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2016

2016 Publications

David Poznik, Yali Xue, Fernando Mendez, Thomas Willems, Andrea Massaia, Melissa Sayres, Qasim Ayub, Shane McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham Ritchie, Eliza Cerveira, Tomas Fitzgerald, Erik Garrison, Anthony Marcketta, David Mittelman, Mallory Romanovitch, Chengsheng Zhang, Xiangqun Zheng-Bradley, Gonçalo Abecasis, Steven McCarroll, Paul Flicek, Peter Underhill, Lachlan Coin, Daniel Zerbino, Fengtang Yang, Charles Lee, Laura Clarke, Adam Auton, Yaniv Erlich, Robert Handsaker, 1000 Consortium, Carlos Bustamante, Chris Tyler-Smith .  2016.   Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.. Nat Genet. ▶ Go to Pubmed
Shuo Yang, Shai Carmi, Itsik Pe'er .  2016.   Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.. J Comput Biol. ▶ Go to Pubmed
Antonio Gomes, Harris Wang .  2016.   The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.. PLoS Comput Biol. 12 (4) :e1004891 ▶ Go to Pubmed
Yeh-Hsing Lao, Chun-Wei Chi, Sarah Friedrich, Konan Peck, Tza-Huei Wang, Kam Leong, Lin-Chi Chen .  2016.   Signal-On Protein Detection via Dye Translocation between Aptamer and Quantum Dot.. ACS Appl Mater Interfaces. ▶ Go to Pubmed
David Beck, Megan Cho, Francisca Millan, Carin Yates, Mark Hannibal, Bridget O'Connor, Marwan Shinawi, Anne Connolly, Darrel Waggoner, Sara Halbach, Brad Angle, Victoria Sanders, Yufeng Shen, Kyle Retterer, Amber Begtrup, Renkui Bai, Wendy Chung .  2016.   A recurrent de novo CTBP1 mutation is associated with developmental delay, hypotonia, ataxia, and tooth enamel defects.. Neurogenetics. ▶ Go to Pubmed
Shengpeng Wang, Yingqi Xu, Hon Chan, Hae-Won Kim, Yitao Wang, Kam Leong, Meiwan Chen .  2016.   phicaNanoparticle-mediated inhibition of survivin to overcome drug resistance in cancer therapy.. J Control Release. ▶ Go to Pubmed
Nathan Johns, Tomasz Blazejewski, Antonio Gomes, Harris Wang .  2016.   Principles for designing synthetic microbial communities.. Curr Opin Microbiol. 31 :146-153 ▶ Go to Pubmed
Genevera Allen, Nicola Amoroso, Catalina Anghel, Venkat Balagurusamy, Christopher Bare, Derek Beaton, Roberto Bellotti, David Bennett, Kevin Boehme, Paul Boutros, Laura Caberlotto, Cristian Caloian, Frederick Campbell, Elias Neto, Yu-Chuan Chang, Beibei Chen, Chien-Yu Chen, Ting-Ying Chien, Tim Clark, Sudeshna Das, Christos Davatzikos, Jieyao Deng, Donna Dillenberger, Richard Dobson, Qilin Dong, Jimit Doshi, Denise Duma, Rosangela Errico, Guray Erus, Evan Everett, David Fardo, Stephen Friend, Holger Fröhlich, Jessica Gan, Peter St George-Hyslop, Satrajit Ghosh, Enrico Glaab, Robert Green, Yuanfang Guan, Ming-Yi Hong, Chao Huang, Jinseub Hwang, Joseph Ibrahim, Paolo Inglese, Qijia Jiang, Yuriko Katsumata, John Kauwe, Arno Klein, Dehan Kong, Roland Krause, Emilie Lalonde, Mario Lauria, Eunjee Lee, Xihui Lin, Zhandong Liu, Julie Livingstone, Benjamin Logsdon, Simon Lovestone, Anandhi Lyappan, Michelle Ma, Ashutosh Malhotra, Lara Mangravite, Taylor Maxwell, Emily Merrill, John Nagorski, Aishwarya Namasivayam, Manjari Narayan, Mufassra Naz, Stephen Newhouse, Thea Norman, Ramil Nurtdinov, Yen-Jen Oyang, Yudi Pawitan, Shengwen Peng, Mette Peters, Stephen Piccolo, Paurush Praveen, Corrado Priami, Veronica Sabelnykova, Philipp Senger, Xia Shen, Andrew Simmons, Aristeidis Sotiras, Gustavo Stolovitzky, Sabina Tangaro, Andrea Tateo, Yi-An Tung, Nicholas Tustison, Erdem Varol, George Vradenburg, Michael Weiner, Guanghua Xiao, Lei Xie, Yang Xie, Jia Xu, Hojin Yang, Xiaowei Zhan, Yunyun Zhou, Fan Zhu, Hongtu Zhu, Shanfeng Zhu, Alzheimer's Initiative .  2016.   Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.. Alzheimers Dement. ▶ Go to Pubmed
