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2014

2014 Publications

Hossein Khiabanian, Zachary Carpenter, Jeffrey Kugelman, Joseph Chan, Vladimir Trifonov, Elyse Nagle, Travis Warren, Patrick Iversen, Sina Bavari, Gustavo Palacios, Raul Rabadan .  2014.   Viral diversity and clonal evolution from unphased genomic data.. BMC Genomics. 15 (Suppl 6) :S17 ▶ Go to Pubmed
F Abate, M Todaro, J-A van der Krogt, M Boi, I Landra, R Machiorlatti, F Tabbò, K Messana, C Abele, A Barreca, D Novero, M Gaudiano, S Aliberti, F Di Giacomo, T Tousseyn, E Lasorsa, R Crescenzo, L Bessone, E Ficarra, A Acquaviva, A Rinaldi, M Ponzoni, D Longo, S Aime, M Cheng, B Ruggeri, P Piccaluga, S Pileri, E Tiacci, B Falini, B Pera-Gresely, L Cerchietti, J Iqbal, W Chan, L Shultz, I Kwee, R Piva, I Wlodarska, R Rabadan, F Bertoni, G Inghirami, the Group .  2014.   A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation.. Leukemia. ▶ Go to Pubmed
Jonathan Chang, Sarah Gilman, Andrew Chiang, Stephan Sanders, Dennis Vitkup .  2014.   Genotype to phenotype relationships in autism spectrum disorders.. Nat Neurosci. ▶ Go to Pubmed
Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski .  2014.   The Cyni framework for network inference in Cytoscape.. Bioinformatics. ▶ Go to Pubmed
Jiguang Wang, Hossein Khiabanian, Davide Rossi, Giulia Fabbri, Valter Gattei, Francesco Forconi, Luca Laurenti, Roberto Marasca, Giovanni Del Poeta, Robin Foá, Laura Pasqualucci, Gianluca Gaidano, Raul Rabadan .  2014.   Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.. Elife. 3 ▶ Go to Pubmed
Raajit Rampal, Altuna Alkalin, Jozef Madzo, Aparna Vasanthakumar, Elodie Pronier, Jay Patel, Yushan Li, Jihae Ahn, Omar Abdel-Wahab, Alan Shih, Chao Lu, Patrick Ward, Jennifer Tsai, Todd Hricik, Valeria Tosello, Jacob Tallman, Xinyang Zhao, Danette Daniels, Qing Dai, Luisa Ciminio, Iannis Aifantis, Chuan He, Francois Fuks, Martin Tallman, Adolfo Ferrando, Stephen Nimer, Elisabeth Paietta, Craig Thompson, Jonathan Licht, Christopher Mason, Lucy Godley, Ari Melnick, Maria Figueroa, Ross Levine .  2014.   DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia.. Cell Rep. ▶ Go to Pubmed
Konstantin Popadin, Maria Gutierrez-Arcelus, Tuuli Lappalainen, Alfonso Buil, Julia Steinberg, Sergey Nikolaev, Samuel Lukowski, Georgii Bazykin, Vladimir Seplyarskiy, Panagiotis Ioannidis, Evgeny Zdobnov, Emmanouil Dermitzakis, Stylianos Antonarakis .  2014.   Gene age predicts the strength of purifying selection acting on gene expression variation in humans.. Am J Hum Genet. 95 (6) :660-74 ▶ Go to Pubmed
Alfonso Buil, Andrew Brown, Tuuli Lappalainen, Ana Viñuela, Matthew Davies, Hou-Feng Zheng, Brent Richards, Daniel Glass, Kerrin Small, Richard Durbin, Timothy Spector, Emmanouil Dermitzakis .  2014.   Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.. Nat Genet. ▶ Go to Pubmed
Felix Sanchez-Garcia, Patricia Villagrasa, Junji Matsui, Dylan Kotliar, Verónica Castro, Uri-David Akavia, Bo-Juen Chen, Laura Saucedo-Cuevas, Ruth Barrueco, David Llobet-Navas, Jose Silva, Dana Pe'er .  2014.   Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers.. Cell. ▶ Go to Pubmed
Santiago Vilar, Eugenio Uriarte, Lourdes Santana, Carol Friedman, Nicholas Tatonetti .  2014.   State of the Art and Development of a Drug-Drug Interaction Large Scale Predictor Based on 3D Pharmacophoric Similarity.. Curr Drug Metab. 15 (5) :490-501 ▶ Go to Pubmed
