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2014

2014 Publications

Panos Oikonomou, Hani Goodarzi, Saeed Tavazoie .  2014.   Systematic Identification of Regulatory Elements in Conserved 3' UTRs of Human Transcripts.. Cell Rep. ▶ Go to Pubmed
Jan-Willem van de Meent, Jonathan Bronson, Chris Wiggins, Ruben Gonzalez .  2014.   Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments.. Biophys J. 106 (6) :1327-37 ▶ Go to Pubmed
Keith Hoffman, Mo Dimbil, Colin Erdman, Nicholas Tatonetti, Brian Overstreet .  2014.   The Weber Effect and the United States Food and Drug Administration's Adverse Event Reporting System (FAERS): Analysis of Sixty-Two Drugs Approved from 2006 to 2010.. Drug Saf. ▶ Go to Pubmed
Adam Sonabend, Arthur Carminucci, Benjamin Amendolara, Mukesh Bansal, Richard Leung, Liang Lei, Ronald Realubit, Hai Li, Charles Karan, Jonathan Yun, Christopher Showers, Robert Rothcock, Jane O, Andrea Califano, Peter Canoll, Jeffrey Bruce .  2014.   Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma.. Neuro Oncol. ▶ Go to Pubmed
David Llobet-Navas, Ruth Rodriguez-Barrueco, Verónica Castro, Alejandro Ugalde, Pavel Sumazin, Damian Jacob-Sendler, Berna Demircan, Mireia Castillo-Martin, Preeti Putcha, Netonia Marshall, Patricia Villagrasa, Joseph Chan, Felix Sanchez-Garcia, Dana Pe'er, Raul Rabadan, Antonio Iavarone, Carlos Cordon-Cardo, Andrea Califano, Carlos López-Otín, Elena Ezhkova, Jose Silva .  2014.   The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.. Genes Dev. ▶ Go to Pubmed
Maria Matos, Patricia Janeiro, Rosa Franco, Santiago Vilar, Nicholas Tatonetti, Lourdes Santana, Eugenio Uriarte, Fernanda Borges, José Fontenla, Dolores Viña .  2014.   Synthesis, pharmacological study and docking calculations of new benzo[f]coumarin derivatives as dual inhibitors of enzymatic systems involved in neurodegenerative diseases.. Future Med Chem. 6 (4) :371-83 ▶ Go to Pubmed
Christopher Sundling, Zhenhai Zhang, Ganesh Phad, Zizhang Sheng, Yimeng Wang, John Mascola, Yuxing Li, Richard Wyatt, Lawrence Shapiro, Gunilla Hedestam .  2014.   Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization.. J Immunol. ▶ Go to Pubmed
Sebastien Weyn-Vanhentenryck, Aldo Mele, Qinghong Yan, Shuying Sun, Natalie Farny, Zuo Zhang, Chenghai Xue, Margaret Herre, Pamela Silver, Michael Zhang, Adrian Krainer, Robert Darnell, Chaolin Zhang .  2014.   HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism.. Cell Rep. ▶ Go to Pubmed
Rachid Skouta, Scott Dixon, Jianlin Wang, Denise Dunn, Marina Orman, Kenichi Shimada, Paul Rosenberg, Donald Lo, Joel Weinberg, Andreas Linkermann, Brent Stockwell .  2014.   Ferrostatins inhibit oxidative lipid damage and cell death in diverse disease models.. J Am Chem Soc. ▶ Go to Pubmed
Monica Messina, Ilaria Del Giudice, Hossein Khiabanian, Davide Rossi, Sabina Chiaretti, Silvia Rasi, Valeria Spina, Antony Holmes, Marilisa Marinelli, Giulia Fabbri, Alfonso Piciocchi, Francesca Mauro, Anna Guarini, Gianluca Gaidano, Riccardo Dalla-Favera, Laura Pasqualucci, Raul Rabadan, Robin Foá .  2014.   Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness.. Blood. ▶ Go to Pubmed
Fei Song, Carmen Del Pozo, Rosa Rosario, Yu Zou, Radha Ananthakrishnan, Xiaoyuan Xu, Payal Patel, Vivian Benoit, Shi Yan, Huilin Li, Richard Friedman, Jason Kim, Ravichandran Ramasamy, Anthony Ferrante, Ann Schmidt .  2014.   RAGE Regulates the Metabolic and Inflammatory Response to High Fat Feeding in Mice.. Diabetes. ▶ Go to Pubmed
Konrad Karczewski, Michael Snyder, Russ Altman, Nicholas Tatonetti .  2014.   Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association.. PLoS Genet. 10 (2) :e1004122 ▶ Go to Pubmed
Davide Rossi, Hossein Khiabanian, Valeria Spina, Carmela Ciardullo, Alessio Bruscaggin, Rosella Famà, Silvia Rasi, Sara Monti, Clara Deambrogi, Lorenzo De Paoli, Jiguang Wang, Valter Gattei, Anna Guarini, Robin Foá, Raul Rabadan, Gianluca Gaidano .  2014.   Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.. Blood. ▶ Go to Pubmed
