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2016

2016 Publications

Kai Wang, Kam Leong, Yong Yang .  2016.   Expanding Nanopatterned Substrates Using Stitch Technique for Nanotopographical Modulation of Cell Behavior.. J Vis Exp. (118) ▶ Go to Pubmed
Jaewoo Lee, Jennifer Jackman, Jean Kwun, Miriam Manook, Angelo Moreno, Eric Elster, Allan Kirk, Kam Leong, Bruce Sullenger .  2016.   Nucleic acid scavenging microfiber mesh inhibits trauma-induced inflammation and thrombosis.. Biomaterials. 120 :94-102 ▶ Go to Pubmed
Katherine Xu, Paul Rosenstiel, Neal Paragas, Christian Hinze, Xiaobo Gao, Tian Shen, Max Werth, Catherine Forster, Rong Deng, Efrat Bruck, Roger Boles, Alexandra Tornato, Tejashree Gopal, Madison Jones, Justin Konig, Jacob Stauber, Vivette D'Agati, Hediye Erdjument-Bromage, Subodh Saggi, Gebhard Wagener, Kai Schmidt-Ott, Nicholas Tatonetti, Paul Tempst, Juan Oliver, Paolo Guarnieri, Jonathan Barasch .  2016.   Unique Transcriptional Programs Identify Subtypes of AKI.. J Am Soc Nephrol. ▶ Go to Pubmed
Joris van Arensbergen, Vincent FitzPatrick, Marcel de Haas, Ludo Pagie, Jasper Sluimer, Harmen Bussemaker, Bas van Steensel .  2016.   Genome-wide mapping of autonomous promoter activity in human cells.. Nat Biotechnol. ▶ Go to Pubmed
Eric Kelsic, Hattie Chung, Niv Cohen, Jimin Park, Harris Wang, Roy Kishony .  2016.   RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq.. Cell Syst. 3 (6) :563-571.e6 ▶ 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 :180-182 ▶ Go to Pubmed
Zeynep Koşaloğlu, Inka Zörnig, Niels Halama, Iris Kaiser, Ivo Buchhalter, Niels Grabe, Roland Eils, Matthias Schlesner, Andrea Califano, Dirk Jäger .  2016.   Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases.. Oncoimmunology. 5 (11) :e1213931 ▶ Go to Pubmed
Abdulkadir Elmas, Tai-Hsien Yang, Xiaodong Wang, Dimitris Anastassiou .  2016.   Discovering Genome-Wide Tag SNPs Based on the Mutual Information of the Variants.. PLoS One. 11 (12) :e0167994 ▶ Go to Pubmed
Andrea Califano, Mariano Alvarez .  2016.   The recurrent architecture of tumour initiation, progression and drug sensitivity.. Nat Rev Cancer. ▶ Go to Pubmed
Victoria Stockman, Lila Ghamsari, Gorka Lasso, Barry Honig, Sagi Shapira, Harris Wang .  2016.   A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions.. PLoS One. 11 (12) :e0167617 ▶ Go to Pubmed
Akshata Udyavar, David Wooten, Megan Hoeksema, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Santiago Schnell, Jonathan Irish, Pierre Massion, Vito Quaranta .  2016.   Novel hybrid phenotype revealed in Small Cell Lung Cancer by a transcription factor network model that can explain tumor heterogeneity.. Cancer Res. ▶ Go to Pubmed
Akshata Udyavar, David Wooten, Megan Hoeksema, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Santiago Schnell, Jonathan Irish, Pierre Massion, Vito Quaranta .  2016.   Novel hybrid phenotype revealed in Small Cell Lung Cancer by a transcription factor network model that can explain tumor heterogeneity.. Cancer Res. ▶ Go to Pubmed
Daniel Rosenbloom, Pablo Camara, Tim Chu, Raul Rabadan .  2016.   Evolutionary scalpels for dissecting tumor ecosystems.. Biochim Biophys Acta. ▶ Go to Pubmed