Mukesh Bansal, Jichen Yang, Charles Karan, Michael Menden, James Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura Heiser, Ronald Realubit, Michela Mattioli, Mariano Alvarez, Yao Shen, NCI-DREAM Community, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, Andrea Califano, NCI-DREAM Community .  2014.   A community computational challenge to predict the activity of pairs of compounds.. Nat Biotechnol. ▶ Go to Pubmed
Andrea Califano .  2014.   Predicting protein networks in cancer.. Nat Genet. 46 (12) :1252-3 ▶ Go to Pubmed
Joseph Thome, Naomi Yudanin, Yoshiaki Ohmura, Masaru Kubota, Boris Grinshpun, Taheri Sathaliyawala, Tomoaki Kato, Harvey Lerner, Yufeng Shen, Donna Farber .  2014.   Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life.. Cell. 159 (4) :814-28 ▶ Go to Pubmed
Ziyue Gao, Molly Przeworski, Guy Sella .  2014.   Footprints of ancient balanced polymorphisms in genetic variation data from closely related species.. Evolution. ▶ Go to Pubmed
Jose Angeli, Manuela Schneider, Bettina Proneth, Yulia Tyurina, Vladimir Tyurin, Victoria Hammond, Nadja Herbach, Michaela Aichler, Axel Walch, Elke Eggenhofer, Devaraj Basavarajappa, Olof Rådmark, Sho Kobayashi, Tobias Seibt, Heike Beck, Frauke Neff, Irene Esposito, Rüdiger Wanke, Heidi Förster, Olena Yefremova, Marc Heinrichmeyer, Georg Bornkamm, Edward Geissler, Stephen Thomas, Brent Stockwell, Valerie O'Donnell, Valerian Kagan, Joel Schick, Marcus Conrad .  2014.   Inactivation of the ferroptosis regulator Gpx4 triggers acute renal failure in mice.. Nat Cell Biol. 16 (12) :1180-91 ▶ Go to Pubmed
Christian Munck, Heidi Gumpert, Annika Wallin, Harris Wang, Morten Sommer .  2014.   Prediction of resistance development against drug combinations by collateral responses to component drugs.. Sci Transl Med. 6 (262) :262ra156 ▶ Go to Pubmed
Andreas Linkermann, Rachid Skouta, Nina Himmerkus, Shrikant Mulay, Christin Dewitz, Federica De Zen, Agnes Prokai, Gabriele Zuchtriegel, Fritz Krombach, Patrick-Simon Welz, Ricardo Weinlich, Tom Berghe, Peter Vandenabeele, Manolis Pasparakis, Markus Bleich, Joel Weinberg, Christoph Reichel, Jan Bräsen, Ulrich Kunzendorf, Hans-Joachim Anders, Brent Stockwell, Douglas Green, Stefan Krautwald .  2014.   Synchronized renal tubular cell death involves ferroptosis.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Hua-Sheng Chiu, David Llobet-Navas, Xuerui Yang, Wei-Jen Chung, Alberto Ambesi-Impiombato, Archana Iyer, Hyunjae Kim, Elena Seviour, Zijun Luo, Vasudha Sehgal, Tyler Moss, Yiling Lu, Prahlad Ram, Jose Silva, Gordon Mills, Andrea Califano, Pavel Sumazin .  2014.   Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.. Genome Res. ▶ Go to Pubmed
Michael Mingueneau, Smita Krishnaswamy, Matthew Spitzer, Sean Bendall, Erica Stone, Stephen Hedrick, Dana Pe'er, Diane Mathis, Garry Nolan, Christophe Benoist .  2014.   Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
César Mendes, Soumya Rajendren V, Imre Bartos, Szabolcs Márka, Richard Mann .  2014.   Kinematic Responses to Changes in Walking Orientation and Gravitational Load in Drosophila melanogaster.. PLoS One. 9 (10) :e109204 ▶ Go to Pubmed
David-Emlyn Parfitt, Michael Shen .  2014.   From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis.. Philos Trans R Soc Lond B Biol Sci. 369 (1657) ▶ Go to Pubmed
Kyung-Ae Yang, Mihaela Barbu, Marlin Halim, Payal Pallavi, Benjamin Kim, Dmitry Kolpashchikov, Stevan Pecic, Steven Taylor, Tilla Worgall, Milan Stojanovic .  2014.   Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors.. Nat Chem. 6 (11) :1003-8 ▶ Go to Pubmed
