Search Publications

Filter Publications

By Year
Rose Orenbuch, Ioan Filip, Raul Rabadan .  2020.   HLA Typing from RNA Sequencing and Applications to Cancer.. Methods Mol Biol. 2120 :71-92 ▶ Go to Pubmed
Wenyan Jiang, Panos Oikonomou, Saeed Tavazoie .  2020.   Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.. Cell. 180 (5) :1002-1017.e31 ▶ Go to Pubmed
Kaiyi Zhu, Dimitris Anastassiou .  2020.   2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions.. Bioinformatics. 36 (11) :3588-3589 ▶ Go to Pubmed
Indrajyoti Indra, Regina Troyanovsky, Lawrence Shapiro, Barry Honig, Sergey Troyanovsky .  2020.   Sensing Actin Dynamics through Adherens Junctions.. Cell Rep. 30 (8) :2820-2833.e3 ▶ Go to Pubmed
Oliver Harrison, Julia Brasch, Phinikoula Katsamba, Goran Ahlsen, Alex Noble, Hanbin Dan, Rosemary Sampogna V, Clinton Potter, Bridget Carragher, Barry Honig, Lawrence Shapiro .  2020.   Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.. Cell Rep. 30 (8) :2655-2671.e7 ▶ Go to Pubmed
Oyetunji Ogundijo, Kaiyi Zhu, Xiaodong Wang, Dimitris Anastassiou .  2021.   Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption.. IEEE/ACM Trans Comput Biol Bioinform. 18 (6) :2271-2280 ▶ Go to Pubmed
Eugenia Lyashenko, Mario Niepel, Purushottam Dixit, Sang Lim, Peter Sorger, Dennis Vitkup .  2020.   Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.. Elife. 9 ▶ Go to Pubmed
K Öberg, A Califano, J Strosberg, S Ma, U Pape, L Bodei, G Kaltsas, C Toumpanakis, J Goldenring, A Frilling, S Paulson .  2020.   A meta-analysis of the accuracy of a neuroendocrine tumor mRNA genomic biomarker (NETest) in blood.. Ann Oncol. 31 (2) :202-212 ▶ Go to Pubmed
Robyn Gartrell-Corrado, Andrew Chen, Emanuelle Rizk, Douglas Marks, Margaret Bogardus, Thomas Hart, Andrew Silverman, Claire -Audrey Y Bayan, Grace Finkel, Luke Barker, Kimberly Komatsubara, Richard Carvajal, Basil Horst, Rui Chang, Anthea Monod, Raul Rabadan, Yvonne Saenger .  2020.   Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma.. Cancer Res. 80 (5) :1078-1087 ▶ Go to Pubmed
Purushottam Dixit, Eugenia Lyashenko, Mario Niepel, Dennis Vitkup .  2020.   Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.. Cell Syst. 10 (2) :204-212.e8 ▶ Go to Pubmed
Rachael Vaubel, Shulan Tian, Dioval Remonde, Mark Schroeder, Ann Mladek, Gaspar Kitange, Alissa Caron, Thomas Kollmeyer, Rebecca Grove, Sen Peng, Brett Carlson, Daniel Ma, Gobinda Sarkar, Lisa Evers, Paul Decker, Huihuang Yan, Harshil Dhruv, Michael Berens, Qianghu Wang, Bianca Marin, Eric Klee, Andrea Califano, Daniel LaChance, Jeanette Eckel-Passow, Roel Verhaak, Erik Sulman, Terry Burns, Fredrick Meyer, Brian O'Neill, Nhan Tran, Caterina Giannini, Robert Jenkins, Ian Parney, Jann Sarkaria .  2020.   Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma.. Clin Cancer Res. 26 (5) :1094-1104 ▶ Go to Pubmed
Brian Ji, Ravi Sheth, Purushottam Dixit, Yiming Huang, Andrew Kaufman, Harris Wang, Dennis Vitkup .  2019.   Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.. Nat Methods. 16 (8) :731-736 ▶ Go to Pubmed
Judith Kribelbauer, Chaitanya Rastogi, Harmen Bussemaker, Richard Mann .  2019.   Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.. Annu Rev Cell Dev Biol. 35 :357-379 ▶ Go to Pubmed
Steven Cook, Travis Jarrell, Christopher Brittin, Yi Wang, Adam Bloniarz, Maksim Yakovlev, Ken Nguyen, Leo Tang, Emily Bayer, Janet Duerr, Hannes Bülow, Oliver Hobert, David Hall, Scott Emmons .  2019.   Whole-animal connectomes of both Caenorhabditis elegans sexes.. Nature. 571 (7763) :63-71 ▶ Go to Pubmed
Anna Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Justin Taylor, Robert Myers, Ghaith Abu-Zeinah, Ryan Brand, Nathaniel Omans, Alicia Alonso, Caroline Sheridan, Marisa Mariani, Xiaoguang Dai, Eoghan Harrington, Alessandro Pastore, Juan Cubillos-Ruiz, Wayne Tam, Ronald Hoffman, Raul Rabadan, Joseph Scandura, Omar Abdel-Wahab, Peter Smibert, Dan Landau .  2019.   Somatic mutations and cell identity linked by Genotyping of Transcriptomes.. Nature. 571 (7765) :355-360 ▶ Go to Pubmed