Anthony Clark, Tatyana Gindin, Baoshan Zhang, Lingle Wang, Robert Abel, Colleen Murret, Fang Xu, Amy Bao, Nina Lu, Tongqing Zhou, Peter Kwong, Lawrence Shapiro, Barry Honig, Richard Friesner .  2016.   Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1.. J Mol Biol. ▶ Go to Pubmed
Khader Shameer, Kipp Johnson, Alexandre Yahi, Riccardo Miotto, L Li, Doran Ricks, Jebakumar Jebakaran, Patricia Kovatch, Partho Sengupta, Sengupta Gelijns, Alan Moskovitz, Bruce Darrow, David David, Andrew Kasarskis, Nicholas Tatonetti, Sean Pinney, Joel Dudley .  2016.   Predictive modelling of hospital readmission rates using electronic medical record-wide machine learning: a case-study using Mount Sinai heart failure cohort. Pac Symp Biocomput. 22 :276-287 ▶ Go to Pubmed
Konrad Karczewski, Nicholas Tatonetti, Arjun Manrai, Chirag Patel, Titus Brown, John Ioannidis .  2016.   Methods to ensure the reproducibility of biomedical research. Pac Symp Biocomput. 22 :117-119 ▶ Go to Pubmed
Rachel Melamed, Iraz Aydin, Geena Rajan, Robert Phelps, David Silvers, Kevin Emmett, Georg Brunner, Raul Rabadan, Julide Celebi .  2016.   Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma.. J Invest Dermatol. ▶ Go to Pubmed
Oliver Hobert, Lori Glenwinkel, John White .  2016.   Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans.. Curr Biol. 26 (22) :R1197-R1203 ▶ Go to Pubmed
Sarah Kim-Hellmuth, Tuuli Lappalainen .  2016.   Concerted Genetic Function in Blood Traits.. Cell. 167 (5) :1167-1169 ▶ Go to Pubmed
Chaolin Zhang, Yufeng Shen .  2016.   A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes.. Hum Mutat. ▶ Go to Pubmed
Jinghe Huang, Byong Kang, Elise Ishida, Tongqing Zhou, Trevor Griesman, Zizhang Sheng, Fan Wu, Nicole Doria-Rose, Baoshan Zhang, Krisha McKee, Sijy O'Dell, Gwo-Yu Chuang, Aliaksandr Druz, Ivelin Georgiev, Chaim Schramm, Anqi Zheng, Gordon Joyce, Mangaiarkarasi Asokan, Amy Ransier, Sam Darko, Stephen Migueles, Robert Bailer, Mark Louder, Munir Alam, Robert Parks, Garnett Kelsoe, Tarra Von Holle, Barton Haynes, Daniel Douek, Vanessa Hirsch, Michael Seaman, Lawrence Shapiro, John Mascola, Peter Kwong, Mark Connors .  2016.   Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.. Immunity. 45 (5) :1108-1121 ▶ Go to Pubmed
Filemon Cruz, Daniel Diolaiti, Andrew Turk, Allison Rainey, Alberto Ambesi-Impiombato, Stuart Andrews, Mahesh Mansukhani, Peter Nagy, Mariano Alvarez, Andrea Califano, Farhad Forouhar, Beata Modzelewski, Chelsey Mitchell, Darrell Yamashiro, Lianna Marks, Julia Bender, Andrew Kung .  2016.   A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma.. Genome Med. 8 (1) :116 ▶ Go to Pubmed
Ankeeta Shah, Yingzhi Qian, Sebastien Weyn-Vanhentenryck, Chaolin Zhang .  2016.   CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.. Bioinformatics. ▶ Go to Pubmed
Weiqian Jiang, Mingqiang Li, Zaozao Chen, Kam Leong .  2016.   Cell-laden microfluidic microgels for tissue regeneration.. Lab Chip. 16 (23) :4482-4506 ▶ Go to Pubmed
Changchun Deng, Mark Lipstein, Luigi Scotto, Xavier Serrano, Michael Mangone, Shirong Li, Jeremie Vendome, Yun Hao, Xiaoming Xu, Shi-Xian Deng, Ronald Realubit, Nicholas Tatonetti, Charles Karan, Suzanne Lentzsch, David Fruman, Barry Honig, Donald Landry, Owen O'Connor .  2016.   Silencing c-Myc translation as a therapeutic strategy through targeting PI3K delta and CK1 epsilon in hematological malignancies.. Blood. ▶ Go to Pubmed