Smita Krishnaswamy, Matthew Spitzer, Michael Mingueneau, Sean Bendall, Oren Litvin, Erica Stone, Dana Pe'er, Garry Nolan .  2014.   Conditional density-based analysis of T cell signaling in single-cell data.. Science. ▶ Go to Pubmed
Ritu Kushwaha, Nirmala Jagadish, Manjunath Kustagi, Mark Tomishima, Geetu Mendiratta, Mukesh Bansal, Hyunjae Kim, Pavel Sumazin, Mariano Alvarez, Celine Lefebvre, Patricia Villagrasa-Gonzalez, Agnes Viale, James Korkola, Jane Houldsworth, Darren Feldman, George Bosl, Andrea Califano, R Chaganti .  2014.   Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.. Stem Cells. ▶ Go to Pubmed
Andreas Linkermann, Brent Stockwell, Stefan Krautwald, Hans-Joachim Anders .  2014.   Regulated cell death and inflammation: an auto-amplification loop causes organ failure.. Nat Rev Immunol. ▶ Go to Pubmed
Ana Machado, Tianyin Zhou, Satyanarayan Rao, Pragya Goel, Chaitanya Rastogi, Allan Lazarovici, Harmen Bussemaker, Remo Rohs .  2014.   Evolving insights on how cytosine methylation affects protein-DNA binding.. Brief Funct Genomics. ▶ Go to Pubmed
Paul Boutros, Adam Margolin, Joshua Stuart, Andrea Califano, Gustavo Stolovitzky .  2014.   Toward better benchmarking: challenge-based methods assessment in cancer genomics.. Genome Biol. 15 (9) :462 ▶ Go to Pubmed
Federico Giorgi, Gonzalo Lopez, Jung Woo, Brygida Bisikirska, Andrea Califano, Mukesh Bansal .  2014.   Inferring protein modulation from gene expression data using conditional mutual information.. PLoS One. 9 (10) :e109569 ▶ Go to Pubmed
Yaara Oren, Mark Smith, Nathan Johns, Millie Zeevi, Dvora Biran, Eliora Ron, Jukka Corander, Harris Wang, Eric Alm, Tal Pupko .  2014.   Transfer of noncoding DNA drives regulatory rewiring in bacteria.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
James Chen, Mariano Alvarez, Flaminia Talos, Harshil Dhruv, Gabrielle Rieckhof, Archana Iyer, Kristin Diefes, Kenneth Aldape, Michael Berens, Michael Shen, Andrea Califano .  2014.   Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.. Cell. 159 (2) :402-14 ▶ Go to Pubmed
Albert Lee, Hossein Khiabanian, Jeffrey Kugelman, Oliver Elliott, Elyse Nagle, Guo-Yun Yu, Travis Warren, Gustavo Palacios, Raul Rabadan .  2014.   Transcriptome reconstruction and annotation of cynomolgus and African green monkey.. BMC Genomics. 15 (1) :846 ▶ Go to Pubmed
Ranjan Batra, Konstantinos Charizanis, Mini Manchanda, Apoorva Mohan, Moyi Li, Dustin Finn, Marianne Goodwin, Chaolin Zhang, Krzysztof Sobczak, Charles Thornton, Maurice Swanson .  2014.   Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease.. Mol Cell. ▶ Go to Pubmed
Olivier Julien, Martin Kampmann, Michael Bassik, Julie Zorn, Vincent Venditto, Kazutaka Shimbo, Nicholas Agard, Kenichi Shimada, Arnold Rheingold, Brent Stockwell, Jonathan Weissman, James Wells .  2014.   Unraveling the mechanism of cell death induced by chemical fibrils.. Nat Chem Biol. ▶ Go to Pubmed
Keith Hoffman, Andrea Demakas, Mo Dimbil, Nicholas Tatonetti, Colin Erdman .  2014.   Stimulated Reporting: The Impact of US Food and Drug Administration-Issued Alerts on the Adverse Event Reporting System (FAERS).. Drug Saf. ▶ Go to Pubmed
Jeremie Vendome, Klara Felsovalyi, Hang Song, Zhongyu Yang, Xiangshu Jin, Julia Brasch, Oliver Harrison, Goran Ahlsen, Fabiana Bahna, Anna Kaczynska, Phinikoula Katsamba, Darwin Edmond, Wayne Hubbell, Lawrence Shapiro, Barry Honig .  2014.   Structural and energetic determinants of adhesive binding specificity in type I cadherins.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
