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2009

2009 Publications

A Mugler, E Ziv, I Nemenman, C Wiggins .  2009.   Quantifying evolvability in small biological networks.. IET Syst Biol. 3 (5) :379-87 ▶ Go to Pubmed
Spiro Pantazatos, Jianrong Li, Paul Pavlidis, Yves Lussier .  2009.   Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes.. Cancer Inform. 8 :75-94 ▶ Go to Pubmed
Mariano Alvarez, Pavel Sumazin, Presha Rajbhandari, Andrea Califano .  2009.   Correlating measurements across samples improves accuracy of large-scale expression profile experiments.. Genome Biol. 10 (12) :R143 ▶ Go to Pubmed
Hossein Khiabanian, Vladimir Trifonov, Raul Rabadan .  2009.   Reassortment patterns in Swine influenza viruses.. PLoS Curr. 1 :RRN1008 ▶ Go to Pubmed
Philip Effraim, Jiangning Wang, Michael Englander, Josh Avins, Thomas Leyh, Ruben Gonzalez, Virginia Cornish .  2009.   Natural amino acids do not require their native tRNAs for efficient selection by the ribosome.. Nat Chem Biol. 5 (12) :947-53 ▶ Go to Pubmed
Andrew Mugler, Aleksandra Walczak, Chris Wiggins .  2009.   Spectral solutions to stochastic models of gene expression with bursts and regulation.. Phys Rev E Stat Nonlin Soft Matter Phys. 80 (4 Pt 1) :041921 ▶ Go to Pubmed
Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen Millen, Andrey Rzhetsky .  2009.   Looking at cerebellar malformations through text-mined interactomes of mice and humans.. PLoS Comput Biol. 5 (11) :e1000559 ▶ Go to Pubmed
Bo-Juen Chen, Helen Causton, Denesy Mancenido, Noel Goddard, Ethan Perlstein, Dana Pe'er .  2009.   Harnessing gene expression to identify the genetic basis of drug resistance.. Mol Syst Biol. 5 :310 ▶ Go to Pubmed
Remo Rohs, Sean West, Alona Sosinsky, Peng Liu, Richard Mann, Barry Honig .  2009.   The role of DNA shape in protein-DNA recognition.. Nature. 461 (7268) :1248-53 ▶ Go to Pubmed
Hossein Khiabanian, Vladimir Trifonov, Raul Rabadan .  2009.   Reassortment patterns in Swine influenza viruses.. PLoS One. 4 (10) :e7366 ▶ Go to Pubmed
Donald Petrey, Markus Fischer, Barry Honig .  2009.   Structural relationships among proteins with different global topologies and their implications for function annotation strategies.. Proc Natl Acad Sci U S A. 106 (41) :17377-82 ▶ Go to Pubmed
Kai Wang, Masumichi Saito, Brygida Bisikirska, Mariano Alvarez, Wei Lim, Presha Rajbhandari, Qiong Shen, Ilya Nemenman, Katia Basso, Adam Margolin, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano .  2009.   Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.. Nat Biotechnol. 27 (9) :829-39 ▶ Go to Pubmed
Hossein Khiabanian, Gregory Farrell, Kirsten St George, Raul Rabadan .  2009.   Differences in patient age distribution between influenza A subtypes.. PLoS One. 4 (8) :e6832 ▶ Go to Pubmed
Xudong Zhao, Domenico Arca, Wei Lim, Manisha Brahmachary, Maria Carro, Thomas Ludwig, Carlos Cardo, Francois Guillemot, Ken Aldape, Andrea Califano, Antonio Iavarone, Anna Lasorella .  2009.   The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain.. Dev Cell. 17 (2) :210-21 ▶ Go to Pubmed
Harris Wang, Farren Isaacs, Peter Carr, Zachary Sun, George Xu, Craig Forest, George Church .  2009.   Programming cells by multiplex genome engineering and accelerated evolution.. Nature. 460 (7257) :894-898 ▶ Go to Pubmed