Tyler Joseph, Itsik Pe'er .  2019.   Inference of Population Structure from Time-Series Genotype Data.. Am J Hum Genet. 105 (2) :317-333 ▶ Go to Pubmed
Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke Baltissen, Federico Comoglio, Robin van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen Bussemaker, Bas van Steensel .  2019.   High-throughput identification of human SNPs affecting regulatory element activity.. Nat Genet. 51 (7) :1160-1169 ▶ Go to Pubmed
Wenji Ma, Jaeyop Lee, Daniel Backenroth, Yu Zhou, Erin Bush, Peter Sims, Kang Liu, Yufeng Shen .  2019.   Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose.. BMC Mol Cell Biol. 20 (1) :20 ▶ Go to Pubmed
Huijuan Feng, Suying Bao, Mohammad Rahman, Sebastien Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise Flynn, Adrian Krainer, Chaolin Zhang .  2019.   Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.. Mol Cell. 74 (6) :1189-1204.e6 ▶ Go to Pubmed
Benjamin Glicksberg, Boris Oskotsky, Phyllis Thangaraj, Nicholas Giangreco, Marcus Badgeley, Kipp Johnson, Debajyoti Datta, Vivek Rudrapatna, Nadav Rappoport, Mark Shervey, Riccardo Miotto, Theodore Goldstein, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel Dudley, Nicholas Tatonetti, Atul Butte .  2019.   PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.. Bioinformatics. ▶ Go to Pubmed
Ela Elyada, Mohan Bolisetty, Pasquale Laise, William Flynn, Elise Courtois, Richard Burkhart, Jonathan Teinor, Pascal Belleau, Giulia Biffi, Matthew Lucito, Santhosh Sivajothi, Todd Armstrong, Dannielle Engle, Kenneth Yu, Yuan Hao, Christopher Wolfgang, Youngkyu Park, Jonathan Preall, Elizabeth Jaffee, Andrea Califano, Paul Robson, David Tuveson .  2019.   Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.. Cancer Discov. 9 (8) :1102-1123 ▶ Go to Pubmed
Liat Shenhav, Mike Thompson, Tyler Joseph, Leah Briscoe, Ori Furman, David Bogumil, Itzhak Mizrahi, Itsik Pe'er, Eran Halperin .  2019.   FEAST: fast expectation-maximization for microbial source tracking.. Nat Methods. 16 (7) :627-632 ▶ Go to Pubmed
R Orenbuch, I Filip, D Comito, J Shaman, I Pe'er, R Rabadan .  2019.   arcasHLA: high resolution HLA typing from RNAseq.. Bioinformatics. ▶ Go to Pubmed
Maher Hanoun, Anna Arnal-Estapé, Maria Maryanovich, Ali Zahalka, Sarah Bergren, Chee Chua, Avigdor Leftin, Patrik Brodin, Michael Shen, Chandan Guha, Paul Frenette .  2019.   NestinNG2 Cells Form a Reserve Stem Cell Population in the Mouse Prostate.. Stem Cell Reports. 12 (6) :1201-1211 ▶ Go to Pubmed
Donna Farber, Peter Sims .  2019.   Dissecting lung development and fibrosis at single-cell resolution.. Genome Med. 11 (1) :33 ▶ Go to Pubmed
Benjamin Hobson, Peter Sims .  2019.   Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry.. eNeuro. 6 (3) ▶ Go to Pubmed
Leslie Beh, Galia Debelouchina, Derek Clay, Robert Thompson, Kelsi Lindblad, Elizabeth Hutton, John Bracht, Robert Sebra, Tom Muir, Laura Landweber .  2019.   Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.. Cell. 177 (7) :1781-1796.e25 ▶ Go to Pubmed
Stanley Ahalt, Christopher Chute, Karamarie Fecho, Gustavo Glusman, Jennifer Hadlock, Casey Taylor, Emily Pfaff, Peter Robinson, Harold Solbrig, Casey Ta, Nicholas Tatonetti, Chunhua Weng, Biomedical Consortium .  2019.   Clinical Data: Sources and Types, Regulatory Constraints, Applications.. Clin Transl Sci. 12 (4) :329-333 ▶ Go to Pubmed
Paola Nicoletti, Sarah Barrett, Laurence McEvoy, Ann Daly, Guruprasad Aithal, Isabel Lucena, Raul Andrade, Mia Wadelius, Pär Hallberg, Camilla Stephens, Einar Bjornsson, Peter Friedmann, Kati Kainu, Tarja Laitinen, Anthony Marson, Mariam Molokhia, Elizabeth Phillips, Werner Pichler, Antonino Romano, Neil Shear, Graeme Sills, Luciana Tanno, Ashley Swale, Aris Floratos, Yufeng Shen, Matthew Nelson, Paul Watkins, Mark Daly, Andrew Morris, Ana Alfirevic, Munir Pirmohamed .  2019.   Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.. Clin Pharmacol Ther. 106 (5) :1028-1036 ▶ Go to Pubmed