S Vilar, P Ryan, D Madigan, P Stang, M Schuemie, C Friedman, N Tatonetti, G Hripcsak .  2014.   Similarity-based modeling applied to signal detection in pharmacovigilance.. CPT Pharmacometrics Syst Pharmacol. 3 :e137 ▶ Go to Pubmed
Tai-Hsien Yang, Wei-Yi Cheng, Tian Zheng, Matthew Maurer, Dimitris Anastassiou .  2014.   Breast Cancer Prognostic Biomarker Using Attractor Metagenes and the FGD3-SUSD3 Metagene.. Cancer Epidemiol Biomarkers Prev. ▶ Go to Pubmed
Chee Chua, Maho Shibata, Ming Lei, Roxanne Toivanen, Lamont Barlow, Sarah Bergren, Ketan Badani, James McKiernan, Mitchell Benson, Hanina Hibshoosh, Michael Shen .  2014.   Single luminal epithelial progenitors can generate prostate organoids in culture.. Nat Cell Biol. ▶ Go to Pubmed
Nikolaos Panousis, Maria Gutierrez-Arcelus, Emmanouil Dermitzakis, Tuuli Lappalainen .  2014.   Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies.. Genome Biol. 15 (9) :467 ▶ Go to Pubmed
Anat Kreimer, Itsik Pe'er .  2014.   Co-regulated Transcripts Associated to Cooperating eSNPs Define Bi-fan Motifs in Human Gene Networks.. PLoS Genet. 10 (9) :e1004587 ▶ Go to Pubmed
Joseph Glessner, Alexander Bick, Kaoru Ito, Jason Homsy, Laura Rodriguez-Murillo, Menachem Fromer, Erica Mazaika, Badri Vardarajan, Michael Italia, Jeremy Leipzig, Steven DePalma, Ryan Golhar, Stephan Sanders, Boris Yamrom, Michael Ronemus, Ivan Iossifov, A Willsey, Matthew State, Jonathan Kaltman, Peter White, Yufeng Shen, Dorothy Warburton, Martina Brueckner, Christine Seidman, Elizabeth Goldmuntz, Bruce Gelb, Richard Lifton, Jonathan Seidman, Hakon Hakonarson, Wendy Chung .  2014.   Increased Frequency of De Novo Copy Number Variations in Congenital Heart Disease by Integrative Analysis of SNP Array and Exome Sequence Data.. Circ Res. ▶ Go to Pubmed
Shai Carmi, Ken Hui, Ethan Kochav, Xinmin Liu, James Xue, Fillan Grady, Saurav Guha, Kinnari Upadhyay, Dan Ben-Avraham, Semanti Mukherjee, Monica Bowen, Tinu Thomas, Joseph Vijai, Marc Cruts, Guy Froyen, Diether Lambrechts, Stéphane Plaisance, Christine Van Broeckhoven, Philip Van Damme, Herwig Van Marck, Nir Barzilai, Ariel Darvasi, Kenneth Offit, Susan Bressman, Laurie Ozelius, Inga Peter, Judy Cho, Harry Ostrer, Gil Atzmon, Lorraine Clark, Todd Lencz, Itsik Pe'er .  2014.   Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.. Nat Commun. 5 :4835 ▶ Go to Pubmed
Daniel Herranz, Alberto Ambesi-Impiombato, Teresa Palomero, Stephanie Schnell, Laura Belver, Agnieszka Wendorff, Luyao Xu, Mireia Castillo-Martin, David Llobet-Navas, Carlos Cordon-Cardo, Emmanuelle Clappier, Jean Soulier, Adolfo Ferrando .  2014.   A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia.. Nat Med. 20 (10) :1130-7 ▶ Go to Pubmed
Ye Zhang, Kenian Chen, Steven Sloan, Mariko Bennett, Anja Scholze, Sean O'Keeffe, Hemali Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben Barres, Jia Wu .  2014.   An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex.. J Neurosci. 34 (36) :11929-47 ▶ Go to Pubmed
Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami, Raul Rabadan .  2014.   Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.. BMC Syst Biol. 8 (1) :97 ▶ Go to Pubmed
Zhu Wang, Roxanne Toivanen, Sarah Bergren, Pierre Chambon, Michael Shen .  2014.   Luminal Cells Are Favored as the Cell of Origin for Prostate Cancer.. Cell Rep. ▶ Go to Pubmed