Kerry Goodman, Rotem Rubinstein, Chan Thu, Seetha Mannepalli, Fabiana Bahna, Goran Ahlsen, Chelsea Rittenhouse, Tom Maniatis, Barry Honig, Lawrence Shapiro .  2016.   γ-Protocadherin structural diversity and functional implications.. Elife. 5 ▶ Go to Pubmed
José Garzón, Lei Deng, Diana Murray, Sagi Shapira, Donald Petrey, Barry Honig .  2016.   A computational interactome and functional annotation for the human proteome.. Elife. 5 ▶ Go to Pubmed
Priya Moorjani, Ziyue Gao, Molly Przeworski .  2016.   Human Germline Mutation and the Erratic Evolutionary Clock.. PLoS Biol. 14 (10) :e2000744 ▶ Go to Pubmed
Yuval Simons, Guy Sella .  2016.   The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.. Curr Opin Genet Dev. 41 :150-158 ▶ Go to Pubmed
Jennifer Jackman, Hemraj Juwarker, Luke Poveromo, Howard Levinson, Kam Leong, Bruce Sullenger .  2016.   Polycationic Nanofibers for Nucleic Acid Scavenging.. Biomacromolecules. ▶ Go to Pubmed
Marie Gendrel, Emily Atlas, Oliver Hobert .  2016.   A cellular and regulatory map of the GABAergic nervous system of C. elegans.. Elife. 5 ▶ Go to Pubmed
Sheng-Han Kuo, Chi-Ying Lin, Jie Wang, Peter Sims, Ming-Kai Pan, Jyun-You Liou, Danielle Lee, William Tate, Geoffrey Kelly, Elan Louis, Phyllis Faust .  2016.   Climbing fiber-Purkinje cell synaptic pathology in tremor and cerebellar degenerative diseases.. Acta Neuropathol. ▶ Go to Pubmed
Jinzhou Yuan, Peter Sims .  2016.   An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq.. Sci Rep. 6 :33883 ▶ Go to Pubmed
David McKean, Jason Homsy, Hiroko Wakimoto, Neil Patel, Joshua Gorham, Steven DePalma, James Ware, Samir Zaidi, Wenji Ma, Nihir Patel, Richard Lifton, Wendy Chung, Richard Kim, Yufeng Shen, Martina Brueckner, Elizabeth Goldmuntz, Andrew Sharp, Christine Seidman, Bruce Gelb, J Seidman .  2016.   Loss of RNA expression and allele-specific expression associated with congenital heart disease.. Nat Commun. 7 :12824 ▶ Go to Pubmed
Koichi Oshima, Hossein Khiabanian, Ana da Silva-Almeida, Gannie Tzoneva, Francesco Abate, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Zachary Carpenter, Alex Penson, Arianne Perez-Garcia, Cornelia Eckert, Concepción Nicolas, Milagros Balbin, Maria Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie Gastier-Foster, Meenakshi Devidas, Mignon Loh, Renate Kirschner-Schwabe, Teresa Palomero, Raul Rabadan, Adolfo Ferrando .  2016.   Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Kerry Goodman, Masahito Yamagata, Xiangshu Jin, Seetha Mannepalli, Phinikoula Katsamba, Goran Ahlsen, Alina Sergeeva, Barry Honig, Joshua Sanes, Lawrence Shapiro .  2016.   Molecular basis of sidekick-mediated cell-cell adhesion and specificity.. Elife. 5 ▶ Go to Pubmed
Donglai Wang, Ning Kon, Gorka Lasso, Le Jiang, Wenchuan Leng, Wei-Guo Zhu, Jun Qin, Barry Honig, Wei Gu .  2016.   Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode.. Nature. ▶ Go to Pubmed
Li Li, Mary Boland, Riccardo Miotto, Nicholas Tatonetti, Joel Dudley .  2016.   Replicating Cardiovascular Condition-Birth Month Associations.. Sci Rep. 6 :33166 ▶ Go to Pubmed
Omid Tavana, Dawei Li, Chao Dai, Gonzalo Lopez, Debarshi Banerjee, Ning Kon, Chao Chen, Andrea Califano, Darrell Yamashiro, Hongbin Sun, Wei Gu .  2016.   HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma.. Nat Med. ▶ Go to Pubmed