Paola Nicoletti, Sarah Barrett, Laurence McEvoy, Ann Daly, Guruprasad Aithal, Isabel Lucena, Raul Andrade, Mia Wadelius, Pär Hallberg, Camilla Stephens, Einar Bjornsson, Peter Friedmann, Kati Kainu, Tarja Laitinen, Anthony Marson, Mariam Molokhia, Elizabeth Phillips, Werner Pichler, Antonino Romano, Neil Shear, Graeme Sills, Luciana Tanno, Ashley Swale, Aris Floratos, Yufeng Shen, Matthew Nelson, Paul Watkins, Mark Daly, Andrew Morris, Ana Alfirevic, Munir Pirmohamed .  2019.   Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.. Clinical pharmacology and therapeutics. 106 (5) :1028-1036 ▶ Go to Pubmed
Jing Zhang, Francesca Caruso, Jason Sa, Sune Justesen, Do-Hyun Nam, Peter Sims, Michele Ceccarelli, Anna Lasorella, Antonio Iavarone .  2019.   The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival.. Commun Biol. 2 :135 ▶ Go to Pubmed
Ziyue Gao, Priya Moorjani, Thomas Sasani, Brent Pedersen, Aaron Quinlan, Lynn Jorde, Guy Amster, Molly Przeworski .  2019.   Overlooked roles of DNA damage and maternal age in generating human germline mutations.. Proc Natl Acad Sci U S A. 116 (19) :9491-9500 ▶ Go to Pubmed
Luciano Cascione, Andrea Rinaldi, Alessio Bruscaggin, Chiara Tarantelli, Alberto Arribas, Ivo Kwee, Lorenza Pecciarini, Afua Mensah, Valeria Spina, Elaine Chung, Lodovico di Bergamo, Stephan Dirnhofer, Alexandar Tzankov, Roberto Miranda, Kenneth Young, Alexandra Traverse-Glehen, Gianluca Gaidano, Steven Swerdlow, Randy Gascoyne, Raul Rabadan, Maurilio Ponzoni, Govind Bhagat, Davide Rossi, Emanuele Zucca, Francesco Bertoni .  2019.   Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses.. Haematologica. ▶ Go to Pubmed
Gloria Echeverria V, Zhongqi Ge, Sahil Seth, Xiaomei Zhang, Sabrina Jeter-Jones, Xinhui Zhou, Shirong Cai, Yizheng Tu, Aaron McCoy, Michael Peoples, Yuting Sun, Huan Qiu, Qing Chang, Christopher Bristow, Alessandro Carugo, Jiansu Shao, Xiaoyan Ma, Angela Harris, Prabhjot Mundi, Rosanna Lau, Vandhana Ramamoorthy, Yun Wu, Mariano Alvarez, Andrea Califano, Stacy Moulder, William Symmans, Joseph Marszalek, Timothy Heffernan, Jeffrey Chang, Helen Piwnica-Worms .  2019.   Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.. Sci Transl Med. 11 (488) ▶ Go to Pubmed
María Blasco, Carolina Navas, Guillermo Martín-Serrano, Osvaldo Graña-Castro, Carmen Lechuga, Laura Martín-Díaz, Magdolna Djurec, Jing Li, Lucia Morales-Cacho, Laura Esteban-Burgos, Javier Perales-Patón, Emilie Bousquet-Mur, Eva Castellano, Harrys Jacob, Lavinia Cabras, Monica Musteanu, Matthias Drosten, Sagrario Ortega, Francisca Mulero, Bruno Sainz, Nelson Dusetti, Juan Iovanna, Francisco Sanchez-Bueno, Manuel Hidalgo, Hossein Khiabanian, Raul Rabadan, Fátima Al-Shahrour, Carmen Guerra, Mariano Barbacid .  2019.   Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.. Cancer Cell. 35 (4) :573-587.e6 ▶ Go to Pubmed
David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal .  2019.   Structural variation in the gut microbiome associates with host health.. Nature. 568 (7750) :43-48 ▶ Go to Pubmed
Sohani Sharma, Jordan Metz, Hongyu Li, Benjamin Hobson, Nicholas Hornstein, David Sulzer, Guomei Tang, Peter Sims .  2019.   Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice.. Cell Rep. 26 (12) :3313-3322.e5 ▶ Go to Pubmed
Emily Slotkin, Daniel Diolaiti, Neerav Shukla, Filemon Cruz, Jennifer Clark, Gunes Gundem, Venkata Yellapantula, Max Levine, Daoqi You, Peilin Ma, Sagarika Pachhal, Glorymar Sanchez, Ryma Benayed, Achim Jungbluth, Lillian Smyth, Audrey Mauguen, Irena Gushterova, Hongxu Ding, Lee Spraggon, Robert Darnell, Andrea Califano, Marc Ladanyi, Elli Papaemmanuil, Andrew Kung, David Hyman, Stephen Roberts .  2019.   Patient-driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-driven Cancer.. Cancer Discov. ▶ Go to Pubmed