Mitja Kurki, Emília Gaál, Johannes Kettunen, Tuuli Lappalainen, Androniki Menelaou, Verneri Anttila, Femke Hof, Mikael Fraunberg, Seppo Helisalmi, Mikko Hiltunen, Hanna Lehto, Aki Laakso, Riku Kivisaari, Timo Koivisto, Antti Ronkainen, Jaakko Rinne, Lambertus Kiemeney, Sita Vermeulen, Mari Kaunisto, Johan Eriksson, Arpo Aromaa, Markus Perola, Terho Lehtimäki, Olli Raitakari, Veikko Salomaa, Murat Gunel, Emmanouil Dermitzakis, Ynte Ruigrok, Gabriel Rinkel, Mika Niemelä, Juha Hernesniemi, Samuli Ripatti, Paul de Bakker, Aarno Palotie, Juha Jääskeläinen .  2014.   High risk population isolate reveals low frequency variants predisposing to intracranial aneurysms.. PLoS Genet. 10 (1) :e1004134 ▶ Go to Pubmed
Stefano Piana, John Klepeis, David Shaw .  2014.   Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.. Curr Opin Struct Biol. 24C :98-105 ▶ Go to Pubmed
Yakov Chudnovsky, Dohoon Kim, Siyuan Zheng, Warren Whyte, Mukesh Bansal, Mark-Anthony Bray, Shuba Gopal, Matthew Theisen, Steve Bilodeau, Prathapan Thiru, Julien Muffat, Omer Yilmaz, Maya Mitalipova, Kevin Woolard, Jeongwu Lee, Riko Nishimura, Nobuo Sakata, Howard Fine, Anne Carpenter, Serena Silver, Roel Verhaak, Andrea Califano, Richard Young, Keith Ligon, Ingo Mellinghoff, David Root, David Sabatini, William Hahn, Milan Chheda .  2014.   ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State.. Cell Rep. ▶ Go to Pubmed
Wan Yang, Rohitha Sriramaratnam, Matthew Welsch, Kenichi Shimada, Rachid Skouta, Vasanthi Viswanathan, Jaime Cheah, Paul Clemons, Alykhan Shamji, Clary Clish, Lewis Brown, Albert Girotti, Virginia Cornish, Stuart Schreiber, Brent Stockwell .  2014.   Regulation of Ferroptotic Cancer Cell Death by GPX4.. Cell. 156 (1-2) :317-31 ▶ Go to Pubmed
Aruna Kode, John Manavalan, Ioanna Mosialou, Govind Bhagat, Chozha Rathinam V, Na Luo, Hossein Khiabanian, Albert Lee, Vundavalli Murty V, Richard Friedman, Andrea Brum, David Park, Naomi Galili, Siddhartha Mukherjee, Julie Teruya-Feldstein, Azra Raza, Raul Rabadan, Ellin Berman, Stavroula Kousteni .  2014.   Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts.. Nature. ▶ Go to Pubmed
Teresa Palomero, Lucile Couronné, Hossein Khiabanian, Mi-Yeon Kim, Alberto Ambesi-Impiombato, Arianne Perez-Garcia, Zachary Carpenter, Francesco Abate, Maddalena Allegretta, Erika Haydu, Xiaoyu Jiang, Izidore Lossos, Concha Nicolas, Milagros Balbin, Christian Bastard, Govind Bhagat, Miguel Piris, Elias Campo, Olivier Bernard, Raul Rabadan, Adolfo Ferrando .  2014.   Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.. Nat Genet. ▶ Go to Pubmed
Michael Moore, Chaolin Zhang, Emily Gantman, Aldo Mele, Jennifer Darnell, Robert Darnell .  2014.   Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.. Nat Protoc. 9 (2) :263-93 ▶ Go to Pubmed
Ronald Tepper, Coleen Murphy, Harmen Bussemaker .  2014.   DAF-16 and PQM-1: Partners in longevity.. Aging (Albany NY). ▶ Go to Pubmed
Adam Sonabend, Mukesh Bansal, Paolo Guarnieri, Liang Lei, Benjamin Amendolara, Craig Soderquist, Richard Leung, Jonathan Yun, Benjamin Kennedy, Julia Sisti, Samuel Bruce, Rachel Bruce, Reena Shakya, Thomas Ludwig, Steven Rosenfeld, Peter Sims, Jeffrey Bruce, Andrea Califano, Peter Canoll .  2014.   The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected During Tumor Progression.. Cancer Res. ▶ Go to Pubmed
Laura Pasqualucci, Hossein Khiabanian, Marco Fangazio, Mansi Vasishtha, Monica Messina, Antony Holmes, Peter Ouillette, Vladimir Trifonov, Davide Rossi, Fabrizio Tabbò, Maurilio Ponzoni, Amy Chadburn, Vundavalli Murty V, Govind Bhagat, Gianluca Gaidano, Giorgio Inghirami, Sami Malek, Raul Rabadan, Riccardo Dalla-Favera .  2014.   Genetics of follicular lymphoma transformation.. Cell Rep. 6 (1) :130-40 ▶ Go to Pubmed
Lan Yu, James Bennett, Julia Wynn, Gemma Carvill, Yee Cheung, Yufeng Shen, George Mychaliska, Kenneth Azarow, Timothy Crombleholme, Dai Chung, Douglas Potoka, Brad Warner, Brian Bucher, Foong-Yen Lim, John Pietsch, Charles Stolar, Gudrun Aspelund, Marc Arkovitz, University Genomics, Heather Mefford, Wendy Chung .  2014.   Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia.. J Med Genet. ▶ Go to Pubmed
Shula Shazman, Hunjoong Lee, Yakov Socol, Richard Mann, Barry Honig .  2014.   OnTheFly: a Database of Drosophila melanogaster Transcription Factors and Their Binding Sites.. Nucleic Acids Res. 42 (1) :D167-71 ▶ Go to Pubmed
Sebastian Waszak, Helena Kilpinen, Andreas Gschwind, Andrea Orioli, Sunil Raghav, Robert Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez, Alexandre Reymond, Emmanouil Dermitzakis, Bart Deplancke .  2014.   Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.. Bioinformatics. 30 (2) :165-71 ▶ Go to Pubmed