Pedro Ferreira, Martin Oti, Matthias Barann, Thomas Wieland, Suzana Ezquina, Marc Friedländer, Manuel Rivas, Anna Esteve-Codina, Geuvadis consortium, Philip Rosenstiel, Tim Strom, Tuuli Lappalainen, Roderic Guigo, Michael Sammeth .  2016.   Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.. Sci Rep. 6 :32406 ▶ Go to Pubmed
Ming Tian, Cheng Cheng, Xuejun Chen, Hongying Duan, Hwei-Ling Cheng, Mai Dao, Zizhang Sheng, Michael Kimble, Lingshu Wang, Sherry Lin, Stephen Schmidt, Zhou Du, Gordon Joyce, Yiwei Chen, Brandon DeKosky, Yimin Chen, Erica Normandin, Elizabeth Cantor, Rita Chen, Nicole Doria-Rose, Yi Zhang, Wei Shi, Wing-Pui Kong, Misook Choe, Amy Henry, Farida Laboune, Ivelin Georgiev, Pei-Yi Huang, Suvi Jain, Andrew McGuire, Eric Georgeson, Sergey Menis, Daniel Douek, William Schief, Leonidas Stamatatos, Peter Kwong, Lawrence Shapiro, Barton Haynes, John Mascola, Frederick Alt .  2016.   Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires.. Cell. 166 (6) :1471-1484.e18 ▶ Go to Pubmed
Jared Mayers, Margaret Torrence, Laura Danai V, Thales Papagiannakopoulos, Shawn Davidson, Matthew Bauer, Allison Lau, Brian Ji, Purushottam Dixit, Aaron Hosios, Alexander Muir, Christopher Chin, Elizaveta Freinkman, Tyler Jacks, Brian Wolpin, Dennis Vitkup, Matthew Heiden .  2016.   Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers.. Science. 353 (6304) :1161-5 ▶ Go to Pubmed
Stephane Castel, Pejman Mohammadi, Wendy Chung, Yufeng Shen, Tuuli Lappalainen .  2016.   Rare variant phasing and haplotypic expression from RNA sequencing with phASER.. Nat Commun. 7 :12817 ▶ Go to Pubmed
Priya Moorjani, Carlos Amorim, Peter Arndt, Molly Przeworski .  2016.   Variation in the molecular clock of primates.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Ricky Joshi, Paras Garg, Noah Zaitlen, Tuuli Lappalainen, Corey Watson, Nidha Azam, Daniel Ho, Xin Li, Stylianos Antonarakis, Han Brunner, Karin Buiting, Sau Cheung, Bradford Coffee, Thomas Eggermann, David Francis, Joep Geraedts, Giorgio Gimelli, Samuel Jacobson, Cedric Le Caignec, Nicole de Leeuw, Thomas Liehr, Deborah Mackay, Stephen Montgomery, Alistair Pagnamenta, Peter Papenhausen, David Robinson, Claudia Ruivenkamp, Charles Schwartz, Bernhard Steiner, David Stevenson, Urvashi Surti, Thomas Wassink, Andrew Sharp .  2016.   DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome.. Am J Hum Genet. 99 (3) :555-66 ▶ Go to Pubmed
Yunting Chen, Oliver Clarke, Jonathan Kim, Sean Stowe, Youn-Kyung Kim, Zahra Assur, Michael Cavalier, Raquel Godoy-Ruiz, Desiree von Alpen, Chiara Manzini, William Blaner, Joachim Frank, Loredana Quadro, David Weber, Lawrence Shapiro, Wayne Hendrickson, Filippo Mancia .  2016.   Structure of the STRA6 receptor for retinol uptake.. Science. 353 (6302) ▶ Go to Pubmed
Robert Reid, Xing Du, Ivana Sunjevaric, Vinayak Rayannavar, John Dittmar, Eric Bryant, Matthew Maurer, Rodney Rothstein .  2016.   A Yeast Synthetic Dosage Lethal Screen Identifies a Conserved Interaction between PLK1 and CKS1B Affecting Cancer Cell Viability.. Genetics. ▶ Go to Pubmed