Mark Snyder, Michael Finlayson, Thomas Connors, Pranay Dogra, Takashi Senda, Erin Bush, Dustin Carpenter, Charles Marboe, Luke Benvenuto, Lori Shah, Hilary Robbins, Jaime Hook, Megan Sykes, Frank D'Ovidio, Matthew Bacchetta, Joshua Sonett, David Lederer, Selim Arcasoy, Peter Sims, Donna Farber .  2019.   Generation and persistence of human tissue-resident memory T cells in lung transplantation.. Sci Immunol. 4 (33) ▶ Go to Pubmed
Lalanti Venkatasubramanian, Richard Mann .  2019.   The development and assembly of the Drosophila adult ventral nerve cord.. Curr Opin Neurobiol. 56 :135-143 ▶ Go to Pubmed
Chen Wang, Oliver Hobert .  2019.   Sex-specific pheromone responses in .. EMBO Rep. 20 (3) ▶ Go to Pubmed
Marta Galanti, Ruthie Birger, Minhaz Ud-Dean, Ioan Filip, Haruka Morita, Devon Comito, Simon Anthony, Greg Freyer, Sadiat Ibrahim, Benjamin Lane, Chanel Ligon, Raul Rabadan, Atinuke Shittu, Eudosie Tagne, Jeffrey Shaman .  2019.   Longitudinal active sampling for respiratory viral infections across age groups.. Influenza Other Respir Viruses. ▶ Go to Pubmed
Junfei Zhao, Andrew Chen, Robyn Gartrell, Andrew Silverman, Luis Aparicio, Tim Chu, Darius Bordbar, David Shan, Jorge Samanamud, Aayushi Mahajan, Ioan Filip, Rose Orenbuch, Morgan Goetz, Jonathan Yamaguchi, Michael Cloney, Craig Horbinski, Rimas Lukas V, Jeffrey Raizer, Ali Rae, Jinzhou Yuan, Peter Canoll, Jeffrey Bruce, Yvonne Saenger, Peter Sims, Fabio Iwamoto, Adam Sonabend, Raul Rabadan .  2019.   Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.. Nat Med. 25 (3) :462-469 ▶ Go to Pubmed
Andrew Anzalone V, Sakellarios Zairis, Annie Lin, Raul Rabadan, Virginia Cornish .  2019.   Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection.. Biochemistry. 58 (8) :1167-1178 ▶ Go to Pubmed
Abhishek Bhattacharya, Ulkar Aghayeva, Emily Berghoff, Oliver Hobert .  2019.   Plasticity of the Electrical Connectome of C. elegans.. Cell. 176 (5) :1174-1189.e16 ▶ Go to Pubmed
Mythily Ganapathi, Leah Padgett, Kentaro Yamada, Orrin Devinsky, Rebecca Willaert, Richard Person, Ping-Yee Au, Julia Tagoe, Marie McDonald, Danielle Karlowicz, Barry Wolf, Joanna Lee, Yufeng Shen, Volkan Okur, Liyong Deng, Charles Leduc, Jiayao Wang, Ashleigh Hanner, Raghavendra Mirmira, Myung Park, Teresa Mastracci, Wendy Chung .  2019.   Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder.. Am J Hum Genet. 104 (2) :287-298 ▶ Go to Pubmed
Carlo Maurer, Sam Holmstrom, Jing He, Pasquale Laise, Tao Su, Aqeel Ahmed, Hanina Hibshoosh, John Chabot, Paul Oberstein, Antonia Sepulveda, Jeanine Genkinger, Jiapeng Zhang, Alina Iuga, Mukesh Bansal, Andrea Califano, Kenneth Olive .  2019.   Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes.. Gut. ▶ Go to Pubmed
Hannah Klein, Giedrė Bačinskaja, Jun Che, Anais Cheblal, Rajula Elango, Anastasiya Epshtein, Devon Fitzgerald, Belén Gómez-González, Sharik Khan, Sandeep Kumar, Bryan Leland, Léa Marie, Qian Mei, Judith Miné-Hattab, Alicja Piotrowska, Erica Polleys, Christopher Putnam, Elina Radchenko, Anissia Saada, Cynthia Sakofsky, Eun Shim, Mathew Stracy, Jun Xia, Zhenxin Yan, Yi Yin, Andrés Aguilera, Juan Argueso, Catherine Freudenreich, Susan Gasser, Dmitry Gordenin, James Haber, Grzegorz Ira, Sue Jinks-Robertson, Megan King, Richard Kolodner, Andrei Kuzminov, Sarah Lambert, Sang Lee, Kyle Miller, Sergei Mirkin, Thomas Petes, Susan Rosenberg, Rodney Rothstein, Lorraine Symington, Pawel Zawadzki, Nayun Kim, Michael Lisby, Anna Malkova .  2019.   Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.. Microb Cell. 6 (1) :1-64 ▶ Go to Pubmed
Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kustagi, Archana Iyer, Michael Comb, Michael White, John Minna, Andrea Califano .  2019.   Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.. PLoS One. 14 (1) :e0208646 ▶ Go to Pubmed
Jinzhou Yuan, Jenny Sheng, Peter Sims .  2018.   SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.. Genome Biol. 19 (1) :227 ▶ Go to Pubmed
