Research Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis (2009)
Serafim Batzoglou, Bonnie Berger, Jill Mesirov, Eric S. L
One approach to sequencing a large genome is (1) to sequence a collection of nonoverlapping “seeds ” chosen from a genomic library of large-insert clones [such as bacterial artificial chromosomes...
Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. L
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
And The Canine Genome Mapping Community: (2008)
Elaine A. Ostr, Kerstin Lindblad-toh, Eric S. L, Gregory M. Acl, Gustavo D. Aguirre, Matthew M. Binns, ...
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ARTICLE An STS-Based Map of the Human Genome (2008)
Thomas J. Hudson, Lincoln D. Stein, Sebastian S. Gerety, Junli Ma, Andrew B. Castle, ...
A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid...
Methods Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 (2008)
David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-toh, Jill P. Mesirov, ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
I POLICY FORUM::: 7- II, Assessing Mapping Progress in the (2008)
David R. Cox, Eric D. Green, Eric S. L, Daniel Cohen, Richard M. Myers
Project in the United States is to construct a physical map of the human genome, con-sisting of unique genomic landmarks at an average spacing of 100 kilobases (kb). When completed (which is...
Abstract Class Prediction and Discovery Using Gene Expression Data (2008)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Abstract A Dictionary Based Approach for Gene Annotation (2008)
Serafim Batzoglouti Vale, In I. Spitkovsky, William S. Beebee, Eric S. L, Er Bonnie Berger*q, Daniel J. Kleitmanll
This paper describes a fast and fully automated dic-tionary based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and...
Leonid Kruglyak, Mark J. Daly, Eric S. Lander, Eric S. L
this paper allows very rapid multipoint likelihood calculation in nuclear families (with or without parental consanguinity), and the accompanying software package makes multipoint mapping feasible in...
SUPPLEMENTARY INFORMATION Multi-class Cancer Diagnosis Using Tumor Gene Expression Signatures (2007)
Sridhar Ramaswamy, Pablo Tamayo, Ryan Rifkin, Sayan Mukherjee, Hsiang Yeang, ...
This document provides supplementary information and details not included in the paper "Multiclass Cancer Diagnosis Using Tumor Gene Expression Signatures." Other sources of information can...
Bradley E. Bernstein, Tarjei S. Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J. Huebert, James Cuff, ...
The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that...
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...
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
An analytical method for multiclass molecular cancer classification (2003)
Ryan Rifkin, Sayan Mukherjee, Pablo Tamayo, Sridhar Ramaswamy, Chen-hsiang Yeang, Michael Angelo, ...
Abstract. Modern cancer treatment relies upon microscopic tissue examination to classify tumors according to anatomical site of origin. This approach is effective but subjective and variable even...
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
Class Prediction and Discovery Using Gene Expression Data (2000)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Recent Developments in Computational Gene Recognition (1998)
Serafim Batzoglou, Bonnie Berger, Daniel J. Kleitman, Eric S. Lander, Eric S. L, Lior Pachter
. We survey recent mathematical and computational work in the field of gene recognition, focusing on the techniques that have been developed to tackle the problem of identifying protein coding...