Phinikoula Katsamba, Kilpatrick Carroll, Goran Ahlsen, Fabiana Bahna, Jeremie Vendome, Shoshana Posy, M Rajebhosale, Stephen Price, Thomas Jessell, Avinoam Ben-Shaul, Lawrence Shapiro, Barry Honig .  2009.   Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.. Proc Natl Acad Sci U S A. 106 (28) :11594-9 ▶ Go to Pubmed
Masumichi Saito, Urban Novak, Erich Piovan, Katia Basso, Pavel Sumazin, Christof Schneider, Marta Crespo, Qiong Shen, Govind Bhagat, Andrea Califano, Amy Chadburn, Laura Pasqualucci, Riccardo Dalla-Favera .  2009.   BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma.. Proc Natl Acad Sci U S A. 106 (27) :11294-9 ▶ Go to Pubmed
Ann Daly, Peter Donaldson, Pallav Bhatnagar, Yufeng Shen, Itsik Pe'er, Aris Floratos, Mark Daly, David Goldstein, Sally John, Matthew Nelson, Julia Graham, Kevin Park, John Dillon, William Bernal, Heather Cordell, Munir Pirmohamed, Guruprasad Aithal, Christopher Day, DILIGEN Study, International Consortium .  2009.   HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.. Nat Genet. 41 (7) :816-9 ▶ Go to Pubmed
Ann Daly, Peter Donaldson, Pallav Bhatnagar, Yufeng Shen, Itsik Pe'er, Aris Floratos, Mark Daly, David Goldstein, Sally John, Matthew Nelson, Julia Graham, Kevin Park, John Dillon, William Bernal, Heather Cordell, Munir Pirmohamed, Guruprasad Aithal, Christopher Day, DILIGEN Study, International Consortium .  2009.   HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.. Nature genetics. 41 (7) :816-9 ▶ Go to Pubmed
Vladimir Trifonov, Hossein Khiabanian, Raul Rabadan .  2009.   Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus.. N Engl J Med. 361 (2) :115-9 ▶ Go to Pubmed
Aly Khan, Doron Betel, Martin Miller, Chris Sander, Christina Leslie, Debora Marks .  2009.   Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.. Nat Biotechnol. 27 (6) :549-55 ▶ Go to Pubmed
Snehit Prabhu, Itsik Pe'er .  2009.   Overlapping pools for high-throughput targeted resequencing.. Genome Res. 19 (7) :1254-61 ▶ Go to Pubmed
Katia Basso, Pavel Sumazin, Pavel Morozov, Christof Schneider, Roy Maute, Yukiko Kitagawa, Jonathan Mandelbaum, Joseph Haddad, Chang-Zheng Chen, Andrea Califano, Riccardo Dalla-Favera .  2009.   Identification of the human mature B cell miRNome.. Immunity. 30 (5) :744-52 ▶ Go to Pubmed
Trifonov V, Hossein Khiabanian, B Greenbaum, Raul Rabadan .  2009.   The origin of the recent swine influenza A(H1N1) virus infecting humans.. Euro Surveill. 14 (17) ▶ Go to Pubmed
Mara Compagno, Wei Lim, Adina Grunn, Subhadra Nandula V, Manisha Brahmachary, Qiong Shen, Francesco Bertoni, Maurilio Ponzoni, Marta Scandurra, Andrea Califano, Govind Bhagat, Amy Chadburn, Riccardo Dalla-Favera, Laura Pasqualucci .  2009.   Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma.. Nature. 459 (7247) :717-21 ▶ Go to Pubmed
Remo Rohs, Sean West, Peng Liu, Barry Honig .  2009.   Nuance in the double-helix and its role in protein-DNA recognition.. Curr Opin Struct Biol. 19 (2) :171-7 ▶ Go to Pubmed
Aleksandra Walczak, Andrew Mugler, Chris Wiggins .  2009.   A stochastic spectral analysis of transcriptional regulatory cascades.. Proc Natl Acad Sci U S A. 106 (16) :6529-34 ▶ Go to Pubmed
David Waltz, Bruce Buchanan .  2009.   Computer science. Automating science.. Science. 324 (5923) :43-4 ▶ Go to Pubmed
Donald Petrey, Barry Honig .  2009.   Is protein classification necessary? Toward alternative approaches to function annotation.. Curr Opin Struct Biol. 19 (3) :363-8 ▶ Go to Pubmed