Chan Thu, Weisheng Chen V, Rotem Rubinstein, Maxime Chevee, Holly Wolcott, Klara Felsovalyi, Juan Tapia, Lawrence Shapiro, Barry Honig, Tom Maniatis .  2014.   Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins.. Cell. 158 (5) :1045-59 ▶ Go to Pubmed
Joris van Arensbergen, Bas van Steensel, Harmen Bussemaker .  2014.   In search of the determinants of enhancer-promoter interaction specificity.. Trends Cell Biol. ▶ Go to Pubmed
Marios Agelopoulos, Daniel McKay, Richard Mann .  2014.   cgChIP: A Cell Type- and Gene-Specific Method for Chromatin Analysis.. Methods Mol Biol. 1196 :291-306 ▶ Go to Pubmed
Todd Riley, Matthew Slattery, Namiko Abe, Chaitanya Rastogi, Dahong Liu, Richard Mann, Harmen Bussemaker .  2014.   SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes.. Methods Mol Biol. 1196 :255-78 ▶ Go to Pubmed
Ambrose Carr, Dana Pe'er .  2014.   Broadening horizons: holistic viewpoints from the Biology of Genomes.. Genome Biol. 15 (7) :416 ▶ Go to Pubmed
Liliana Greger, Jing Su, Johan Rung, Pedro Ferreira, Geuvadis consortium, Tuuli Lappalainen, Emmanouil Dermitzakis, Alvis Brazma .  2014.   Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.. PLoS One. 9 (8) :e104567 ▶ Go to Pubmed
Christian Gonzalez, Jennifer Sims, Nicholas Hornstein, Angeliki Mela, Franklin Garcia, Liang Lei, David Gass, Benjamin Amendolara, Jeffrey Bruce, Peter Canoll, Peter Sims .  2014.   Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors.. J Neurosci. 34 (33) :10924-36 ▶ Go to Pubmed
Alicia Martin, Helio Costa, Tuuli Lappalainen, Brenna Henn, Jeffrey Kidd, Muh-Ching Yee, Fabian Grubert, Howard Cann, Michael Snyder, Stephen Montgomery, Carlos Bustamante .  2014.   Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.. PLoS Genet. 10 (8) :e1004549 ▶ Go to Pubmed
Stephanie Johnson, Jan-Willem van de Meent, Rob Phillips, Chris Wiggins, Martin Lindén .  2014.   Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.. Nucleic Acids Res. 42 (16) :10265-77 ▶ Go to Pubmed
Evangelos Pefanis, Jiguang Wang, Gerson Rothschild, Junghyun Lim, Jaime Chao, Raul Rabadan, Aris Economides, Uttiya Basu .  2014.   Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.. Nature. ▶ Go to Pubmed
Brian Gill, David Pisapia, Hani Malone, Hannah Goldstein, Liang Lei, Adam Sonabend, Jonathan Yun, Jorge Samanamud, Jennifer Sims, Matei Banu, Athanassios Dovas, Andrew Teich, Sameer Sheth, Guy McKhann, Michael Sisti, Jeffrey Bruce, Peter Sims, Peter Canoll .  2014.   MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.. Proc Natl Acad Sci U S A. 111 (34) :12550-5 ▶ Go to Pubmed
Jingqiang Wang, Cory Abate-Shen .  2014.   Analyses of tumor-suppressor genes in germline mouse models of cancer.. Cold Spring Harb Protoc. 2014 (8) :pdb.top069773 ▶ Go to Pubmed
Elaine Lim, Peter Würtz, Aki Havulinna, Priit Palta, Taru Tukiainen, Karola Rehnström, Tõnu Esko, Reedik Mägi, Michael Inouye, Tuuli Lappalainen, Yingleong Chan, Rany Salem, Monkol Lek, Jason Flannick, Xueling Sim, Alisa Manning, Claes Ladenvall, Suzannah Bumpstead, Eija Hämäläinen, Kristiina Aalto, Mikael Maksimow, Marko Salmi, Stefan Blankenberg, Diego Ardissino, Svati Shah, Benjamin Horne, Ruth McPherson, Gerald Hovingh, Muredach Reilly, Hugh Watkins, Anuj Goel, Martin Farrall, Domenico Girelli, Alex Reiner, Nathan Stitziel, Sekar Kathiresan, Stacey Gabriel, Jeffrey Barrett, Terho Lehtimäki, Markku Laakso, Leif Groop, Jaakko Kaprio, Markus Perola, Mark McCarthy, Michael Boehnke, David Altshuler, Cecilia Lindgren, Joel Hirschhorn, Andres Metspalu, Nelson Freimer, Tanja Zeller, Sirpa Jalkanen, Seppo Koskinen, Olli Raitakari, Richard Durbin, Daniel MacArthur, Veikko Salomaa, Samuli Ripatti, Mark Daly, Aarno Palotie, Sequencing Project .  2014.   Distribution and medical impact of loss-of-function variants in the Finnish founder population.. PLoS Genet. 10 (7) :e1004494 ▶ Go to Pubmed
