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2018

2018 Publications

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
Ravi Sheth, Harris Wang .  2018.   DNA-based memory devices for recording cellular events.. Nature reviews. Genetics. 19 (11) :718-732 ▶ 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
Stephanie Pavlovich, Sean Lovett, Galina Koroleva, Jonathan Guito, Catherine Arnold, Elyse Nagle, Kirsten Kulcsar, Albert Lee, Francoise Thibaud-Nissen, Adam Hume, Elke Mühlberger, Luke Uebelhoer, Jonathan Towner, Raul Rabadan, Mariano Sanchez-Lockhart, Thomas Kepler, Gustavo Palacios .  2018.   The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity.. Cell. 173 (5) :1098-1110.e18 ▶ Go to Pubmed
Hua-Sheng Chiu, María Martínez, Elena Komissarova V, David Llobet-Navas, Mukesh Bansal, Evan Paull, Jose Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano .  2018.   The number of titrated microRNA species dictates ceRNA regulation.. Nucleic Acids Res. 46 (9) :4354-4369 ▶ Go to Pubmed
Neda Masoudi, Saeed Tavazoie, Lori Glenwinkel, Leesun Ryu, Kyuhyung Kim, Oliver Hobert .  2018.   Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity.. PLoS Biol. 16 (4) :e2004979 ▶ Go to Pubmed
Hongxu Ding, Eugene Douglass, Adam Sonabend, Angeliki Mela, Sayantan Bose, Christian Gonzalez, Peter Canoll, Peter Sims, Mariano Alvarez, Andrea Califano .  2018.   Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.. Nat Commun. 9 (1) :1471 ▶ Go to Pubmed
Juan Arriaga, Cory Abate-Shen .  2018.   Genetically Engineered Mouse Models of Prostate Cancer in the Postgenomic Era.. Cold Spring Harb Perspect Med. ▶ Go to Pubmed
Weijun Luo, Chaolin Zhang, Yong-Hui Jiang, Cory Brouwer .  2018.   Systematic reconstruction of autism biology from massive genetic mutation profiles.. Sci Adv. 4 (4) :e1701799 ▶ Go to Pubmed
Enrico Tiacci, Erik Ladewig, Gianluca Schiavoni, Alex Penson, Elisabetta Fortini, Valentina Pettirossi, Yuchun Wang, Ariele Rosseto, Alessandra Venanzi, Sofija Vlasevska, Roberta Pacini, Simonetta Piattoni, Alessia Tabarrini, Alessandra Pucciarini, Barbara Bigerna, Alessia Santi, Alessandro Gianni, Simonetta Viviani, Antonello Cabras, Stefano Ascani, Barbara Crescenzi, Cristina Mecucci, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini .  2018.   Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.. Blood. 131 (22) :2454-2465 ▶ Go to Pubmed
Patrick Cimino, Youngmi Kim, Hua-Jun Wu, Jes Alexander, Hans-Georg Wirsching, Frank Szulzewsky, Ken Pitter, Tatsuya Ozawa, Jiguang Wang, Julio Vazquez, Sonali Arora, Raul Rabadan, Ross Levine, Franziska Michor, Eric Holland .  2018.   Increased expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.. Genes Dev. 32 (7-8) :512-523 ▶ Go to Pubmed
Marcella Cesana, Michael Guo, Davide Cacchiarelli, Lara Wahlster, Jessica Barragan, Sergei Doulatov, Linda Vo, Beatrice Salvatori, Cole Trapnell, Kendell Clement, Patrick Cahan, Kaloyan Tsanov, Patricia Sousa, Barbara Tazon-Vega, Adriano Bolondi, Federico Giorgi, Andrea Califano, John Rinn, Alexander Meissner, Joel Hirschhorn, George Daley .  2018.   A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.. Cell Stem Cell. 22 (4) :575-588.e7 ▶ Go to Pubmed
Suk Lee, Wenhuo Hu, Justin Matulay, Mark Silva V, Tomasz Owczarek, Kwanghee Kim, Chee Chua, Lamont Barlow, Cyriac Kandoth, Alanna Williams, Sarah Bergren, Eugene Pietzak, Christopher Anderson, Mitchell Benson, Jonathan Coleman, Barry Taylor, Cory Abate-Shen, James McKiernan, Hikmat Al-Ahmadie, David Solit, Michael Shen .  2018.   Tumor Evolution and Drug Response in Patient-Derived Organoid Models of Bladder Cancer.. Cell. 173 (2) :515-528.e17 ▶ Go to Pubmed
Peter Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie .  2018.   Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.. Elife. 7 ▶ Go to Pubmed
