Results 1 - 10 of 11,329

Functional discovery via a compendium of expression profiles.

by Timothy R Hughes , Matthew J Marton , Allan R Jones , Christopher J Roberts , Roland Stoughton , Christopher D Armour , Holly A Bennett , Ernest Coffey , Hongyue Dai , Ross-Macdonald , Yudong D He , Matthew J Kidd , Amy M King , Michael R Meyer , David Slade , Pek Y Lum , Sergey B Stepaniants , Daniel D Shoemaker , Julian Simon , Martin Bard - Cell, , 2000
"... provided that the cellular transcriptional response to frames encode proteins required for sterol metabodisruption of different steps in the same pathway is lism, cell wall function, mitochondrial respiration, or similar, and that there are sufficiently unique transcripprotein synthesis. We also sh ..."
Abstract - Cited by 547 (9 self) - Add to MetaCart
show that the compendium tional responses to the perturbation of most cellular can be used to characterize pharmacological perturpathways, systematic characterization of novel mutants bations by identifying a novel target of the commonly could be carried out with a single genome-wide expresused drug

Fast and accurate short read alignment with Burrows-Wheeler transform

by Heng Li, Richard Durbin - BIOINFORMATICS, 2009, ADVANCE ACCESS , 2009
"... Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hashtable based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to a ..."
Abstract - Cited by 2096 (24 self) - Add to MetaCart
of individuals. Results: We implemented BWA, a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space

MATRIX FACTORIZATION TECHNIQUES FOR RECOMMENDER SYSTEMS

by Yehuda Koren, Robert Bell, Chris Volinsky - IEEE COMPUTER , 2009
"... As the Netflix Prize competition has demonstrated, matrix factorization models are superior to classic nearest-neighbor techniques for producing product recommendations, allowing the incorporation of additional information such as implicit feedback, temporal effects, and confidence levels. Modern co ..."
Abstract - Cited by 593 (4 self) - Add to MetaCart
As the Netflix Prize competition has demonstrated, matrix factorization models are superior to classic nearest-neighbor techniques for producing product recommendations, allowing the incorporation of additional information such as implicit feedback, temporal effects, and confidence levels. Modern

A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes

by Pierre Baldi, Anthony D. Long - Bioinformatics , 2001
"... Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory ..."
Abstract - Cited by 491 (6 self) - Add to MetaCart
Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory

In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector

by Luigi Naldini, Ulrike Blomer, Daniel Ory, Richard Mulligan, Fred H. Gage, Inder M. Verma, Didier Trono - Science , 1996
"... A retroviral vector system based on the human immunodeficiency virus (HIV) was de-veloped that, in contrast to a murine leukemia virus-based counterpart, transduced heterologous sequences into HeLa cells and rat fibroblasts blocked in the cell cycle, as well as into human primary macrophages. Additi ..."
Abstract - Cited by 478 (17 self) - Add to MetaCart
. Additionally, the HIV vector could mediate stable in vivo gene transfer into terminally differentiated neurons. The ability of HIV-based viral vectors to deliver genes in vivo into nondividing cells could increase the applicability of retroviral vectors in human gene therapy. Until now, gene therapy protocols

KEGG: Kyoto Encyclopedia of Genes and Genomes

by Hiroyuki Ogata, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono - Nucl. Acids Res , 1999
"... Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known me ..."
Abstract - Cited by 408 (0 self) - Add to MetaCart
and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/ genome databases

by Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holl, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne Paley, Pallavi Subhraveti, Daniel S. Weaver, Deepika Weerasinghe, Peifen Zhang, Peter D. Karp - Nucleic Acids Res , 2012
"... The MetaCyc database (MetaCyc.org) is a compre-hensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scien-tific literature. ..."
Abstract - Cited by 404 (15 self) - Add to MetaCart
metabolic network of one organism, including metabolites, enzymes, reac-tions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome

A Bayesian networks approach for predicting protein-protein interactions from genomic data

by Ronald Jansen, Haiyuan Yu, Dov Greenbaum, Yuval Kluger, Nevan J Krogan, Sambath Chung, Andrew Emili, Michael Snyder, Jack F Greenblatt, Mark Gerstein - SCIENCE , 2003
"... We developed an approach using Bayesian networks to predict protein-protein interactions genome-wide in yeast. Our method naturally weights and combines into reliable predictions genomic features only weakly associated with interaction (e.g., mRNA co-expression, co-essentiality and co-localization). ..."
Abstract - Cited by 294 (11 self) - Add to MetaCart
We developed an approach using Bayesian networks to predict protein-protein interactions genome-wide in yeast. Our method naturally weights and combines into reliable predictions genomic features only weakly associated with interaction (e.g., mRNA co-expression, co-essentiality and co

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

by Nevan J Krogan , Gerard Cagney , Haiyuan Yu , Gouqing Zhong , Xinghua Guo , Alexandr Ignatchenko , Joyce Li , Shuye Pu , Nira Datta , Aaron P Tikuisis , Thanuja Punna , José M Peregrín-Alvarez , Michael Shales , Xin Zhang , Michael Davey , Mark D Robinson , Alberto Paccanaro , James E Bray , Anthony Sheung , Bryan Beattie , Dawn P Richards , Veronica Canadien , Atanas Lalev , Frank Mena , Peter Wong , Andrei Starostine , Myra M Canete , James Vlasblom , Samuel Wu , Chris Orsi , Sean R Collins , Shamanta Chandran , Robin Haw , Jennifer J Rilstone , Kiran Gandi , Natalie J Thompson , Gabe Musso , Peter St Onge , Shaun Ghanny , Mandy H Y Lam , Gareth Butland , Amin M Altaf-Ul , Shigehiko Kanaya , Ali Shilatifard , Erin O'shea , Jonathan S Weissman , C James Ingles , Timothy R Hughes , John Parkinson , Mark Gerstein , Shoshana J Wodak , Andrew Emili , Jack F Greenblatt - Nature , 2006
"... Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation ..."
Abstract - Cited by 296 (9 self) - Add to MetaCart
into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics

Sequencing technologies - the next generation.

by Michael L Metzker , Michael L Metzker - Nature Reviews , 2010
"... Abstract | Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the ..."
Abstract - Cited by 286 (2 self) - Add to MetaCart
Abstract | Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data
Results 1 - 10 of 11,329