Pruitt, Kim D., Harrow, Jennifer, Harte, Rachel A., Wallin, Craig, Diekhans, Mark, Maglott, Donna R., ...
Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can...
HST.480: BIOINFORMATICS AND PROTEOMICS: AN ENGINEERING-BASED PROBLEM SOLVING APPROACH (2008)
Interdisciplinary and hands-on approach the topics of bioinformatics and proteomics. Lectures and labs cover sequence analysis, microarray expression analysis, Bayesian methods, control theory,...
Special review for the Encyclopedia of Genomics, Proteomics, and Bioinformatics. (2008)
Manolis Kellis, John Wiley, (in Press
Three years after the initial sequencing of the human genome, the actual number of functional human genes remains uncertain. Several expression-based analyses still argue for a hundred thousand...
A Classification Approach to Comparative Gene Finding in Mammals (2008)
Evolutionary conservation is a powerful signal that can be used to identify protein-coding genes within related genomes. Promising early approaches ([1], [3], [4], [5]) considered conservation...
Presser, Aviva, Elowitz, Michael B., Kellis, Manolis, Kishony, Roy
Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate....
Conservation of small RNA pathways in platypus (2008)
Murchison, Elizabeth Prody, Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, ...
Copyright © 2008 by Cold Spring Harbor Laboratory Press
Conservation of small RNA pathways in platypus (2008)
Murchison, Elizabeth Prody, Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, ...
Copyright © 2008 by Cold Spring Harbor Laboratory Press
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Warren, Wesley C., Hillier, LaDeana W., Marshall Graves, Jennifer A., Birney, Ewan, Ponting, Chris P., Grützner, Frank, ...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a...
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands (2008)
Stark, Alexander, Bushati, Natascha, Jan, Calvin H., Kheradpour, Pouya, Hodges, Emily, Brennecke, Julius, ...
MicroRNAs (miRNAs) are ∼22-nucleotide RNAs that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression....
Conservation of small RNA pathways in platypus (2008)
Murchison, Elizabeth P., Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, ...
Small RNA pathways play evolutionarily conserved roles in gene regulation and defense from parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout...
Downloaded From, Er Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Emily Hodges, ...
data
Network motif discovery using subgraph enumeration and symmetry-breaking (2007)
Joshua A. Grochow, Manolis Kellis
Abstract. The study of biological networks and network motifs can yield significant new insights into systems biology. Previous methods of discovering network motifs – network-centric subgraph...
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes (2007)
Lin, Michael F., Carlson, Joseph W., Crosby, Madeline A., Matthews, Beverley B., Yu, Charles, Park, Soo, ...
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have...
Ruby, J. Graham, Stark, Alexander, Johnston, Wendy K., Kellis, Manolis, Bartel, David P., Lai, Eric C.
MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing...
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes (2007)
Stark, Alexander, Kheradpour, Pouya, Parts, Leopold, Brennecke, Julius, Hodges, Emily, Hannon, Gregory J., ...
MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3′ untranslated regions (3′ UTRs). They are one of the most abundant classes of regulators,...
Reliable prediction of regulator targets using 12 Drosophila genomes (2007)
Kheradpour, Pouya, Stark, Alexander, Roy, Sushmita, Kellis, Manolis
Gene expression is regulated pre- and post-transcriptionally via cis-regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome sequences is a major...
Rasmussen, Matthew D., Kellis, Manolis
Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses,...
Zeitlinger, Julia, Zinzen, Robert P., Stark, Alexander, Kellis, Manolis, Zhang, Hailan, Young, Richard A., ...
Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determined...
Joshua A. Grochow, Manolis Kellis, Joshua A. Grochow
The study of protein interactions from the networks point of view has yielded new insights into systems biology [Bar03, MA03, RSM + 02, WS98]. In particular, “network motifs ” become apparent as...
Large-scale discovery and validation of functional elements in the human genome (2005)
Bernstein, Bradley E, Kellis, Manolis
A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
The changing face of genomics (2004)
A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
Introduction to Bioinformatics (2004)
Neil C. Jones, Pavel A. Pevzner, Manolis Kellis
Comparative genomics reveals unusually long motifs in mammalian genomes Vol. 22 no. 14 2006, pages e236–e242 doi:10.1093/bioinformatics/btl265
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. L
In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M., Chiang, Derek Y., Kellis, Manolis, Lander, Eric S., Eisen, Michael B.
Background: The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content...
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
2003 Chiang et Volume al. 4, Issue 7, Article R43 Open Access (2003)
Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S L, Michael B Eisen
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
Large-scale discovery and validation of functional elements in the human genome
Bernstein, Bradley E, Kellis, Manolis
A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
A report on the 5th annual Advances in Genome Biology and Technology (AGBT) and Automation in DNA Mapping and Sequencing (AMS) meeting, Marco Island, USA, 4-7 February 2004.
Large-scale discovery and validation of functional elements in the human genome
Bernstein, Bradley E, Kellis, Manolis
A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004.
Zeitlinger, Julia, Zinzen, Robert P., Stark, Alexander, Kellis, Manolis, Zhang, Hailan, Young, Richard A., ...
Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determined...
Xie, Xiaohui, Mikkelsen, Tarjei S., Gnirke, Andreas, Lindblad-Toh, Kerstin, Kellis, Manolis, Lander, Eric S.
Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Experimental evidence suggests that...
Lin, Michael F., Deoras, Ameya N., Rasmussen, Matthew D., Kellis, Manolis
Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here,...
Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F., ...
Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative...
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
Lin, Michael F., Carlson, Joseph W., Crosby, Madeline A., Matthews, Beverley B., Yu, Charles, Park, Soo, ...
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have...
Ruby, J. Graham, Stark, Alexander, Johnston, Wendy K., Kellis, Manolis, Bartel, David P., Lai, Eric C.
MicroRNA (miRNA) genes give rise to small regulatory RNAs in a wide variety of organisms. We used computational methods to predict miRNAs conserved among Drosophila species and large-scale sequencing...
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
Stark, Alexander, Kheradpour, Pouya, Parts, Leopold, Brennecke, Julius, Hodges, Emily, Hannon, Gregory J., ...
MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3′ untranslated regions (3′ UTRs). They are one of the most abundant classes of regulators,...
Reliable prediction of regulator targets using 12 Drosophila genomes
Kheradpour, Pouya, Stark, Alexander, Roy, Sushmita, Kellis, Manolis
Gene expression is regulated pre- and post-transcriptionally via cis-regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome sequences is a major...
Rasmussen, Matthew D., Kellis, Manolis
Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses,...
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands
Stark, Alexander, Bushati, Natascha, Jan, Calvin H., Kheradpour, Pouya, Hodges, Emily, Brennecke, Julius, ...
MicroRNAs (miRNAs) are ∼22-nucleotide RNAs that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression....
Presser, Aviva, Elowitz, Michael B., Kellis, Manolis, Kishony, Roy
Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate....
Conservation of small RNA pathways in platypus
Murchison, Elizabeth P., Kheradpour, Pouya, Sachidanandam, Ravi, Smith, Carly, Hodges, Emily, Xuan, Zhenyu, ...
Small RNA pathways play evolutionarily conserved roles in gene regulation and defense from parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout...