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2015

2015 Publications

Fernanda Polubriaginof, Nicholas Tatonetti, David Vawdrey .  2015.   An Assessment of Family History Information Captured in an Electronic Health Record.. AMIA Annu Symp Proc. 2015 :2035-42 ▶ Go to Pubmed
Daniel Gallego-Perez, Jose Otero, Catherine Czeisler, Junyu Ma, Cristina Ortiz, Patrick Gygli, Fay Catacutan, Hamza Gokozan, Aaron Cowgill, Thomas Sherwood, Subhadip Ghatak, Veysi Malkoc, Xi Zhao, Wei-Ching Liao, Surya Gnyawali, Xinmei Wang, Andrew Adler, Kam Leong, Brian Wulff, Traci Wilgus, Candice Askwith, Savita Khanna, Cameron Rink, Chandan Sen, James Lee .  2015.   Deterministic transfection drives efficient nonviral reprogramming and uncovers reprogramming barriers.. Nanomedicine. ▶ Go to Pubmed
Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi Mayo, David Hall, John White, Brigitte LeBoeuf, Rene Garcia, Uri Alon, Oliver Hobert .  2015.   A cellular and regulatory map of the cholinergic nervous system of C.elegans.. Elife. 4 ▶ Go to Pubmed
Michael Hart, Oliver Hobert .  2015.   Sexual Dimorphism: Mystery Neurons Control Sex-Specific Behavioral Plasticity.. Curr Biol. 25 (24) :R1170-2 ▶ Go to Pubmed
Todd Riley, Allan Lazarovici, Richard Mann, Harmen Bussemaker .  2015.   Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.. Elife. 4 ▶ Go to Pubmed
Keith Hoffman, Mo Dimbil, Robert Kyle, Nicholas Tatonetti, Colin Erdman, Andrea Demakas, Dingguo Chen, Brian Overstreet .  2015.   A Drug Safety Rating System Based on Postmarketing Costs Associated with Adverse Events and Patient Outcomes.. J Manag Care Spec Pharm. 21 (12) :1134-43 ▶ Go to Pubmed
Hailan Zhang, Tian Zheng, Chee Chua, Michael Shen, Edward Gelmann .  2015.   Nkx3.1 controls the DNA repair response in the mouse prostate.. Prostate. ▶ Go to Pubmed
Wan Yang, Brent Stockwell .  2015.   Ferroptosis: Death by Lipid Peroxidation.. Trends Cell Biol. ▶ Go to Pubmed
Anupama Khare, Saeed Tavazoie .  2015.   Multifactorial Competition and Resistance in a Two-Species Bacterial System.. PLoS Genet. 11 (12) :e1005715 ▶ Go to Pubmed
Albert Lee, Kirsten Kulcsar, Oliver Elliott, Hossein Khiabanian, Elyse Nagle, Megan Jones, Brian Amman, Mariano Sanchez-Lockhart, Jonathan Towner, Gustavo Palacios, Raul Rabadan .  2015.   De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.. BMC Genomics. 16 :1033 ▶ Go to Pubmed
Preeti Putcha, Jiyang Yu, Ruth Rodriguez-Barrueco, Laura Saucedo-Cuevas, Patricia Villagrasa, Eva Murga-Penas, Steven Quayle, Min Yang, Verónica Castro, David Llobet-Navas, Daniel Birnbaum, Pascal Finetti, Wendy Woodward, François Bertucci, Mary Alpaugh, Andrea Califano, Jose Silva .  2015.   HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.. Breast Cancer Res. 17 (1) :149 ▶ Go to Pubmed
Melissa Gymrek, Thomas Willems, Audrey Guilmatre, Haoyang Zeng, Barak Markus, Stoyan Georgiev, Mark Daly, Alkes Price, Jonathan Pritchard, Andrew Sharp, Yaniv Erlich .  2015.   Abundant contribution of short tandem repeats to gene expression variation in humans.. Nat Genet. ▶ Go to Pubmed
Michael Shen .  2015.   Illuminating the Properties of Prostate Luminal Progenitors.. Cell Stem Cell. 17 (6) :644-6 ▶ Go to Pubmed
Elise Morton, Joshua Lynch, Alain Froment, Sophie Lafosse, Evelyne Heyer, Molly Przeworski, Ran Blekhman, Laure Segurel .  2015.   Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence.. PLoS Genet. 11 (11) :e1005658 ▶ Go to Pubmed
Brian Kidd, Aleksandra Wroblewska, Mary Boland, Judith Agudo, Miriam Merad, Nicholas Tatonetti, Brian Brown, Joel Dudley .  2015.   Mapping the effects of drugs on the immune system.. Nat Biotechnol. ▶ Go to Pubmed
Joseph Romano, Nicholas Tatonetti .  2015.   VenomKB, a new knowledge base for facilitating the validation of putative venom therapies.. Sci Data. 2 :150065 ▶ Go to Pubmed
Ilaria Del Giudice, Marilisa Marinelli, Jiguang Wang, Silvia Bonina, Monica Messina, Sabina Chiaretti, Caterina Ilari, Luciana Cafforio, Sara Raponi, Francesca Mauro, Valeria Di Maio, Maria De Propris, Mauro Nanni, Carmela Ciardullo, Davide Rossi, Gianluca Gaidano, Anna Guarini, Raul Rabadan, Robin Foá .  2015.   Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments.. Br J Haematol. ▶ Go to Pubmed
Paola Arlotta, Oliver Hobert .  2015.   Homeotic Transformations of Neuronal Cell Identities.. Trends Neurosci. ▶ Go to Pubmed
Brygida Bisikirska, Mukesh Bansal, Yao Shen, Julie Teruya-Feldstein, Raju Chaganti, Andrea Califano .  2015.   Elucidation and pharmacological targeting of novel molecular drivers of follicular lymphoma progression.. Cancer Res. ▶ Go to Pubmed
Sonal Singhal, Ellen Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel Hooper, Alva Strand, Qiye Li, Brian Raney, Christopher Balakrishnan, Simon Griffith, Gil McVean, Molly Przeworski .  2015.   Stable recombination hotspots in birds.. Science. 350 (6263) :928-32 ▶ Go to Pubmed
Pier Palamara, Laurent Francioli, Peter Wilton, Giulio Genovese, Alexander Gusev, Hilary Finucane, Sriram Sankararaman, Genome Consortium, Shamil Sunyaev, Paul de Bakker, John Wakeley, Itsik Pe'er, Alkes Price .  2015.   Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.. Am J Hum Genet. ▶ Go to Pubmed
Ana Almeida, Francesco Abate, Hossein Khiabanian, Estela Martinez-Escala, Joan Guitart, Cornelis Tensen, Maarten Vermeer, Raul Rabadan, Adolfo Ferrando, Teresa Palomero .  2015.   The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome.. Nat Genet. ▶ Go to Pubmed
Jianbo Sun, Jiguang Wang, Evangelos Pefanis, Jaime Chao, Gerson Rothschild, Isao Tachibana, Jun Chen, Ivaylo Ivanov, Raul Rabadan, Yoshito Takeda, Uttiya Basu .  2015.   Transcriptomics Identify CD9 as a Marker of Murine IL-10-Competent Regulatory B Cells.. Cell Rep. ▶ Go to Pubmed
Oliver Clarke, David Tomasek, Carla Jorge, Meagan Dufrisne, Minah Kim, Surajit Banerjee, Kanagalaghatta Rajashankar, Lawrence Shapiro, Wayne Hendrickson, Helena Santos, Filippo Mancia .  2015.   Structural basis for phosphatidylinositol-phosphate biosynthesis.. Nat Commun. 6 :8505 ▶ Go to Pubmed
Xinmin Liu, Nora Hernandez, Sergey Kisselev, Aris Floratos, Ashley Sawle, Iuliana Ionita-Laza, Ruth Ottman, Elan Louis, Lorraine Clark .  2015.   Identification of candidate genes for familial early-onset essential tremor.. Eur J Hum Genet. ▶ Go to Pubmed
