Results 1 - 10 of 7,924

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
dyclonine. sion measurement. Using a comprehensive database of reference profiles, the pathway(s) perturbed by an Introduction uncharacterized mutation would be ascertained by simply asking which expression patterns in the database Systematic approaches for identifying the biological its profile most

Muscle: multiple sequence alignment with high accuracy and high throughput

by Robert C. Edgar - NUCLEIC ACIDS RES , 2004
"... We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree-dependent r ..."
Abstract - Cited by 2509 (7 self) - Add to MetaCart
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree

Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
Abstract - Cited by 771 (13 self) - Add to MetaCart
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI Gen

A mammalian microRNA expression atlas based on small RNA library sequencing.

by Pablo Landgraf , Mirabela Rusu , Robert Sheridan , Alain Sewer , Nicola Iovino , Alexei Aravin , Sé Bastien Pfeffer , Amanda Rice , Alice O Kamphorst , Markus Landthaler , Carolina Lin , Nicholas D Socci , Leandro Hermida , Valerio Fulci , Sabina Chiaretti , Robin Foà , Julia Schliwka , Uta Fuchs , Astrid Novosel , Roman-Ulrich Mü , Bernhard Schermer , Ute Bissels , Jason Inman , Quang Phan , David B Weir , Ruchi Choksi , Gabriella De Vita , Daniela Frezzetti , Hans-Ingo Trompeter , Veit Hornung , Grace Teng , Gunther Hartmann , Miklos Palkovits , Roberto Di Lauro , Peter Wernet , Giuseppe Macino , Charles E Rogler , James W Nagle , Jingyue Ju , F Nina Papavasiliou , Thomas Benzing , Peter Lichter , Wayne Tam , Michael J Brownstein , Andreas Bosio , James J Russo , Chris Sander , Mihaela Zavolan , Thomas Tuschl - Cell, , 2007
"... SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ sy ..."
Abstract - Cited by 418 (4 self) - Add to MetaCart
of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units

Protein homology detection by HMM-HMM comparison

by Johannes Söding - BIOINFORMATICS , 2005
"... Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile H ..."
Abstract - Cited by 401 (8 self) - Add to MetaCart
Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile

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
efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available

Godzik A: FFAS03: a server for profile--profile sequence alignments

by Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, Adam Godzik - Nucleic Acids Res 2005, 33(Web Server
"... alignments ..."
Abstract - Cited by 80 (8 self) - Add to MetaCart
alignments

Biological identifications through DNA barcodes

by Paul D. N. Hebert, Alina Cywinska, Shelley L. Ball, Jeremy R. Dewaard - Proc. Biol. Sci , 2003
"... Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. In this study, we establish that ..."
Abstract - Cited by 335 (3 self) - Add to MetaCart
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon ‘barcodes’. In this study, we establish

HMMER web server: interactive sequence similarity searching

by Robert D. Finn, Jody Clements, Sean R. Eddy - Nucleic Acids Research , 2011
"... HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed gai ..."
Abstract - Cited by 260 (0 self) - Add to MetaCart
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed

Temperament and development

by Pam J. Thomas, Immunopathology Unit, Centre Stevenage Herts , 1977
"... The genome sequences of two virulent strains of Mycobacterium tuberculosis (H37Rv and CDC 1551) are now available. CDC 1551 is a recent clinical isolate and H37Rv is a commonly used lab strain which has been subject to in vitro passage. The two strains have been shown to display differing phenotypes ..."
Abstract - Cited by 290 (0 self) - Add to MetaCart
The genome sequences of two virulent strains of Mycobacterium tuberculosis (H37Rv and CDC 1551) are now available. CDC 1551 is a recent clinical isolate and H37Rv is a commonly used lab strain which has been subject to in vitro passage. The two strains have been shown to display differing
Results 1 - 10 of 7,924