Guy Nimrod, András Szilágyi, Christina Leslie, Nir Ben-Tal .  2009.   Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.. J Mol Biol. 387 (4) :1040-53 ▶ Go to Pubmed
Oren Litvin, Helen Causton, Bo-Juen Chen, Dana Pe'er .  2009.   Modularity and interactions in the genetics of gene expression.. Proc Natl Acad Sci U S A. 106 (16) :6441-6 ▶ Go to Pubmed
Wei Lim, Eugenia Lyashenko, Andrea Califano .  2009.   Master regulators used as breast cancer metastasis classifier.. Pac Symp Biocomput. :504-15 ▶ Go to Pubmed
Kai Wang, Mariano Alvarez, Brygida Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla-Favera, Andrea Califano .  2009.   Dissecting the interface between signaling and transcriptional regulation in human B cells.. Pac Symp Biocomput. :264-75 ▶ Go to Pubmed
Lee Sam, Eneida Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves Lussier .  2009.   PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.. BMC Bioinformatics. 10 Suppl 2 :S8 ▶ Go to Pubmed
Yang Liu, Lee Sam, Jianrong Li, Yves Lussier .  2009.   Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.. BMC Bioinformatics. 10 Suppl 2 :S11 ▶ Go to Pubmed
Jennifer Lowe, Julian Maller, Itsik Pe'er, Benjamin Neale, Jacqueline Salit, Eimear Kenny, Jessica Shea, Ralph Burkhardt, Gustav Smith, Weizhen Ji, Martha Noel, Jia Foo, Maude Blundell, Vita Skilling, Laura Garcia, Marcia Sullivan, Heather Lee, Anna Labek, Hope Ferdowsian, Steven Auerbach, Richard Lifton, Christopher Newton-Cheh, Jan Breslow, Markus Stoffel, Mark Daly, David Altshuler, Jeffrey Friedman .  2009.   Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.. PLoS Genet. 5 (2) :e1000365 ▶ Go to Pubmed
Karen Sachs, Solomon Itani, Jennifer Carlisle, Garry Nolan, Dana Pe'er, Douglas Lauffenburger .  2009.   Learning signaling network structures with sparsely distributed data.. J Comput Biol. 16 (2) :201-12 ▶ Go to Pubmed
Su-In Lee, Aimée Dudley, David Drubin, Pamela Silver, Nevan Krogan, Dana Pe'er, Daphne Koller .  2009.   Learning a prior on regulatory potential from eQTL data.. PLoS Genet. 5 (1) :e1000358 ▶ Go to Pubmed
Jiang Liu, Murad Ghanim, Lei Xue, Christopher Brown, Ivan Iossifov, Cesar Angeletti, Sujun Hua, Nicolas Nègre, Michael Ludwig, Thomas Stricker, Hikmat Al-Ahmadie, Maria Tretiakova, Robert Camp, Montse Perera-Alberto, David Rimm, Tian Xu, Andrey Rzhetsky, Kevin White .  2009.   Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.. Science. 323 (5918) :1218-22 ▶ Go to Pubmed
Nuala Meyer, Yong Huang, Patrick Singleton, Saad Sammani, Jaideep Moitra, Carrie Evenoski, Aliya Husain, Sumegha Mitra, Liliana Moreno-Vinasco, Jeffrey Jacobson, Yves Lussier, Joe Garcia .  2009.   GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling.. FASEB J. 23 (5) :1325-37 ▶ Go to Pubmed
Adam Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo Ferrando, Gustavo Stolovitzky .  2009.   ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.. Proc Natl Acad Sci U S A. 106 (1) :244-9 ▶ Go to Pubmed
Iain Melvin, Jason Weston, Christina Leslie, William Noble .  2009.   RANKPROP: a web server for protein remote homology detection.. Bioinformatics. 25 (1) :121-2 ▶ Go to Pubmed
Alexander Gusev, Jennifer Lowe, Markus Stoffel, Mark Daly, David Altshuler, Jan Breslow, Jeffrey Friedman, Itsik Pe'er .  2009.   Whole population, genome-wide mapping of hidden relatedness.. Genome Res. 19 (2) :318-26 ▶ Go to Pubmed