Suk Lee, Michael Shen .  2015.   Cell types of origin for prostate cancer.. Curr Opin Cell Biol. 37 :35-41 ▶ Go to Pubmed
Rimma Pivovarov, Adler Perotte, Edouard Grave, John Angiolillo, Chris Wiggins, Noémie Elhadad .  2015.   Learning probabilistic phenotypes from heterogeneous EHR data.. J Biomed Inform. ▶ Go to Pubmed
Youngmee Jung, HaYeun Ji, Zaozao Chen, Hon Chan, Leigh Atchison, Bruce Klitzman, George Truskey, Kam Leong .  2015.   Scaffold-free, Human Mesenchymal Stem Cell-Based Tissue Engineered Blood Vessels.. Sci Rep. 5 :15116 ▶ Go to Pubmed
Alexandra Jacunski, Scott Dixon, Nicholas Tatonetti .  2015.   Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality.. PLoS Comput Biol. 11 (10) :e1004506 ▶ Go to Pubmed
Douglas Barrows, Sarah Schoenfeld, Cindy Hodakoski, Antonina Silkov, Barry Honig, Anthony Couvillon, Aliaksei Shymanets, Bernd Nuernberg, John Asara, Ramon Parsons .  2015.   PAK kinases mediate the phosphorylation of PREX2 to initiate feedback inhibition of Rac1.. J Biol Chem. ▶ Go to Pubmed
Nichole O'Connell, Katherine Lelli, Richard Mann, Arthur Palmer .  2015.   Asparagine deamidation reduces DNA-binding affinity of the Drosophila melanogaster Scr homeodomain.. FEBS Lett. ▶ Go to Pubmed
Malgorzata Klauzinska, David McCurdy, Cristina Rangel, Arun Vaidyanath, Nadia Castro, Michael Shen, Monica Gonzales, Daniel Bertolette, Caterina Bianco, Robert Callahan, David Salomon, Ahmed Raafat .  2015.   Cripto-1 Ablation Disrupts Alveolar Development in the Mouse Mammary Gland through a Progesterone Receptor-Mediated Pathway.. Am J Pathol. ▶ Go to Pubmed
Pam Ellis, Sarah Burbridge, Sandrine Soubes, Kyoji Ohyama, Nadav Ben-Haim, Canhe Chen, Kim Dale, Michael Shen, Daniel Constam, Marysia Placzek .  2015.   ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm.. Development. ▶ Go to Pubmed
Jiyang Yu, Jose Silva, Andrea Califano .  2015.   ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.. Bioinformatics. ▶ Go to Pubmed
Wanglong Qiu, Sophia Tang, Sohyae Lee, Andrew Turk, Anthony Sireci, Anne Qiu, Christian Rose, Chuangao Xie, Jan Kitajewski, Hui-Ju Wen, Howard Crawford, Peter Sims, Ralph Hruban, Helen Remotti, Gloria Su .  2015.   Loss of Activin Receptor Type 1B Accelerates Development of Intraductal Papillary Mucinous Neoplasms in Mice With Activated KRAS.. Gastroenterology. ▶ Go to Pubmed
Antonina Mitrofanova, Alvaro Aytes, Min Zou, Michael Shen, Cory Abate-Shen, Andrea Califano .  2015.   Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models.. Cell Rep. ▶ Go to Pubmed
Yunfei Guo, Xiaolei Ding, Yufeng Shen, Gholson Lyon, Kai Wang .  2015.   SeqMule: automated pipeline for analysis of human exome/genome sequencing data.. Sci Rep. 5 :14283 ▶ Go to Pubmed
Stephane Castel, Ami Levy-Moonshine, Pejman Mohammadi, Eric Banks, Tuuli Lappalainen .  2015.   Tools and best practices for data processing in allelic expression analysis.. Genome Biol. 16 (1) :195 ▶ Go to Pubmed