Agnieszka Wendorff, Aidan Quinn, Marissa Rashkovan, Chioma Madubata, Alberto Ambesi-Impiombato, Mark Litzow, Martin Tallman, Elisabeth Paietta, Maddalena Paganin, Giuseppe Basso, Julie Gastier-Foster, Mignon Loh, Raul Rabadan, Pieter Van Vlierberghe, Adolfo Ferrando .  2018.   Phf6 loss enhances HSC self-renewal driving tumor initiation and leukemia stem cell activity in T-ALL.. Cancer Discov. ▶ Go to Pubmed
Jason Sa, Seung Choi, Junfei Zhao, Yeri Lee, Jing Zhang, Doo-Sik Kong, Jung Choi, Ho Seol, Jung-Il Lee, Antonio Iavarone, Raul Rabadan, Do-Hyun Nam .  2018.   Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.. Int J Cancer. ▶ Go to Pubmed
Antonio Moretti, Andrew Stirn, Gabriel Marks, Itsik Pe'er .  2018.   Autoencoding Topographic Factors.. J Comput Biol. ▶ Go to Pubmed
Alvaro Aytes, Arianna Giacobbe, Antonina Mitrofanova, Katia Ruggero, Joanna Cyrta, Juan Arriaga, Luis Palomero, Sonia Farran-Matas, Mark Rubin, Michael Shen, Andrea Califano, Cory Abate-Shen .  2018.   NSD2 is a conserved driver of metastatic prostate cancer progression.. Nat Commun. 9 (1) :5201 ▶ Go to Pubmed
Sonja Billerbeck, James Brisbois, Neta Agmon, Miguel Jimenez, Jasmine Temple, Michael Shen, Jef Boeke, Virginia Cornish .  2018.   A scalable peptide-GPCR language for engineering multicellular communication.. Nat Commun. 9 (1) :5057 ▶ Go to Pubmed
Tonći Šuštić, Sake van Wageningen, Evert Bosdriesz, Robert Reid, John Dittmar, Cor Lieftink, Roderick Beijersbergen, Lodewyk Wessels, Rodney Rothstein, René Bernards .  2018.   A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.. Genome Med. 10 (1) :90 ▶ Go to Pubmed
Casey Ta, Michel Dumontier, George Hripcsak, Nicholas Tatonetti, Chunhua Weng .  2018.   Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records.. Sci Data. 5 :180273 ▶ Go to Pubmed
Filip Cosmanescu, Phinikoula Katsamba, Alina Sergeeva, Goran Ahlsen, Saurabh Patel, Joshua Brewer, Liming Tan, Shuwa Xu, Qi Xiao, Sonal Nagarkar-Jaiswal, Aljoscha Nern, Hugo Bellen, Lawrence Zipursky, Barry Honig, Lawrence Shapiro .  2018.   Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins.. Neuron. 100 (6) :1385-1400.e6 ▶ Go to Pubmed
Shuwa Xu, Qi Xiao, Filip Cosmanescu, Alina Sergeeva, Juyoun Yoo, Ying Lin, Phinikoula Katsamba, Goran Ahlsen, Jonathan Kaufman, Nikhil Linaval, Pei-Tseng Lee, Hugo Bellen, Lawrence Shapiro, Barry Honig, Liming Tan, Lawrence Zipursky .  2018.   Interactions between the Ig-Superfamily Proteins DIP-α and Dpr6/10 Regulate Assembly of Neural Circuits.. Neuron. 100 (6) :1369-1384.e6 ▶ Go to Pubmed
Ahrim Youn, Kyung Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen, Shuang Wang .  2018.   A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.. BMC Med Genomics. 11 (1) :98 ▶ Go to Pubmed
Alireza Khatamian, Evan Paull, Andrea Califano, Jiyang Yu .  2018.   SJARACNe: a scalable software tool for gene network reverse engineering from big data.. Bioinformatics. ▶ Go to Pubmed
Maria Sapienza, Francesco Abate, Federica Melle, Stefania Orecchioni, Fabio Fuligni, Maryam Etebari, Valentina Tabanelli, Maria Laginestra, Alessandro Pileri, Giovanna Motta, Maura Rossi, Claudio Agostinelli, Elena Sabattini, Nicola Pimpinelli, Mauro Truni, Brunangelo Falini, Lorenzo Cerroni, Giovanna Talarico, Rossana Piccioni, Stefano Amente, Valentina Indio, Giuseppe Tarantino, Francesco Brundu, Marco Paulli, Emilio Berti, Fabio Facchetti, Gaetano Dellino, Francesco Bertolini, Claudio Tripodo, Raul Rabadan, Stefano Pileri .  2018.   Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target.. Haematologica. ▶ Go to Pubmed
Leah Zagore, Thomas Sweet, Molly Hannigan, Sebastien Weyn-Vanhentenryck, Raul Jobava, Maria Hatzoglou, Chaolin Zhang, Donny Licatalosi .  2018.   DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions.. Cell Rep. 25 (5) :1225-1240.e6 ▶ Go to Pubmed
Huiyi Liang, Bo Peng, Cong Dong, Lixin Liu, Jiaji Mao, Song Wei, Xinlu Wang, Hanshi Xu, Jun Shen, Hai-Quan Mao, Xiaohu Gao, Kam Leong, Yongming Chen .  2018.   Cationic nanoparticle as an inhibitor of cell-free DNA-induced inflammation.. Nat Commun. 9 (1) :4291 ▶ Go to Pubmed