Jennifer Bain, Megan Cho, Aida Telegrafi, Ashley Wilson, Susan Brooks, Christina Botti, Gordon Gowans, Leigh Autullo, Vidya Krishnamurthy, Marcia Willing, Tomi Toler, Bruria Ben-Zev, Orly Elpeleg, Yufeng Shen, Kyle Retterer, Kristin Monaghan, Wendy Chung .  2016.   Variants in HNRNPH2 on the X Chromosome Are Associated with a Neurodevelopmental Disorder in Females.. Am J Hum Genet. ▶ Go to Pubmed
Eyal Elyashiv, Shmuel Sattath, Tina Hu, Alon Strutsovsky, Graham McVicker, Peter Andolfatto, Graham Coop, Guy Sella .  2016.   A Genomic Map of the Effects of Linked Selection in Drosophila.. PLoS Genet. 12 (8) :e1006130 ▶ Go to Pubmed
Pablo Camara, Arnold Levine, Raul Rabadan .  2016.   Inference of Ancestral Recombination Graphs through Topological Data Analysis.. PLoS Comput Biol. 12 (8) :e1005071 ▶ Go to Pubmed
Joshua Black, Andrew Adler, Hong-Gang Wang, Anthony D'Ippolito, Hunter Hutchinson, Timothy Reddy, Geoffrey Pitt, Kam Leong, Charles Gersbach .  2016.   Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.. Cell Stem Cell. ▶ Go to Pubmed
Yun Hao, Nicholas Tatonetti .  2016.   Predicting G Protein-Coupled Receptor Downstream Signaling by Tissue Expression.. Bioinformatics. ▶ Go to Pubmed
Gordon Joyce, Adam Wheatley, Paul Thomas V, Gwo-Yu Chuang, Cinque Soto, Robert Bailer, Aliaksandr Druz, Ivelin Georgiev, Rebecca Gillespie, Masaru Kanekiyo, Wing-Pui Kong, Kwanyee Leung, Sandeep Narpala, Madhu Prabhakaran, Eun Yang, Baoshan Zhang, Yi Zhang, Mangaiarkarasi Asokan, Jeffrey Boyington, Tatsiana Bylund, Sam Darko, Christopher Lees, Amy Ransier, Chen-Hsiang Shen, Lingshu Wang, James Whittle, Xueling Wu, Hadi Yassine, Celia Santos, Yumiko Matsuoka, Yaroslav Tsybovsky, Ulrich Baxa, NISC Program, James Mullikin, Kanta Subbarao, Daniel Douek, Barney Graham, Richard Koup, Julie Ledgerwood, Mario Roederer, Lawrence Shapiro, Peter Kwong, John Mascola, Adrian McDermott .  2016.   Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.. Cell. 166 (3) :609-23 ▶ Go to Pubmed
Laura Belver, Adolfo Ferrando .  2016.   The genetics and mechanisms of T cell acute lymphoblastic leukaemia.. Nat Rev Cancer. 16 (8) :494-507 ▶ Go to Pubmed
Jeremy Chang, Kayla Quinnies, Ronald Realubit, Charles Karan, Jacob Rand, Nicholas Tatonetti .  2016.   A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient.. Sci Rep. 6 :29387 ▶ Go to Pubmed
Robert Moskovitch, Hyunmi Choi, George Hripcsak, Nicholas Tatonetti .  2016.   Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection.. IEEE/ACM Trans Comput Biol Bioinform. ▶ Go to Pubmed
Timothy Olsen, Jing Zhu, Jinho Kim, Renjun Pei, Milan Stojanovic, Qiao Lin .  2016.   An Integrated Microfluidic SELEX Approach Using Combined Electrokinetic and Hydrodynamic Manipulation.. J Lab Autom. ▶ Go to Pubmed
Julio Saez-Rodriguez, James Costello, Stephen Friend, Michael Kellen, Lara Mangravite, Pablo Meyer, Thea Norman, Gustavo Stolovitzky .  2016.   Crowdsourcing biomedical research: leveraging communities as innovation engines.. Nat Rev Genet. 17 (8) :470-86 ▶ Go to Pubmed