Monica Venere, Craig Horbinski, James Crish, Xun Jin, Amit Vasanji, Jennifer Major, Amy Burrows, Cathleen Chang, John Prokop, Quilian Wu, Peter Sims, Peter Canoll, Matthew Summers, Steven Rosenfeld, Jeremy Rich .  2015.   The mitotic kinesin KIF11 is a driver of invasion, proliferation, and self-renewal in glioblastoma.. Sci Transl Med. 7 (304) :304ra143 ▶ Go to Pubmed
Francine Katz, Stevan Pecic, Timothy Tran, Ilya Trakht, Laura Schneider, Zhengxiang Zhu, Long Ton-That, Michal Luzac, Viktor Zlatanic, Shivani Damera, Joanne Macdonald, Donald Landry, Liang Tong, Milan Stojanovic .  2015.   Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates.. Chembiochem. ▶ Go to Pubmed
Maho Shibata, Michael Shen .  2015.   Stem cells in genetically-engineered mouse models of prostate cancer.. Endocr Relat Cancer. ▶ Go to Pubmed
Amel Alqadah, Yi-Wen Hsieh, Berta Vidal, Chieh Chang, Oliver Hobert, Chiou-Fen Chuang .  2015.   Postmitotic diversification of olfactory neuron types is mediated by differential activities of the HMG-box transcription factor SOX-2.. EMBO J. ▶ Go to Pubmed
Mariano Alvarez, James Chen, Andrea Califano .  2015.   DIGGIT: A Bioconductor package to infer genetic variants driving cellular phenotypes.. Bioinformatics. ▶ Go to Pubmed
Brett Baskovich, Susan Hiraki, Kinnari Upadhyay, Philip Meyer, Shai Carmi, Nir Barzilai, Ariel Darvasi, Laurie Ozelius, Inga Peter, Judy Cho, Gil Atzmon, Lorraine Clark, Jin Yu, Todd Lencz, Itsik Pe'er, Harry Ostrer, Carole Oddoux .  2015.   Expanded genetic screening panel for the Ashkenazi Jewish population.. Genet Med. ▶ Go to Pubmed
Claudio Alarcón, Hani Goodarzi, Hyeseung Lee, Xuhang Liu, Saeed Tavazoie, Sohail Tavazoie .  2015.   HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events.. Cell. ▶ Go to Pubmed
Brent Stockwell, Melissa Stockwell, Michael Cennamo, Elise Jiang .  2015.   Blended Learning Improves Science Education.. Cell. 162 (5) :933-6 ▶ Go to Pubmed
Kaiyu Jiang, Xiaoyun Sun, Yanmin Chen, Yufeng Shen, James Jarvis .  2015.   RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states.. BMC Med Genomics. 8 (1) :55 ▶ Go to Pubmed
Alexandre Yahi, Nicholas Tatonetti .  2015.   A knowledge-based, automated method for phenotyping in the EHR using only clinical pathology reports.. AMIA Jt Summits Transl Sci Proc. 2015 :64-8 ▶ Go to Pubmed
Jessica Ingram, Kevin Knockenhauer, Benedikt Markus, Joseph Mandelbaum, Alexander Ramek, Yibing Shan, David Shaw, Thomas Schwartz, Hidde Ploegh, Sebastian Lourido .  2015.   Allosteric activation of apicomplexan calcium-dependent protein kinases.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Gabriele Gut, Michelle Tadmor, Dana Pe'er, Lucas Pelkmans, Prisca Liberali .  2015.   Trajectories of cell-cycle progression from fixed cell populations.. Nat Methods. ▶ Go to Pubmed
Nikolaos Stefanakis, Ines Carrera, Oliver Hobert .  2015.   Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans.. Neuron. 87 (4) :733-50 ▶ Go to Pubmed
Kabir Biswas, Kevin Hartman, Cheng-Han Yu, Oliver Harrison, Hang Song, Adam Smith, William Huang, Wan-Chen Lin, Zhenhuan Guo, Anup Padmanabhan, Sergey Troyanovsky, Michael Dustin, Lawrence Shapiro, Barry Honig, Ronen Zaidel-Bar, Jay Groves .  2015.   E-cadherin junction formation involves an active kinetic nucleation process.. Proc Natl Acad Sci U S A. 112 (35) :10932-7 ▶ Go to Pubmed
Bo-Juen Chen, Oren Litvin, Lyle Ungar, Dana Pe'er .  2015.   Context Sensitive Modeling of Cancer Drug Sensitivity.. PLoS One. 10 (8) :e0133850 ▶ Go to Pubmed
Rebecca L Y Fan, Sophie Valkenburg, Chloe Wong, Olive Li, John Nicholls, Raul Rabadan, J Peiris, Leo Poon .  2015.   Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias.. J Virol. 89 (21) :10762-73 ▶ Go to Pubmed
Alpan Raval, Stefano Piana, Michael Eastwood, David Shaw .  2015.   Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.. Protein Sci. ▶ Go to Pubmed
Jian Zhang, Yen Lieu, Abdullah Ali, Alex Penson, Kathryn Reggio, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, James Manley .  2015.   Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Chi-Shuo Chen, Soonjin Hong, Indrajyoti Indra, Alina Sergeeva, Regina Troyanovsky, Lawrence Shapiro, Barry Honig, Sergey Troyanovsky .  2015.   α-Catenin-mediated cadherin clustering couples cadherin and actin dynamics.. J Cell Biol. ▶ Go to Pubmed
Marianne Goodwin, Apoorva Mohan, Ranjan Batra, Kuang-Yung Lee, Konstantinos Charizanis, Francisco Gómez, Sabiha Eddarkaoui, Nicolas Sergeant, Luc Buée, Takashi Kimura, Brent Clark, Joline Dalton, Kenji Takamura, Sebastien Weyn-Vanhentenryck, Chaolin Zhang, Tammy Reid, Laura Ranum, John Day, Maurice Swanson .  2015.   MBNL Sequestration by Toxic RNAs and RNA Misprocessing in the Myotonic Dystrophy Brain.. Cell Rep. ▶ Go to Pubmed
Ash Alizadeh, Victoria Aranda, Alberto Bardelli, Cedric Blanpain, Christoph Bock, Christine Borowski, Carlos Caldas, Andrea Califano, Michael Doherty, Markus Elsner, Manel Esteller, Rebecca Fitzgerald, Jan Korbel, Peter Lichter, Christopher Mason, Nicholas Navin, Dana Pe'er, Kornelia Polyak, Charles Roberts, Lillian Siu, Alexandra Snyder, Hannah Stower, Charles Swanton, Roel Verhaak, Jean Zenklusen, Johannes Zuber, Jessica Zucman-Rossi .  2015.   Toward understanding and exploiting tumor heterogeneity.. Nat Med. 21 (8) :846-53 ▶ Go to Pubmed
Huijuan Feng, Xuegong Zhang, Chaolin Zhang .  2015.   mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.. Nat Commun. 6 :7816 ▶ Go to Pubmed
Ruth Rodriguez-Barrueco, Jiyang Yu, Laura Saucedo-Cuevas, Mireia Olivan, David Llobet-Navas, Preeti Putcha, Verónica Castro, Eva Murga-Penas, Ana Collazo-Lorduy, Mireia Castillo-Martin, Mariano Alvarez, Carlos Cordon-Cardo, Kevin Kalinsky, Matthew Maurer, Andrea Califano, Jose Silva .  2015.   Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.. Genes Dev. 29 (15) :1631-48 ▶ Go to Pubmed
Joshua Tasoff, Michael Mee, Harris Wang .  2015.   An Economic Framework of Microbial Trade.. PLoS One. 10 (7) :e0132907 ▶ Go to Pubmed
Xuewen Liu, Yuxia Jia, Mark Stoopler, Yufeng Shen, Haiying Cheng, Jinli Chen, Mahesh Mansukhani, Sanjay Koul, Balazs Halmos, Alain Borczuk .  2015.   Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations.. J Clin Oncol. ▶ Go to Pubmed