Hanna Levitin, Jinzhou Yuan, Peter Sims .  2018.   Single-Cell Transcriptomic Analysis of Tumor Heterogeneity.. Trends Cancer. 4 (4) :264-268 ▶ Go to Pubmed
Hongxu Ding, Wanxin Wang, Andrea Califano .  2018.   iterClust: a statistical framework for iterative clustering analysis.. Bioinformatics. ▶ Go to Pubmed
Jasper Braun, Lukas Nabergall, Rafik Neme, Laura Landweber, Masahico Saito, Nataša Jonoska .  2018.   Russian Doll Genes and Complex Chromosome Rearrangements in.. G3 (Bethesda). ▶ Go to Pubmed
Roumen Voutev, Richard Mann .  2018.   Robust ΦC31-Mediated Genome Engineering inUsing Minimal attP/attB Phage Sites.. G3 (Bethesda). ▶ Go to Pubmed
Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, Ruth Rodriguez-Barrueco, Daniel Martinez, Mark Yarmarkovich, Nina Weichert-Leahey, Brian Abraham, Mariano Alvarez, Archana Iyer, Jo Harenza, Derek Oldridge, Katleen De Preter, Jan Koster, Shahab Asgharzadeh, Robert Seeger, Jun Wei, Javed Khan, Jo Vandesompele, Pieter Mestdagh, Rogier Versteeg, Thomas Look, Richard Young, Antonio Iavarone, Anna Lasorella, Jose Silva, John Maris, Andrea Califano .  2018.   Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma.. Cancer Discov. ▶ Go to Pubmed
Tomas Rube, Chaitanya Rastogi, Judith Kribelbauer, Harmen Bussemaker .  2018.   A unified approach for quantifying and interpreting DNA shape readout by transcription factors.. Mol Syst Biol. 14 (2) :e7902 ▶ Go to Pubmed
Robyn Gartrell, Douglas Marks, Thomas Hart, Gen Li, Danielle Davari, Alan Wu, Zoë Blake, Yan Lu, Kayleigh Askin, Anthea Monod, Camden Esancy, Edward Stack, Dan Jia, Paul Armenta, Yichun Fu, Daisuke Izaki, Bret Taback, Raul Rabadan, Howard Kaufman, Charles Drake, Basil Horst, Yvonne Saenger .  2018.   Quantitative Analysis of Immune Infiltrates in Primary Melanoma.. Cancer Immunol Res. ▶ Go to Pubmed
Joseph Juliano, Orlando Gil, Andrea Hawkins-Daarud, Sonal Noticewala, Russell Rockne, Jill Gallaher, Susan Massey, Peter Sims, Alexander Anderson, Kristin Swanson, Peter Canoll .  2018.   Comparative dynamics of microglial and glioma cell motility at the infiltrative margin of brain tumours.. J R Soc Interface. 15 (139) ▶ Go to Pubmed
Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana Garofalo, Dina Balderes, Lori Sussel, Kenneth Olive, Raul Rabadan .  2018.   Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma.. Gut. ▶ Go to Pubmed
Xichen Bao, Xiangpeng Guo, Menghui Yin, Muqddas Tariq, Yiwei Lai, Shahzina Kanwal, Jiajian Zhou, Na Li, Yuan Lv, Carlos Pulido-Quetglas, Xiwei Wang, Lu Ji, Muhammad Khan, Xihua Zhu, Zhiwei Luo, Changwei Shao, Do-Hwan Lim, Xiao Liu, Nan Li, Wei Wang, Minghui He, Yu-Lin Liu, Carl Ward, Tong Wang, Gong Zhang, Dongye Wang, Jianhua Yang, Yiwen Chen, Chaolin Zhang, Ralf Jauch, Yun-Gui Yang, Yangming Wang, Baoming Qin, Minna-Liisa Anko, Andrew Hutchins, Hao Sun, Huating Wang, Xiang-Dong Fu, Biliang Zhang, Miguel Esteban .  2018.   Capturing the interactome of newly transcribed RNA.. Nat Methods. 15 (3) :213-220 ▶ Go to Pubmed
Kathryn Manheimer, Felix Richter, Lisa Edelmann, Sunita D'Souza, Lisong Shi, Yufeng Shen, Jason Homsy, Marko Boskovski, Angela Tai, Joshua Gorham, Christopher Yasso, Elizabeth Goldmuntz, Martina Brueckner, Richard Lifton, Wendy Chung, Christine Seidman, J Seidman, Bruce Gelb .  2018.   Robust identification of mosaic variants in congenital heart disease.. Hum Genet. 137 (2) :183-193 ▶ Go to Pubmed
Satyanarayan Rao, Tsu-Pei Chiu, Judith Kribelbauer, Richard Mann, Harmen Bussemaker, Remo Rohs .  2018.   Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.. Epigenetics Chromatin. 11 (1) :6 ▶ Go to Pubmed
Martin Jacko, Sebastien Weyn-Vanhentenryck, John Smerdon, Rui Yan, Huijuan Feng, Damian Williams, Joy Pai, Ke Xu, Hynek Wichterle, Chaolin Zhang .  2018.   Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly.. Neuron. ▶ Go to Pubmed
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