Samir Merabet, Richard Mann .  2016.   To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins.. Trends Genet. ▶ Go to Pubmed
Rosemarie Mason, Hugh Welles, Cameron Adams, Bimal Chakrabarti, Jason Gorman, Tongqing Zhou, Richard Nguyen, Sijy O'Dell, Sabrina Lusvarghi, Carole Bewley, Hui Li, George Shaw, Zizhang Sheng, Lawrence Shapiro, Richard Wyatt, Peter Kwong, John Mascola, Mario Roederer .  2016.   Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability.. PLoS Pathog. 12 (4) :e1005537 ▶ Go to Pubmed
Javier Quilez, Audrey Guilmatre, Paras Garg, Gareth Highnam, Melissa Gymrek, Yaniv Erlich, Ricky Joshi, David Mittelman, Andrew Sharp .  2016.   Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.. Nucleic Acids Res. ▶ Go to Pubmed
Rob Patro, Raquel Norel, Robert Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Luštrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford .  2016.   A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.. BMC Bioinformatics. 17 :155 ▶ Go to Pubmed
Benedikt Westphalen, Yoshihiro Takemoto, Takayuki Tanaka, Marina Macchini, Zhengyu Jiang, Bernhard Renz, Xiaowei Chen, Steffen Ormanns, Karan Nagar, Yagnesh Tailor, Randal May, Youngjin Cho, Samuel Asfaha, Daniel Worthley, Yoku Hayakawa, Aleksandra Urbanska, Michael Quante, Maximilian Reichert, Joshua Broyde, Prem Subramaniam, Helen Remotti, Gloria Su, Anil Rustgi, Richard Friedman, Barry Honig, Andrea Califano, Courtney Houchen, Kenneth Olive, Timothy Wang .  2016.   Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis.. Cell Stem Cell. 18 (4) :441-55 ▶ Go to Pubmed
Sophie Zaaijer, Yaniv Erlich .  2016.   Using mobile sequencers in an academic classroom.. Elife. 5 ▶ Go to Pubmed
Mi-Jeong Park, Ren Sheng, Antonina Silkov, Da-Jung Jung, Zhi-Gang Wang, Yao Xin, Hyunjin Kim, Pallavi Thiagarajan-Rosenkranz, Seohyeon Song, Youngdae Yoon, Wonhee Nam, Ilshin Kim, Eui Kim, Dong-Gyu Lee, Yong Chen, Indira Singaram, Li Wang, Myoung Jang, Cheol-Sang Hwang, Barry Honig, Sungho Ryu, Justin Lorieau, You-Me Kim, Wonhwa Cho .  2016.   SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins.. Mol Cell. 62 (1) :7-20 ▶ Go to Pubmed
Hon Chan, Siying Ma, Kam Leong .  2016.   Can microfluidics address biomanufacturing challenges in drug/gene/cell therapies?. Regen Biomater. 3 (2) :87-98 ▶ Go to Pubmed
Erica Peters, Nicolas Christoforou, Kam Leong, George Truskey, Jennifer West .  2016.   Poly(ethylene glycol) Hydrogel Scaffolds Containing Cell-Adhesive and Protease-Sensitive Peptides Support Microvessel Formation by Endothelial Progenitor Cells.. Cell Mol Bioeng. 9 (1) :38-54 ▶ Go to Pubmed
Stefanie Widder, Rosalind Allen, Thomas Pfeiffer, Thomas Curtis, Carsten Wiuf, William Sloan, Otto Cordero, Sam Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry Flint, Andreas Haas, Béatrice Laroche, Jan-Ulrich Kreft, Paul Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan van der Meer, Tobias Groβkopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth Smets, Harris Wang, Isaac Fellows, Orkun Soyer .  2016.   Challenges in microbial ecology: building predictive understanding of community function and dynamics.. ISME J. ▶ Go to Pubmed