Lars Brichta, William Shin, Vernice Jackson-Lewis, Javier Blesa, Ee-Lynn Yap, Zachary Walker, Jack Zhang, Jean-Pierre Roussarie, Mariano Alvarez, Andrea Califano, Serge Przedborski, Paul Greengard .  2015.   Identification of neurodegenerative factors using translatome-regulatory network analysis.. Nat Neurosci. ▶ Go to Pubmed
Xose Puente, Silvia Beà, Rafael Valdés-Mas, Neus Villamor, Jesús Gutiérrez-Abril, José Martín-Subero, Marta Munar, Carlota Rubio-Pérez, Pedro Jares, Marta Aymerich, Tycho Baumann, Renée Beekman, Laura Belver, Anna Carrio, Giancarlo Castellano, Guillem Clot, Enrique Colado, Dolors Colomer, Dolors Costa, Julio Delgado, Anna Enjuanes, Xavier Estivill, Adolfo Ferrando, Josep Gelpí, Blanca González, Santiago González, Marcos González, Marta Gut, Jesús Hernández-Rivas, Mónica López-Guerra, David Martín-García, Alba Navarro, Pilar Nicolás, Modesto Orozco, Ángel Payer, Magda Pinyol, David Pisano, Diana Puente, Ana Queirós, Víctor Quesada, Carlos Romeo-Casabona, Cristina Royo, Romina Royo, María Rozman, Nuria Russiñol, Itziar Salaverría, Kostas Stamatopoulos, Hendrik Stunnenberg, David Tamborero, María Terol, Alfonso Valencia, Nuria López-Bigas, David Torrents, Ivo Gut, Armando López-Guillermo, Carlos López-Otín, Elias Campo .  2015.   Non-coding recurrent mutations in chronic lymphocytic leukaemia.. Nature. ▶ Go to Pubmed
Wynn Meyer, Aarti Venkat, Amir Kermany, Bryce van de Geijn, Sidi Zhang, Molly Przeworski .  2015.   Evolutionary history inferred from the de novo assembly of a non-model organism, the blue-eyed black lemur.. Mol Ecol. ▶ Go to Pubmed
César Mendes, Imre Bartos, Zsuzsanna Márka, Turgay Akay, Szabolcs Márka, Richard Mann .  2015.   Quantification of gait parameters in freely walking rodents.. BMC Biol. 13 :50 ▶ Go to Pubmed
Jung Woo, Yishai Shimoni, Wan Yang, Prem Subramaniam, Archana Iyer, Paola Nicoletti, María Martínez, Gonzalo Lopez, Michela Mattioli, Ronald Realubit, Charles Karan, Brent Stockwell, Mukesh Bansal, Andrea Califano .  2015.   Elucidating Compound Mechanism of Action by Network Perturbation Analysis.. Cell. 162 (2) :441-51 ▶ Go to Pubmed
M Hayano, WS Yang, CK Corn, NC Pagano, BR Stockwell .  2015.   Loss of cysteinyl-tRNA synthetase (CARS) induces the transsulfuration pathway and inhibits ferroptosis induced by cystine deprivation.. Cell Death Differ. ▶ Go to Pubmed
Xiang-Jun Lu, Harmen Bussemaker, Wilma Olson .  2015.   DSSR: an integrated software tool for dissecting the spatial structure of RNA.. Nucleic Acids Res. ▶ Go to Pubmed
Howook Hwang, Donald Petrey, Barry Honig .  2015.   A hybrid method for protein-protein interface prediction.. Protein Sci. ▶ Go to Pubmed
Jonathan Goodwin, Vishal Kothari, Justin Drake, Shuang Zhao, Emanuela Dylgjeri, Jeffry Dean, Matthew Schiewer, Christopher McNair, Jennifer Jones, Alvaro Aytes, Michael Magee, Adam Snook, Ziqi Zhu, Robert Den, Ruth Birbe, Leonard Gomella, Nicholas Graham, Ajay Vashisht, James Wohlschlegel, Thomas Graeber, Jeffrey Karnes, Mandeep Takhar, Elai Davicioni, Scott Tomlins, Cory Abate-Shen, Nima Sharifi, Owen Witte, Felix Feng, Karen Knudsen .  2015.   DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis.. Cancer Cell. 28 (1) :97-113 ▶ Go to Pubmed