Yaniv Erlich, Tal Shor, Itsik Pe'er, Shai Carmi .  2018.   Identity inference of genomic data using long-range familial searches.. Science. 362 (6415) :690-694 ▶ Go to Pubmed
Elizabeth Brunk, Roger Chang, Jing Xia, Hooman Hefzi, James Yurkovich, Donghyuk Kim, Evan Buckmiller, Harris Wang, Byung-Kwan Cho, Chen Yang, Bernhard Palsson, George Church, Nathan Lewis .  2018.   Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.. Proc Natl Acad Sci U S A. 115 (43) :11096-11101 ▶ Go to Pubmed
Paschalis Kratsios, Oliver Hobert .  2018.   Nervous System Development: Flies and Worms Converging on Neuron Identity Control.. Curr Biol. 28 (19) :R1154-R1157 ▶ Go to Pubmed
Jia Li, Michael Shen .  2018.   Prostate Stem Cells and Cancer Stem Cells.. Cold Spring Harb Perspect Med. ▶ Go to Pubmed
Clémentine Le Magnen, Renu Virk, Aditya Dutta, Jaime Kim, Sukanya Panja, Zoila Lopez-Bujanda, Andrea Califano, Charles Drake, Antonina Mitrofanova, Cory Abate-Shen .  2018.   Cooperation of loss of and inflammation in prostate cancer initiation.. Dis Model Mech. 11 (11) ▶ Go to Pubmed
Jin-Ku Lee, Zhaoqi Liu, Jason Sa, Sang Shin, Jiguang Wang, Mykola Bordyuh, Hee Cho, Oliver Elliott, Timothy Chu, Seung Choi, Daniel Rosenbloom, In-Hee Lee, Yong Shin, Hyun Kang, Donggeon Kim, Sun Kim, Moon-Hee Sim, Jusun Kim, Taehyang Lee, Yun Seo, Hyemi Shin, Mijeong Lee, Sung Kim, Yong-Jun Kwon, Jeong-Woo Oh, Minsuk Song, Misuk Kim, Doo-Sik Kong, Jung Choi, Ho Seol, Jung-Il Lee, Seung Kim, Joon Park, Kyoung-Mee Kim, Sang-Yong Song, Jeong-Won Lee, Hee-Cheol Kim, Jeong Lee, Min Choi, Sung Seo, Young Shim, Jae Zo, Byong Jeong, Yeup Yoon, Gyu Ryu, Nayoung Kim, Joon Bae, Woong-Yang Park, Jeongwu Lee, Roel Verhaak, Antonio Iavarone, Jeeyun Lee, Raul Rabadan, Do-Hyun Nam .  2018.   Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.. Nat Genet. 50 (10) :1399-1411 ▶ Go to Pubmed
Khader Shameer, Mercedes Perez-Rodriguez, Roy Bachar, Li Li, Amy Johnson, Kipp Johnson, Benjamin Glicksberg, Milo Smith, Ben Readhead, Joseph Scarpa, Jebakumar Jebakaran, Patricia Kovatch, Sabina Lim, Wayne Goodman, David Reich, Andrew Kasarskis, Nicholas Tatonetti, Joel Dudley .  2018.   Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining.. BMC Med Inform Decis Mak. 18 (Suppl 3) :79 ▶ Go to Pubmed
Tyler Risom, Ellen Langer, Margaret Chapman, Juha Rantala, Andrew Fields, Christopher Boniface, Mariano Alvarez, Nicholas Kendsersky, Carl Pelz, Katherine Johnson-Camacho, Lacey Dobrolecki, Koei Chin, Anil Aswani, Nicholas Wang, Andrea Califano, Michael Lewis, Claire Tomlin, Paul Spellman, Andrew Adey, Joe Gray, Rosalie Sears .  2018.   Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.. Nat Commun. 9 (1) :3815 ▶ Go to Pubmed
Nako Nakatsuka, Kyung-Ae Yang, John Abendroth, Kevin Cheung, Xiaobin Xu, Hongyan Yang, Chuanzhen Zhao, Bowen Zhu, You Rim, Yang Yang, Paul Weiss, Milan Stojanovic, Anne Andrews .  2018.   Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing.. Science. 362 (6412) :319-324 ▶ Go to Pubmed
Michael Smith, Eric Bryant, Rodney Rothstein .  2018.   Increased chromosomal mobility after DNA damage is controlled by interactions between the recombination machinery and the checkpoint.. Genes Dev. 32 (17-18) :1242-1251 ▶ Go to Pubmed
Tim Zeiske, Nithya Baburajendran, Anna Kaczynska, Julia Brasch, Arthur Palmer, Lawrence Shapiro, Barry Honig, Richard Mann .  2018.   Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.. Cell Rep. 24 (9) :2221-2230 ▶ Go to Pubmed
Emily Bayer, Oliver Hobert .  2018.   Past experience shapes sexually dimorphic neuronal wiring through monoaminergic signalling.. Nature. 561 (7721) :117-121 ▶ Go to Pubmed