Adam Wolpaw, Brent Stockwell .  2014.   Multidimensional profiling in the investigation of small-molecule-induced cell death.. Methods Enzymol. 545 :265-302 ▶ Go to Pubmed
Maria Matos, Santiago Vilar, Sonja Kachler, André Fonseca, Lourdes Santana, Eugenio Uriarte, Fernanda Borges, Nicholas Tatonetti, Karl-Norbert Klotz .  2014.   Insight into the Interactions between Novel Coumarin Derivatives and Human A3 Adenosine Receptors.. ChemMedChem. ▶ Go to Pubmed
Hani Goodarzi, Steven Zhang, Colin Buss, Lisa Fish, Saeed Tavazoie, Sohail Tavazoie .  2014.   Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.. Nature. ▶ Go to Pubmed
Casey Overby, George Hripcsak, Yufeng Shen .  2014.   Estimating heritability of drug-induced liver injury from common variants and implications for future study designs.. Sci Rep. 4 :5762 ▶ Go to Pubmed
Daniel Woods, Thomas Ream, Gregory Minevich, Oliver Hobert, Richard Amasino .  2014.   PHYTOCHROME C Is an Essential Light Receptor for Photoperiodic Flowering in the Temperate Grass, Brachypodium distachyon.. Genetics. 198 (1) :397-408 ▶ Go to Pubmed
Hyangyee Oh, Matthew Slattery, Lijia Ma, Kevin White, Richard Mann, Kenneth Irvine .  2014.   Yorkie Promotes Transcription by Recruiting a Histone Methyltransferase Complex.. Cell Rep. ▶ Go to Pubmed
Laure Segurel, Minyoung Wyman, Molly Przeworski .  2014.   Determinants of Mutation Rate Variation in the Human Germline.. Annu Rev Genomics Hum Genet. ▶ Go to Pubmed
Claire Higgins, Lynn Petukhova, Sivan Harel, Yuan Ho, Esther Drill, Lawrence Shapiro, Muhammad Wajid, Angela Christiano .  2014.   FGF5 is a crucial regulator of hair length in humans.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Richard Boyce, Patrick Ryan, Niklas Norén, Martijn Schuemie, Christian Reich, Jon Duke, Nicholas Tatonetti, Gianluca Trifirò, Rave Harpaz, Marc Overhage, Abraham Hartzema, Mark Khayter, Erica Voss, Christophe Lambert, Vojtech Huser, Michel Dumontier .  2014.   Bridging Islands of Information to Establish an Integrated Knowledge Base of Drugs and Health Outcomes of Interest.. Drug Saf. ▶ Go to Pubmed
Vez Repunte-Canonigo, Celine Lefebvre, Olivier George, Tomoya Kawamura, Marisela Morales, George Koob, Andrea Califano, Eliezer Masliah, Pietro Sanna .  2014.   Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats.. Mol Neurodegener. 9 :26 ▶ Go to Pubmed
Hiyaa Ghosh, Michele Ceribelli, Ines Matos, Allan Lazarovici, Harmen Bussemaker, Anna Lasorella, Scott Hiebert, Kang Liu, Louis Staudt, Boris Reizis .  2014.   ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2.. J Exp Med. ▶ Go to Pubmed
The Consortium .  2014.   Whole-genome sequence variation, population structure and demographic history of the Dutch population.. Nat Genet. ▶ Go to Pubmed
Lucas Ward, Junbai Wang, Harmen Bussemaker .  2014.   Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast.. BMC Genomics. 15 (1) :494 ▶ Go to Pubmed
Semanti Mukherjee, Saurav Guha, Masashi Ikeda, Nakao Iwata, Anil Malhotra, Itsik Pe'er, Ariel Darvasi, Todd Lencz .  2014.   Excess of homozygosity in the major histocompatibility complex in schizophrenia.. Hum Mol Genet. ▶ Go to Pubmed