Daniel Freedberg, Nora Toussaint, Sway Chen, Adam Ratner, Susan Whittier, Timothy Wang, Harris Wang, Julian Abrams .  2015.   Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial.. Gastroenterology. ▶ Go to Pubmed
Berta Vidal, Anthony Santella, Esther Serrano-Saiz, Zhirong Bao, Chiou-Fen Chuang, Oliver Hobert .  2015.   C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types.. Development. 142 (14) :2464-77 ▶ Go to Pubmed
Burcin Ikiz, Mariano Alvarez, Diane Ré, Virginia Le Verche, Kristin Politi, Francesco Lotti, Sudarshan Phani, Radhika Pradhan, Changhao Yu, Gist Croft, Arnaud Jacquier, Christopher Henderson, Andrea Califano, Serge Przedborski .  2015.   The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis.. Cell Rep. ▶ Go to Pubmed
R Rabadan .  2015.   WE-D-BRB-03: Geometrization of Tumor Evolution.. Med Phys. 42 (6) :3666 ▶ Go to Pubmed
Matthew Nelson, Hannah Tipney, Jeffery Painter, Judong Shen, Paola Nicoletti, Yufeng Shen, Aris Floratos, Pak Sham, Mulin Li, Junwen Wang, Lon Cardon, John Whittaker, Philippe Sanseau .  2015.   The support of human genetic evidence for approved drug indications.. Nature genetics. 47 (8) :856-60 ▶ Go to Pubmed
Paola Nicoletti, Mukesh Bansal, Celine Lefebvre, Paolo Guarnieri, Yufeng Shen, Itsik Pe'er, Andrea Califano, Aris Floratos .  2015.   ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs.. PloS one. 10 (6) :e0131038 ▶ Go to Pubmed
Paola Nicoletti, Mukesh Bansal, Celine Lefebvre, Paolo Guarnieri, Yufeng Shen, Itsik Pe'er, Andrea Califano, Aris Floratos .  2015.   ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs.. PLoS One. 10 (6) :e0131038 ▶ Go to Pubmed
Satyanarayan Rao, Ana Machado, Tianyin Zhou, Chaitanya Rastogi, Harmen Bussemaker, Remo Rohs .  2015.   22 Evolving insights on how cytosine methylation affects protein-DNA binding.. J Biomol Struct Dyn. 33 Suppl 1 :12 ▶ Go to Pubmed
Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard Mann, Harmen Bussemaker, Raluca Gordân, Remo Rohs .  2015.   14 Quantitative modeling of transcription factor binding specificities using DNA shape.. J Biomol Struct Dyn. 33 Suppl 1 :8-9 ▶ Go to Pubmed
Young Kwon, Marie Pancera, Priyamvada Acharya, Ivelin Georgiev, Emma Crooks, Jason Gorman, Gordon Joyce, Miklos Guttman, Xiaochu Ma, Sandeep Narpala, Cinque Soto, Daniel Terry, Yongping Yang, Tongqing Zhou, Goran Ahlsen, Robert Bailer, Michael Chambers, Gwo-Yu Chuang, Nicole Doria-Rose, Aliaksandr Druz, Mark Hallen, Adam Harned, Tatsiana Kirys, Mark Louder, Sijy O'Dell, Gilad Ofek, Keiko Osawa, Madhu Prabhakaran, Mallika Sastry, Guillaume Stewart-Jones, Jonathan Stuckey, Paul Thomas V, Tishina Tittley, Constance Williams, Baoshan Zhang, Hong Zhao, Zhou Zhou, Bruce Donald, Lawrence Lee, Susan Zolla-Pazner, Ulrich Baxa, Arne Schön, Ernesto Freire, Lawrence Shapiro, Kelly Lee, James Arthos, James Munro, Scott Blanchard, Walther Mothes, James Binley, Adrian McDermott, John Mascola, Peter Kwong .  2015.   Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.. Nat Struct Mol Biol. ▶ Go to Pubmed