Tracey Goldstein, Simon Anthony, Aiah Gbakima, Brian Bird, James Bangura, Alexandre Tremeau-Bravard, Manjunatha Belaganahalli, Heather Wells, Jasjeet Dhanota, Eliza Liang, Michael Grodus, Rohit Jangra, Veronica DeJesus, Gorka Lasso, Brett Smith, Amara Jambai, Brima Kamara, Sorie Kamara, William Bangura, Corina Monagin, Sagi Shapira, Christine Johnson, Karen Saylors, Edward Rubin, Kartik Chandran, Ian Lipkin, Jonna Mazet .  2018.   The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses.. Nat Microbiol. 3 (10) :1084-1089 ▶ Go to Pubmed
Susan Newcomb, Roumen Voutev, Aurelie Jory, Rebecca Delker, Matthew Slattery, Richard Mann .  2018.   cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg.. PLoS Genet. 14 (8) :e1007568 ▶ Go to Pubmed
Estibaliz Castillero, Ziad Ali, Hirokazu Akashi, Nicholas Giangreco, Catherine Wang, Eric Stöhr, Ruiping Ji, Xiaokan Zhang, Nathaniel Kheysin, Joo-Eun Park, Sheetal Hegde, Sanatkumar Patel, Samantha Stein, Carlos Cuenca, Diana Leung, Shunichi Homma, Nicholas Tatonetti, Veli Topkara, Koji Takeda, Paolo Colombo, Yoshifumi Naka, Lee Sweeney, Christian Schulze, Isaac George .  2018.   Structural and Functional Cardiac Profile after Prolonged Duration of Mechanical Unloading: Potential Implications for Myocardial Recovery.. Am J Physiol Heart Circ Physiol. ▶ Go to Pubmed
Stephane Castel, Alejandra Cervera, Pejman Mohammadi, François Aguet, Ferran Reverter, Aaron Wolman, Roderic Guigo, Ivan Iossifov, Ana Vasileva, Tuuli Lappalainen .  2018.   Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk.. Nat Genet. 50 (9) :1327-1334 ▶ Go to Pubmed
Yuan Yuan, Shirley Xie, Jennifer Darnell, Andrew Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth Murphy, Chaolin Zhang, Tom Maniatis, Robert Darnell .  2018.   Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons.. Genome Biol. 19 (1) :117 ▶ Go to Pubmed
Susan DeWolf, Boris Grinshpun, Thomas Savage, Sai Lau, Aleksandar Obradovic, Brittany Shonts, Suxiao Yang, Heather Morris, Julien Zuber, Robert Winchester, Megan Sykes, Yufeng Shen .  2018.   Quantifying size and diversity of the human T cell alloresponse.. JCI Insight. 3 (15) ▶ Go to Pubmed
Hee Cho, Junfei Zhao, Sang Jung, Erik Ladewig, Doo-Sik Kong, Yeon-Lim Suh, Yeri Lee, Donggeon Kim, Sun Ahn, Mykola Bordyuh, Hyun Kang, Jason Sa, Yun Seo, Sung Kim, Do Lim, Yun-Sik Dho, Jung-Il Lee, Ho Seol, Jung Choi, Woong-Yang Park, Chul-Kee Park, Raul Rabadan, Do-Hyun Nam .  2018.   Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma.. Neuro Oncol. ▶ Go to Pubmed
Gilman Dionne, Xufeng Qiu, Micah Rapp, Xiaoping Liang, Bo Zhao, Guihong Peng, Phinikoula Katsamba, Goran Ahlsen, Rotem Rubinstein, Clinton Potter, Bridget Carragher, Barry Honig, Ulrich Müller, Lawrence Shapiro .  2018.   Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture.. Neuron. 99 (3) :480-492.e5 ▶ Go to Pubmed
Fabrizio Spagnolo, Pierre Cristofari, Nicholas Tatonetti, Lev Ginzburg, Daniel Dykhuizen .  2018.   Pathogen population structure can explain hospital outbreaks.. ISME J. 12 (12) :2835-2843 ▶ Go to Pubmed
Raul Rabadan, Gyan Bhanot, Sonia Marsilio, Nicholas Chiorazzi, Laura Pasqualucci, Hossein Khiabanian .  2018.   On statistical modeling of sequencing noise in high depth data to assess tumor evolution.. J Stat Phys. 172 (1) :143-155 ▶ Go to Pubmed
Zeynep Coban-Akdemir, Janson White, Xiaofei Song, Shalini Jhangiani, Jawid Fatih, Tomasz Gambin, Yavuz Bayram, Ivan Chinn, Ender Karaca, Jaya Punetha, Cecilia Poli, Baylor-Hopkins Genomics, Eric Boerwinkle, Chad Shaw, Jordan Orange, Richard Gibbs, Tuuli Lappalainen, James Lupski, Claudia Carvalho .  2018.   Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles.. Am J Hum Genet. 103 (2) :171-187 ▶ Go to Pubmed
Na Zhu, Carrie Welch, Jiayao Wang, Philip Allen, Claudia Gonzaga-Jauregui, Lijiang Ma, Alejandra King, Usha Krishnan, Erika Rosenzweig, Dunbar Ivy, Eric Austin, Rizwan Hamid, Michael Pauciulo, Katie Lutz, William Nichols, Jeffrey Reid, John Overton, Aris Baras, Frederick Dewey, Yufeng Shen, Wendy Chung .  2018.   Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease.. Genome Med. 10 (1) :56 ▶ Go to Pubmed