Nir Nissim, Mary Boland, Nicholas Tatonetti, Yuval Elovici, George Hripcsak, Yuval Shahar, Robert Moskovitch .  2016.   Improving Condition Severity Classification with an Efficient Active Learning Based Framework.. J Biomed Inform. ▶ Go to Pubmed
Rebecca Lescarbeau, Liang Lei, Katrina Bakken, Peter Sims, Jann Sarkaria, Peter Canoll, Forest White .  2016.   Quantitative phosphoproteomics reveals Wee1 kinase as a therapeutic target in a model of proneural glioblastoma.. Mol Cancer Ther. ▶ Go to Pubmed
Paula van Mourik, Jannie de Jong, Danielle Agpalo, Clémence Claussin, Rodney Rothstein, Michael Chang .  2016.   Recombination-Mediated Telomere Maintenance in Saccharomyces cerevisiae Is Not Dependent on the Shu Complex.. PLoS One. 11 (3) :e0151314 ▶ Go to Pubmed
Oliver Hobert .  2016.   Terminal Selectors of Neuronal Identity.. Curr Top Dev Biol. 116 :455-75 ▶ Go to Pubmed
Mina Fazlollahi, Ivor Muroff, Eunjee Lee, Helen Causton, Harmen Bussemaker .  2016.   Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Sebastien Weyn-Vanhentenryck, Chaolin Zhang .  2016.   mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins.. Methods Mol Biol. 1421 :215-26 ▶ Go to Pubmed
Paola Nicoletti, Anneke Werk, Ashley Sawle, Yufeng Shen, Thomas Urban, Sally Coulthard, Einar Bjornsson, Ingolf Cascorbi, Aris Floratos, Thomas Stammschulte, Ursula Gundert-Remy, Matthew Nelson, Guruprasad Aithal, Ann Daly, International Consortium .  2016.   HLA-DRB1*16: 01-DQB1*05: 02 is a novel genetic risk factor for flupirtine-induced liver injury.. Pharmacogenet Genomics. 26 (5) :218-24 ▶ Go to Pubmed
Habte Nida, Shula Blum, Dina Zielinski, Dhruv Srivastava, Rivka Elbaum, Zhanguo Xin, Yaniv Erlich, Eyal Fridman, Noam Shental .  2016.   Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach.. Plant J. ▶ Go to Pubmed
Roumen Voutev, Richard Mann .  2016.   Streamlined scanning for enhancer elements in Drosophila melanogaster.. Biotechniques. 60 (3) :141-4 ▶ Go to Pubmed
Keith Hoffman, Mo Dimbil, Nicholas Tatonetti, Robert Kyle .  2016.   A Pharmacovigilance Signaling System Based on FDA Regulatory Action and Post-Marketing Adverse Event Reports.. Drug Saf. ▶ Go to Pubmed
Shuqiang Huang, Anna Lee, Ryan Tsoi, Feilun Wu, Ying Zhang, Kam Leong, Lingchong You .  2016.   Coupling spatial segregation with synthetic circuits to control bacterial survival.. Mol Syst Biol. 12 (2) :859 ▶ Go to Pubmed
Ravi Sheth, Vitor Cabral, Sway Chen, Harris Wang .  2016.   Manipulating Bacterial Communities by in situ Microbiome Engineering.. Trends Genet. ▶ Go to Pubmed
Steven Hill, Laura Heiser, Thomas Cokelaer, Michael Unger, Nicole Nesser, Daniel Carlin, Yang Zhang, Artem Sokolov, Evan Paull, Chris Wong, Kiley Graim, Adrian Bivol, Haizhou Wang, Fan Zhu, Bahman Afsari, Ludmila Danilova V, Alexander Favorov V, Wai Lee, Dane Taylor, Chenyue Hu, Byron Long, David Noren, Alexander Bisberg, HPN-DREAM Consortium, Gordon Mills, Joe Gray, Michael Kellen, Thea Norman, Stephen Friend, Amina Qutub, Elana Fertig, Yuanfang Guan, Mingzhou Song, Joshua Stuart, Paul Spellman, Heinz Koeppl, Gustavo Stolovitzky, Julio Saez-Rodriguez, Sach Mukherjee .  2016.   Inferring causal molecular networks: empirical assessment through a community-based effort.. Nat Methods. 13 (4) :310-8 ▶ Go to Pubmed
Clémentine Le Magnen, Aditya Dutta, Cory Abate-Shen .  2016.   Optimizing mouse models for precision cancer prevention.. Nat Rev Cancer. ▶ Go to Pubmed