Patricia Gordon, Oliver Hobert .  2015.   A Competition Mechanism for a Homeotic Neuron Identity Transformation in C. elegans.. Dev Cell. ▶ Go to Pubmed
Jacob Levine, Erin Simonds, Sean Bendall, Kara Davis, El-Ad Amir, Michelle Tadmor, Oren Litvin, Harris Fienberg, Astraea Jager, Eli Zunder, Rachel Finck, Amanda Gedman, Ina Radtke, James Downing, Dana Pe'er, Garry Nolan .  2015.   Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.. Cell. ▶ Go to Pubmed
Kelly Howell, John White, Oliver Hobert .  2015.   Spatiotemporal control of a novel synaptic organizer molecule.. Nature. ▶ Go to Pubmed
Sabrina Murgan, Willi Kari, Ute Rothbächer, Magali Iché-Torres, Pauline Mélénec, Oliver Hobert, Vincent Bertrand .  2015.   Atypical Transcriptional Activation by TCF via a Zic Transcription Factor in C. elegans Neuronal Precursors.. Dev Cell. 33 (6) :737-45 ▶ Go to Pubmed
Santiago Vilar, Tal Lorberbaum, George Hripcsak, Nicholas Tatonetti .  2015.   Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling.. PLoS One. 10 (6) :e0129974 ▶ Go to Pubmed
Lauren Pitt, Anastasia Tikhonova, Hai Hu, Thomas Trimarchi, Bryan King, Yixiao Gong, Marta Sanchez-Martin, Aris Tsirigos, Dan Littman, Adolfo Ferrando, Sean Morrison, David Fooksman, Iannis Aifantis, Susan Schwab .  2015.   CXCL12-Producing Vascular Endothelial Niches Control Acute T Cell Leukemia Maintenance.. Cancer Cell. 27 (6) :755-68 ▶ Go to Pubmed
Hyung-Ok Lee, Xiao He, Jayati Mookerjee-Basu, Dai Zhongping, Xiang Hua, Emmanuelle Nicolas, Maria Sulis, Adolfo Ferrando, Joseph Testa, Dietmar Kappes .  2015.   Disregulated expression of the transcription factor ThPOK during T-cell development leads to high incidence of T-cell lymphomas.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Elizabeth Ostrowski, Yufeng Shen, Xiangjun Tian, Richard Sucgang, Huaiyang Jiang, Jiaxin Qu, Mariko Katoh-Kurasawa, Debra Brock, Christopher Dinh, Fremiet Lara-Garduno, Sandra Lee, Christie Kovar, Huyen Dinh, Viktoriya Korchina, LaRonda Jackson, Shobha Patil, Yi Han, Lesley Chaboub, Gad Shaulsky, Donna Muzny, Kim Worley, Richard Gibbs, Stephen Richards, Adam Kuspa, Joan Strassmann, David Queller .  2015.   Genomic Signatures of Cooperation and Conflict in the Social Amoeba.. Curr Biol. 25 (12) :1661-5 ▶ Go to Pubmed
Sayantan Bose, Zhenmao Wan, Ambrose Carr, Abbas Rizvi, Gregory Vieira, Dana Pe'er, Peter Sims .  2015.   Scalable microfluidics for single cell RNA printing and sequencing.. Genome Biol. 16 (1) :120 ▶ Go to Pubmed
Mary Boland, Zachary Shahn, David Madigan, George Hripcsak, Nicholas Tatonetti .  2015.   Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method.. J Am Med Inform Assoc. ▶ Go to Pubmed
Mukesh Bansal, Geetu Mendiratta, Santosh Anand, Ritu Kushwaha, Ryan Kim, Manju Kustagi, Archana Iyer, Raju Chaganti, Andrea Califano, Pavel Sumazin .  2015.   Direct ChIP-Seq significance analysis improves target prediction.. BMC Genomics. 16 Suppl 5 :S4 ▶ Go to Pubmed
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