Dmytro Ustianenko, Hua-Sheng Chiu, Thomas Treiber, Sebastien Weyn-Vanhentenryck, Nora Treiber, Gunter Meister, Pavel Sumazin, Chaolin Zhang .  2018.   LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.. Mol Cell. 71 (2) :271-283.e5 ▶ Go to Pubmed
Patrick Cimino, Lisa McFerrin, Hans-Georg Wirsching, Sonali Arora, Hamid Bolouri, Raul Rabadan, Michael Weller, Eric Holland .  2018.   Copy number profiling across glioblastoma populations has implications for clinical trial design.. Neuro Oncol. 20 (10) :1368-1373 ▶ Go to Pubmed
Ehud Herbst, Pedro Baldera-Aguayo, Hyunwook Lee, Virginia Cornish .  2018.   A Yeast Three Hybrid Assay for Metabolic Engineering of Tetracycline Derivatives.. Biochemistry. 57 (31) :4726-4734 ▶ Go to Pubmed
Yun Hao, Kayla Quinnies, Ronald Realubit, Charles Karan, Nicholas Tatonetti .  2018.   Tissue-Specific Analysis of Pharmacological Pathways.. CPT Pharmacometrics Syst Pharmacol. ▶ Go to Pubmed
Mariano Alvarez, Prem Subramaniam, Laura Tang, Adina Grunn, Mahalaxmi Aburi, Gabrielle Rieckhof, Elena Komissarova V, Elizabeth Hagan, Lisa Bodei, Paul Clemons, Filemon Cruz, Deepti Dhall, Daniel Diolaiti, Douglas Fraker, Afshin Ghavami, Daniel Kaemmerer, Charles Karan, Mark Kidd, Kyoung Kim, Hee Kim, Lakshmi Kunju, Ülo Langel, Zhong Li, Jeeyun Lee, Hai Li, Virginia LiVolsi, Roswitha Pfragner, Allison Rainey, Ronald Realubit, Helen Remotti, Jakob Regberg, Robert Roses, Anil Rustgi, Antonia Sepulveda, Stefano Serra, Chanjuan Shi, Xiaopu Yuan, Massimo Barberis, Roberto Bergamaschi, Arul Chinnaiyan, Tony Detre, Shereen Ezzat, Andrea Frilling, Merten Hommann, Dirk Jaeger, Michelle Kim, Beatrice Knudsen, Andrew Kung, Emer Leahy, David Metz, Jeffrey Milsom, Young Park, Diane Reidy-Lagunes, Stuart Schreiber, Kay Washington, Bertram Wiedenmann, Irvin Modlin, Andrea Califano .  2018.   A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.. Nat Genet. ▶ Go to Pubmed
Víctor Arrieta, Bernardo Cacho-Díaz, Junfei Zhao, Raul Rabadan, Li Chen, Adam Sonabend .  2018.   The possibility of cancer immune editing in gliomas. A critical review.. Oncoimmunology. 7 (7) :e1445458 ▶ Go to Pubmed
Shuobo Boboila, Gonzalo Lopez, Jiyang Yu, Debarshi Banerjee, Angela Kadenhe-Chiweshe, Eileen Connolly, Jessica Kandel, Presha Rajbhandari, Jose Silva, Andrea Califano, Darrell Yamashiro .  2018.   Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma.. Oncogene. ▶ Go to Pubmed
Sebastien Weyn-Vanhentenryck, Huijuan Feng, Dmytro Ustianenko, Rachel Duffié, Qinghong Yan, Martin Jacko, Jose Martinez, Marianne Goodwin, Xuegong Zhang, Ulrich Hengst, Stavros Lomvardas, Maurice Swanson, Chaolin Zhang .  2018.   Precise temporal regulation of alternative splicing during neural development.. Nat Commun. 9 (1) :2189 ▶ Go to Pubmed
Xinwei Han, Siying Chen, Elise Flynn, Shuang Wu, Dana Wintner, Yufeng Shen .  2018.   Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders.. Nat Commun. 9 (1) :2138 ▶ Go to Pubmed
Yuan Pan, Christina Duron, Erin Bush, Yu Ma, Peter Sims, David Gutmann, Ami Radunskaya, Johanna Hardin .  2018.   Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma.. PLoS One. 13 (5) :e0190001 ▶ Go to Pubmed
Fernanda Polubriaginof, Rami Vanguri, Kayla Quinnies, Gillian Belbin, Alexandre Yahi, Hojjat Salmasian, Tal Lorberbaum, Victor Nwankwo, Li Li, Mark Shervey, Patricia Glowe, Iuliana Ionita-Laza, Mary Simmerling, George Hripcsak, Suzanne Bakken, David Goldstein, Krzysztof Kiryluk, Eimear Kenny, Joel Dudley, David Vawdrey, Nicholas Tatonetti .  2018.   Disease Heritability Inferred from Familial Relationships Reported in Medical Records.. Cell. 173 (7) :1692-1704.e11 ▶ Go to Pubmed
Julia Brasch, Phinikoula Katsamba, Oliver Harrison, Goran Ahlsen, Regina Troyanovsky, Indrajyoti Indra, Anna Kaczynska, Benjamin Kaeser, Sergey Troyanovsky, Barry Honig, Lawrence Shapiro .  2018.   Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior.. Cell Rep. 23 (6) :1840-1852 ▶ Go to Pubmed