Urmila Santanam, Whitney Banach-Petrosky, Cory Abate-Shen, Michael Shen, Eileen White, Robert DiPaola .  2016.   Atg7 cooperates with Pten loss to drive prostate cancer tumor growth.. Genes Dev. 30 (4) :399-407 ▶ Go to Pubmed
Monica Messina, Sabina Chiaretti, Jiguang Wang, Anna Fedullo, Nadia Peragine, Valentina Gianfelici, Alfonso Piciocchi, Fulvia Brugnoletti, Filomena Di Giacomo, Simona Pauselli, Antony Holmes, Maria Puzzolo, Giulia Ceglie, Valerio Apicella, Marco Mancini, Geertruy Kronnie, Anna Testi, Antonella Vitale, Marco Vignetti, Anna Guarini, Raul Rabadan, Robin Foá .  2016.   Prognostic and therapeutic role of targetable lesions in B-lineage acute lymphoblastic leukemia without recurrent fusion genes.. Oncotarget. ▶ Go to Pubmed
HaYeun Ji, Leigh Atchison, Zaozao Chen, Syandan Chakraborty, Youngmee Jung, George Truskey, Nicolas Christoforou, Kam Leong .  2016.   Transdifferentiation of human endothelial progenitors into smooth muscle cells.. Biomaterials. 85 :180-94 ▶ Go to Pubmed
Tal Lorberbaum, Kevin Sampson, Raymond Woosley, Robert Kass, Nicholas Tatonetti .  2016.   An Integrative Data Science Pipeline to Identify Novel Drug Interactions that Prolong the QT Interval.. Drug Saf. ▶ Go to Pubmed
Kenichi Shimada, Miki Hayano, Nen Pagano, Brent Stockwell .  2016.   Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity.. Cell Chem Biol. ▶ Go to Pubmed
Michele Ceccarelli, Floris Barthel, Tathiane Malta, Thais Sabedot, Sofie Salama, Bradley Murray, Olena Morozova, Yulia Newton, Amie Radenbaugh, Stefano Pagnotta, Samreen Anjum, Jiguang Wang, Ganiraju Manyam, Pietro Zoppoli, Shiyun Ling, Arjun Rao, Mia Grifford, Andrew Cherniack, Hailei Zhang, Laila Poisson, Carlos Carlotti, Daniela Tirapelli, Arvind Rao, Tom Mikkelsen, Ching Lau, W Yung, Raul Rabadan, Jason Huse, Daniel Brat, Norman Lehman, Jill Barnholtz-Sloan, Siyuan Zheng, Kenneth Hess, Ganesh Rao, Matthew Meyerson, Rameen Beroukhim, Lee Cooper, Rehan Akbani, Margaret Wrensch, David Haussler, Kenneth Aldape, Peter Laird, David Gutmann, TCGA Network, Houtan Noushmehr, Antonio Iavarone, Roel Verhaak .  2016.   Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.. Cell. 164 (3) :550-63 ▶ Go to Pubmed
Richard Mann, Clare Howard .  2016.   The Importance of Timing.. Cell. 164 (3) :347-8 ▶ Go to Pubmed
Silvia Rasi, Hossein Khiabanian, Carmela Ciardullo, Lodovico Terzi-di-Bergamo, Sara Monti, Valeria Spina, Alessio Bruscaggin, Michaela Cerri, Clara Deambrogi, Lavinia Martuscelli, Alessandra Biasi, Elisa Spaccarotella, Lorenzo De Paoli, Valter Gattei, Robin Foa', Raul Rabadan, Gianluca Gaidano, Davide Rossi .  2016.   Clinical impact of small subclasses harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia.. Haematologica. ▶ Go to Pubmed
Guy Amster, Guy Sella .  2016.   Life history effects on the molecular clock of autosomes and sex chromosomes.. Proc Natl Acad Sci U S A. 113 (6) :1588-93 ▶ Go to Pubmed
Kelly Howell, Oliver Hobert .  2016.   Small Immunoglobulin Domain Proteins at Synapses and the Maintenance of Neuronal Features.. Neuron. 89 (2) :239-41 ▶ Go to Pubmed
Antoni Ribas, Daniel Shin, Jesse Zaretsky, Juliet Frederiksen, Andrew Cornish, Earl Avramis, Elizabeth Seja, Christine Kivork, Janet Siebert, Paula Kaplan-Lefko, Xiaoyan Wang, Bartosz Chmielowski, John Glaspy, Paul Tumeh, Thinle Chodon, Dana Pe'er, Begoña Comin-Anduix .  2016.   PD-1 blockade expands intratumoral T memory cells.. Cancer Immunol Res. ▶ Go to Pubmed