Daniela Gerhard, Paul Clemons, Alykhan Shamji, Cindy Hon, Bridget Wagner, Stuart Schreiber, Alex Krasnitz, Raffaella Sordella, Chris Sander, Scott Lowe, Scott Powers, Kenneth Smith, Mahalaxmi Aburi, Antonio Iavarone, Anna Lasorella, Jose Silva, Brent Stockwell, Andrea Califano, Jesse Boehm, Francisca Vazquez, Barbara Weir, William Hahn, Fadlo Khuri, Carlos Moreno, Margaret Johns, Haian Fu, Olga Nikolova, Eduardo Mendez, Vijayakrishna Gadi, Adam Margolin, Carla Grandori, Christopher Kemp, Edus Warren, Stanley Riddell, Martin McIntosh, Olivier Gevaert, Calvin Kuo, Hanlee Ji, Harshil Dhruv, Darren Finlay, Jeffrey Kiefer, Seungchan Kim, Kristiina Vuori, Michael Berens, Matthew Hangauer, Michael Boettcher, Jonathan Weissman, Trever Bivona, Sourav Bandyopadhyay, Michael McManus, Frank McCormick, Ozlem Aksoy, Erin Simonds, Tina Zheng, Justin Chen, Zhenyi An, Allan Balmain, William Weiss, Ken Chen, Han Liang, Kenneth Scott, Gordon Mills, Bruce Posner, John MacMillan, John Minna, Michael White, Michael Roth, Subhashini Jagu, Jessica Mazerik .  2016.   Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance.. Mol Cancer Res. ▶ Go to Pubmed
M Boland, N Tatonetti .  2016.   Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review.. Pharmacogenomics J. ▶ Go to Pubmed
Esther Berko, Megan Cho, Christine Eng, Yunru Shao, David Sweetser, Jessica Waxler, Nathaniel Robin, Fallon Brewer, Sandra Donkervoort, Payam Mohassel, Carsten Bönnemann, Martin Bialer, Christine Moore, Lynne Wolfe, Cynthia Tifft, Yufeng Shen, Kyle Retterer, Francisca Millan, Wendy Chung .  2016.   De novo missense variants in HECW2 are associated with neurodevelopmental delay and hypotonia.. J Med Genet. ▶ Go to Pubmed
Nicholas Hornstein, Daniela Torres, Sohani Sharma, Guomei Tang, Peter Canoll, Peter Sims .  2016.   Ligation-free ribosome profiling of cell type-specific translation in the brain.. Genome Biol. 17 (1) :149 ▶ Go to Pubmed
Ling-Shiang Chuang, Nicole Villaverde, Ken Hui, Arthur Mortha, Adeeb Rahman, Adam Levine, Talin Haritunians, Sok Ng, Wei Zhang, Nai-Yun Hsu, Jody-Ann Facey, Tramy Luong, Heriberto Fernandez-Hernandez, Dalin Li, Manuel Rivas, Elena Schiff, Alexander Gusev, Phillip Schumm, Beatrice Bowen, Yashoda Sharma, Kaida Ning, Romain Remark, Sacha Gnjatic, Peter Legnani, James George, Bruce Sands, Joanne Stempak, Lisa Datta, Seth Lipka, Seymour Katz, Adam Cheifetz, Nir Barzilai, Nikolas Pontikos, Clara Abraham, Marla Dubinsky, Stephan Targan, Kent Taylor, Jerome Rotter, Ellen Scherl, Robert Desnick, Maria Abreu, Hongyu Zhao, Gil Atzmon, Itsik Pe'er, Subra Kugathasan, Hakon Hakonarson, Jacob McCauley, Todd Lencz, Ariel Darvasi, Vincent Plagnol, Mark Silverberg, Aleixo Muise, Steven Brant, Mark Daly, Anthony Segal, Richard Duerr, Miriam Merad, Dermot McGovern, Inga Peter, Judy Cho .  2016.   A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF.. Gastroenterology. 151 (4) :710-723.e2 ▶ Go to Pubmed
Andrew Anzalone V, Zhixing Chen, Virginia Cornish .  2016.   Synthesis of photoactivatable azido-acyl caged oxazine fluorophores for live-cell imaging.. Chem Commun (Camb). ▶ Go to Pubmed
Hai Li, Takaaki Kuwajima, Derek Oakley, Elena Nikulina, Jianwei Hou, Wan Yang, Emily Lowry, Nuno Lamas, Mackenzie Amoroso, Gist Croft, Raghavendra Hosur, Hynek Wichterle, Said Sebti, Marie Filbin, Brent Stockwell, Christopher Henderson .  2016.   Protein Prenylation Constitutes an Endogenous Brake on Axonal Growth.. Cell Rep. ▶ Go to Pubmed
Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong, Katherine Lintner, Qiong Ding, Zou Wang, Jiang Hu, Depeng Wang, Feng Wang, Lin Wang, Gholson Lyon, Yongtao Guan, Yufeng Shen, Oleg Evgrafov V, James Knowles, Francoise Thibaud-Nissen, Valerie Schneider, Chack-Yung Yu, Libing Zhou, Evan Eichler, Kwok-Fai So, Kai Wang .  2016.   Long-read sequencing and de novo assembly of a Chinese genome.. Nat Commun. 7 :12065 ▶ Go to Pubmed
Pablo Camara, Daniel Rosenbloom, Kevin Emmett, Arnold Levine, Raul Rabadan .  2016.   Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination.. Cell Syst. 3 (1) :83-94 ▶ Go to Pubmed
Xiao Zhao, Keni Yang, Ruifang Zhao, Tianjiao Ji, Xiuchao Wang, Xiao Yang, Yinlong Zhang, Keman Cheng, Shaoli Liu, Jihui Hao, He Ren, Kam Leong, Guangjun Nie .  2016.   Inducing enhanced immunogenic cell death with nanocarrier-based drug delivery systems for pancreatic cancer therapy.. Biomaterials. 102 :187-197 ▶ Go to Pubmed
Aditya Dutta, Clémentine Le Magnen, Antonina Mitrofanova, Xuesong Ouyang, Andrea Califano, Cory Abate-Shen .  2016.   Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.. Science. 352 (6293) :1576-80 ▶ Go to Pubmed
Valeria Spina, Hossein Khiabanian, Monica Messina, Sara Monti, Luciano Cascione, Alessio Bruscaggin, Elisa Spaccarotella, Antony Holmes, Luca Arcaini, Marco Lucioni, Fabrizio Tabbò, Sakellarios Zairis, Fary Diop, Michaela Cerri, Sabina Chiaretti, Roberto Marasca, Maurilio Ponzoni, Silvia Deaglio, Antonio Ramponi, Enrico Tiacci, Laura Pasqualucci, Marco Paulli, Brunangelo Falini, Giorgio Inghirami, Francesco Bertoni, Robin Foá, Raul Rabadan, Gianluca Gaidano, Davide Rossi .  2016.   The genetics of nodal marginal zone lymphoma.. Blood. ▶ Go to Pubmed
Ren Sheng, Da-Jung Jung, Antonina Silkov, Hyunjin Kim, Indira Singaram, Zhi-Gang Wang, Yao Xin, Eui Kim, Mi-Jeong Park, Pallavi Thiagarajan-Rosenkranz, Sean Smrt, Barry Honig, Kwanghee Baek, Sungho Ryu, Justin Lorieau, You-Me Kim, Wonhwa Cho .  2016.   Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain.. J Biol Chem. 291 (34) :17639-50 ▶ Go to Pubmed
Mariano Alvarez, Yao Shen, Federico Giorgi, Alexander Lachmann, Belinda Ding, Hilda Ye, Andrea Califano .  2016.   Functional characterization of somatic mutations in cancer using network-based inference of protein activity.. Nat Genet. ▶ Go to Pubmed
Cameron Palmer, Itsik Pe'er .  2016.   Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation.. PLoS Genet. 12 (6) :e1006091 ▶ Go to Pubmed
Kenta Yamamoto, Jiguang Wang, Lisa Sprinzen, Jun Xu, Christopher Haddock, Chen Li, Brian Lee, Denis Loredan, Wenxia Jiang, Alessandro Vindigni, Dong Wang, Raul Rabadan, Shan Zha .  2016.   Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors.. Elife. 5 ▶ Go to Pubmed
Oliver Harrison, Julia Brasch, Gorka Lasso, Phinikoula Katsamba, Goran Ahlsen, Barry Honig, Lawrence Shapiro .  2016.   Structural basis of adhesive binding by desmocollins and desmogleins.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Vesna Pulko, John Davies, Carmine Martinez, Marion Lanteri, Michael Busch, Michael Diamond, Kenneth Knox, Erin Bush, Peter Sims, Shripad Sinari, Dean Billheimer, Elias Haddad, Kristy Murray, Anne Wertheimer, Janko Nikolich-Žugich .  2016.   Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses.. Nat Immunol. ▶ Go to Pubmed
