rehan Akbani, Rupa S Kanchi, Charles S Rabkin, Joseph E Willis, Kenneth K Wang, Shannon J McCall, Lopa Mishra, Akinyemi I Ojesina, Susan Bullman, Chandra Sekhar Pedamallu, Alexander J Lazar, Ryo Sakai,TCGA consortium, VésteinnThorsson, Adam J.Bass and Peter W.Laird</span>{:.authors}<br>
<span>_Cancer Cell_, 33(4):721-735, April 2018</span>{:.journal}
<span>**URL:**[https://www.sciencedirect.com/science/article/pii/S1535610818301144](https://www.sciencedirect.com/science/article/pii/S1535610818301144)</span>{:.doi}

### 2017

{:.paper}
<span>Integrated genomic characterization of oesophageal carcinoma</span>{:.papertitle}
<span>The Cancer Genome Atlas Research Network</span>{:.authors}<br>
<span>_Nature_, 541(7636), Jan. 2017</span>{:.journal}
<span>**URL:**[https://www.nature.com/articles/nature20805](https://www.nature.com/articles/nature20805)</span>{:.doi}

### 2014

{:.paper}
<span>Canonical correlation analysis for gene-based pleiotropy discovery</span>{:.papertitle}
<span>**Jose A Seoane**, Colin Campbell, Ian NM Day, Juan P Casas, Tom R Gaunt</span>{:.authors}<br>
<span>_PLoS Computational Biology_, 10(10), Oct. 2014</span>{:.journal}
<span>**URL:**[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003876](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003876)</span>{:.doi}

{:.paper}
<span>A pathway-based data integration framework for prediction of disease progression</span>{:.papertitle}
<span>**Jose A Seoane**, Ian NM Day, Tom R Gaunt, Colin Campbell</span>{:.authors}<br>
<span>_Bioinformatics_, 30(6):838-845, Mar. 2014</span>{:.journal}
<span>**URL:**[https://academic.oup.com/bioinformatics/article-abstract/30/6/838/285849](https://academic.oup.com/bioinformatics/article-abstract/30/6/838/285849)</span>{:.doi}




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