Arjun Manrai, Chirag Patel, Nils Gehlenborg, Nicholas Tatonetti, John Ioannidis, Isaac Kohane .  2016.   Methods to enhance the reproducibility of precision medicine. Pac Symp Biocomput. 21 :180-2 ▶ Go to Pubmed
Marcus Conrad, José Angeli, Peter Vandenabeele, Brent Stockwell .  2016.   Regulated necrosis: disease relevance and therapeutic opportunities.. Nat Rev Drug Discov. ▶ Go to Pubmed
Richard Marcotte, Azin Sayad, Kevin Brown, Felix Sanchez-Garcia, Jüri Reimand, Maliha Haider, Carl Virtanen, James Bradner, Gary Bader, Gordon Mills, Dana Pe'er, Jason Moffat, Benjamin Neel .  2016.   Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance.. Cell. 164 (1-2) :293-309 ▶ Go to Pubmed
Jorge Sepulveda, Jorge Gutierrez-Pajares, Aesis Luna, Yuan Yao, John Tobias, Steven Thomas, Yanghee Woo, Federico Giorgi, Elena Komissarova V, Andrea Califano, Timothy Wang, Antonia Sepulveda .  2016.   High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing.. Mod Pathol. ▶ Go to Pubmed
Ziyue Gao, Minyoung Wyman, Guy Sella, Molly Przeworski .  2016.   Interpreting the Dependence of Mutation Rates on Age and Time.. PLoS Biol. 14 (1) :e1002355 ▶ Go to Pubmed
Susan DeWolf, Yufeng Shen, Megan Sykes .  2016.   A New Window into the Human Alloresponse.. Transplantation. ▶ Go to Pubmed
Sang Lee, Veronique Frattini, Mukesh Bansal, Angelica Castano, Dan Sherman, Keino Hutchinson, Jeffrey Bruce, Andrea Califano, Guangchao Liu, Timothy Cardozo, Antonio Iavarone, Anna Lasorella .  2016.   An ID2-dependent mechanism for VHL inactivation in cancer.. Nature. 529 (7585) :172-7 ▶ Go to Pubmed
Chiara Ardiccioni, Oliver Clarke, David Tomasek, Habon Issa, Desiree von Alpen, Heather Pond, Surajit Banerjee, Kanagalaghatta Rajashankar, Qun Liu, Ziqiang Guan, Chijun Li, Brian Kloss, Renato Bruni, Edda Kloppmann, Burkhard Rost, Chiara Manzini, Lawrence Shapiro, Filippo Mancia .  2016.   Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.. Nat Commun. 7 :10175 ▶ Go to Pubmed
Teresa Amato, Francesco Abate, Pierpaolo Piccaluga, Michele Iacono, Chiara Fallerini, Alessandra Renieri, Giulia De Falco, Maria Ambrosio, Vaselious Mourmouras, Martin Ogwang, Valeria Calbi, Roul Rabadan, Michael Hummel, Stefano Pileri, Lorenzo Leoncini, Cristiana Bellan .  2016.   Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma.. Am J Clin Pathol. 145 (1) :116-27 ▶ Go to Pubmed
Elizabeth Lorden, Kyle Miller, Mohamed Ibrahim, Latif Bashirov, Ellen Hammett, Syandan Chakraborty, Carlos Quiles-Torres, Angelica Selim, Kam Leong, Howard Levinson .  2016.   Biostable electrospun microfibrous scaffolds mitigate hypertrophic scar contraction in an immune-competent murine model.. Acta Biomater. 32 :100-9 ▶ Go to Pubmed
Jason Gorman, Cinque Soto, Max Yang, Thaddeus Davenport, Miklos Guttman, Robert Bailer, Michael Chambers, Gwo-Yu Chuang, Brandon DeKosky, Nicole Doria-Rose, Aliaksandr Druz, Michael Ernandes, Ivelin Georgiev, Marissa Jarosinski, Gordon Joyce, Thomas Lemmin, Sherman Leung, Mark Louder, Jonathan McDaniel, Sandeep Narpala, Marie Pancera, Jonathan Stuckey, Xueling Wu, Yongping Yang, Baoshan Zhang, Tongqing Zhou, Nisc Program, James Mullikin, Ulrich Baxa, George Georgiou, Adrian McDermott, Mattia Bonsignori, Barton Haynes, Penny Moore, Lynn Morris, Kelly Lee, Lawrence Shapiro, John Mascola, Peter Kwong .  2016.   Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.. Nat Struct Mol Biol. 23 (1) :81-90 ▶ Go to Pubmed