Jiguang Wang, Emanuela Cazzato, Erik Ladewig, Veronique Frattini, Daniel Rosenbloom, Sakellarios Zairis, Francesco Abate, Zhaoqi Liu, Oliver Elliott, Yong-Jae Shin, Jin-Ku Lee, In-Hee Lee, Woong-Yang Park, Marica Eoli, Andrew Blumberg, Anna Lasorella, Do-Hyun Nam, Gaetano Finocchiaro, Antonio Iavarone, Raul Rabadan .  2016.   Clonal evolution of glioblastoma under therapy.. Nat Genet. ▶ Go to Pubmed
Kaitlyn Gayvert, Etienne Dardenne, Cynthia Cheung, Mary Boland, Tal Lorberbaum, Jackline Wanjala, Yu Chen, Mark Rubin, Nicholas Tatonetti, David Rickman, Olivier Elemento .  2016.   A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors.. Cell Rep. 15 (11) :2348-56 ▶ Go to Pubmed
Jennifer Sims, Boris Grinshpun, Yaping Feng, Timothy Ung, Justin Neira, Jorge Samanamud, Peter Canoll, Yufeng Shen, Peter Sims, Jeffrey Bruce .  2016.   Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Clara Soria-Valles, Ana Gutiérrez-Fernández, Fernando Osorio, Dido Carrero, Adolfo Ferrando, Enrique Colado, Soledad Fernández-García, Elena Bonzon-Kulichenko, Jesús Vázquez, Antonio Fueyo, Carlos López-Otín .  2016.   MMP-25 Metalloprotease Regulates Innate Immune Response through NF-κB Signaling.. J Immunol. ▶ Go to Pubmed
Jef Boeke, George Church, Andrew Hessel, Nancy Kelley, Adam Arkin, Yizhi Cai, Rob Carlson, Aravinda Chakravarti, Virginia Cornish, Liam Holt, Farren Isaacs, Todd Kuiken, Marc Lajoie, Tracy Lessor, Jeantine Lunshof, Matthew Maurano, Leslie Mitchell, Jasper Rine, Susan Rosser, Neville Sanjana, Pamela Silver, David Valle, Harris Wang, Jeffrey Way, Luhan Yang .  2016.   The Genome Project-Write.. Science. ▶ Go to Pubmed
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Maddalena Paganin, Barbara Buldini, Giuseppe Germano, Elena Seganfreddo, Annamaria di Meglio, Elisa Magrin, Francesca Grillo, Martina Pigazzi, Carmelo Rizzari, Giovanni Cazzaniga, Hossein Khiabanian, Teresa Palomero, Raul Rabadan, Adolfo Ferrando, Giuseppe Basso .  2016.   A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia.. Pediatr Blood Cancer. ▶ Go to Pubmed
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Manu Setty, Michelle Tadmor, Shlomit Reich-Zeliger, Omer Angel, Tomer Salame, Pooja Kathail, Kristy Choi, Sean Bendall, Nir Friedman, Dana Pe'er .  2016.   Wishbone identifies bifurcating developmental trajectories from single-cell data.. Nat Biotechnol. ▶ Go to Pubmed
Jose Utrilla, Edward O'Brien, Ke Chen, Douglas McCloskey, Jacky Cheung, Harris Wang, Dagoberto Armenta-Medina, Adam Feist, Bernhard Palsson .  2016.   Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.. Cell Syst. 2 (4) :260-71 ▶ Go to Pubmed
Ritu Kushwaha, Nirmala Jagadish, Manjunath Kustagi, Geetu Mendiratta, Marco Seandel, Rekha Soni, James Korkola, Venkata Thodima, Andrea Califano, George Bosl, R Chaganti .  2016.   Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification.. Stem Cell Reports. ▶ Go to Pubmed
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Tea Kaartokallio, Inkeri Lokki, Hanna Peterson, Katja Kivinen, Leena Hiltunen, Elina Salmela, Tuuli Lappalainen, Paula Maanselkä, Sanna Heino, Sakari Knuutila, Ayat Sayed, Lucilla Poston, Shaun Brennecke, Matthew Johnson, Linda Morgan, Eric Moses, Juha Kere, Hannele Laivuori .  2016.   Preeclampsia does not share common risk alleles in 9p21 with coronary artery disease and type 2 diabetes.. Ann Med. :1-7 ▶ Go to Pubmed