Mina Fazlollahi, Eunjee Lee, Ivor Muroff, Xiang-Jun Lu, Pilar Gomez-Alcala, Helen Causton, Harmen Bussemaker .  2014.   Harnessing Natural Sequence Variation to Dissect Post-Transcriptional Regulatory Networks in Yeast.. G3 (Bethesda). ▶ Go to Pubmed
Giuliano Sciara, Oliver Clarke, David Tomasek, Brian Kloss, Shantelle Tabuso, Rushelle Byfield, Raphael Cohn, Surajit Banerjee, Kanagalaghatta Rajashankar, Vesna Slavkovic, Joseph Graziano, Lawrence Shapiro, Filippo Mancia .  2014.   Structural basis for catalysis in a CDP-alcohol phosphotransferase.. Nat Commun. 5 :4068 ▶ Go to Pubmed
Yibing Shan, Kavitha Gnanasambandan, Daniela Ungureanu, Eric Kim, Henrik Hammarén, Kazuo Yamashita, Olli Silvennoinen, David Shaw, Stevan Hubbard .  2014.   Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase.. Nat Struct Mol Biol. ▶ Go to Pubmed
Donald Petrey, Barry Honig .  2014.   Structural bioinformatics of the interactome.. Annu Rev Biophys. 43 :193-210 ▶ Go to Pubmed
James Costello, Laura Heiser, Elisabeth Georgii, Mehmet Gönen, Michael Menden, Nicholas Wang, Mukesh Bansal, Muhammad Ammad-Ud-Din, Petteri Hintsanen, Suleiman Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI Community, James Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe Gray, Gustavo Stolovitzky .  2014.   A community effort to assess and improve drug sensitivity prediction algorithms.. Nat Biotechnol. ▶ Go to Pubmed
Milan Stojanovic, Darko Stefanovic, Sergei Rudchenko .  2014.   Exercises in Molecular Computing.. Acc Chem Res. ▶ Go to Pubmed
Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang .  2014.   A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.. EURASIP J Bioinform Syst Biol. 2014 (1) :7 ▶ Go to Pubmed
Mads Bonde, Sriram Kosuri, Hans Genee, Kira Sarup-Lytzen, George Church, Morten Sommer, Harris Wang .  2014.   Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides.. ACS Synth Biol. ▶ Go to Pubmed
Scott Dixon, Darpan Patel, Matthew Welsch, Rachid Skouta, Eric Lee, Miki Hayano, Ajit Thomas, Caroline Gleason, Nicholas Tatonetti, Barbara Slusher, Brent Stockwell .  2014.   Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis.. Elife. :e02523 ▶ Go to Pubmed
Vladimir Vacic, Laurie Ozelius, Lorraine Clark, Anat Bar-Shira, Mali Gana-Weisz, Tanya Gurevich, Alexander Gusev, Merav Kedmi, Eimear Kenny, Xinmin Liu, Helen Mejia-Santana, Anat Mirelman, Deborah Raymond, Rachel Saunders-Pullman, Robert Desnick, Gil Atzmon, Edward Burns, Harry Ostrer, Hakon Hakonarson, Aviv Bergman, Nir Barzilai, Ariel Darvasi, Inga Peter, Saurav Guha, Todd Lencz, Nir Giladi, Karen Marder, Itsik Pe'er, Susan Bressman, Avi Orr-Urtreger .  2014.   Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.. Hum Mol Genet. ▶ Go to Pubmed
Stephanie Yaung, George Church, Harris Wang .  2014.   Recent progress in engineering human-associated microbiomes.. Methods Mol Biol. 1151 :3-25 ▶ Go to Pubmed
Iraz Aydin, Rachel Melamed, Sarah Adams, Mireia Castillo-Martin, Ahu Demir, Diana Bryk, Georg Brunner, Carlos Cordon-Cardo, Iman Osman, Raul Rabadan, Julide Celebi .  2014.   FBXW7 Mutations in Melanoma and a New Therapeutic Paradigm.. J Natl Cancer Inst. 106 (6) ▶ Go to Pubmed
Mads Bonde, Michael Klausen, Mads Anderson V, Annika Wallin, Harris Wang, Morten Sommer .  2014.   MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.. Nucleic Acids Res. ▶ Go to Pubmed
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