Longo, Mark S, Carone, Dawn M, Green, Eric D, O'Neill, Michael J, O'Neill, Rachel J
Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype...
The value of avian genomics to the conservation of wildlife (2009)
Romanov, Michael N, Tuttle, Elaina M, Houck, Marlys L, Modi, William S, Chemnick, Leona G, Korody, Marisa L, ...
Abstract Background Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for...
Reconstructing the Evolutionary History of Complex Human Gene Clusters (2009)
Yu Zhang, Giltae Song, Eric D. Green, Adam Siepel, Webb Miller
Abstract. Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such...
Dynamic evolution of V1R putative pheromone receptors between Mus musculus and Mus spretus (2009)
Kurzweil, Vanessa C, Getman, Mike, Green, Eric D, Lane, Robert P
Abstract Background The mammalian vomeronasal organ (VNO) expresses two G-protein coupled receptor gene families that mediate pheromone responses, the V1R and V2R receptor genes. In rodents, there...
Article Identification and Characterization of Multi-Species Conserved Sequences (2009)
Elliott H. Margulies, Mathieu Blanchette, David Haussler, Eric D. Green
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
Rudd, M. Katharine, Endicott, RaeLynn M., Friedman, Cynthia, Walker, Megan, Young, Janet M., Osoegawa, Kazutoyo, ...
Subtelomeres are concentrations of interchromosomal segmental duplications capped by telomeric repeats at the ends of chromosomes. The nature of the segments shared by different sets of human...
The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine (2009)
Biesecker, Leslie G., Mullikin, James C., Facio, Flavia M., Turner, Clesson, Cherukuri, Praveen F., Blakesley, Robert W., ...
ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human...
Tsipouri, Vicky, Schueler, Mary G, Hu, Sufen, Dutra, Amalia, Pak, Evgenia, ...
Abstract Background Indian muntjac ( Muntiacus muntjak vaginalis ) has an extreme mammalian karyotype, with only six and seven chromosomes in the female and male, respectively. Chinese muntjac (...
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...
Article Distribution and intensity of constraint in mammalian genomic sequence (2008)
Gregory M. Cooper, Eric A. Stone, George Asimenos, Nisc Comparative, Sequencing Program, Eric D. Green, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Resource Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner (2008)
Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski, Krishna M. Roskin, ...
We define a “threaded blockset, ” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) builds a...
Hughes, Inna, Binkley, Jonathan, Hurle, Belen, Green, Eric D, Sidow, Arend, ...
Abstract Background Otopetrin 1 (Otop1) encodes a multi-transmembrane domain protein with no homology to known transporters, channels, exchangers, or receptors. Otop1 is necessary for the formation...
for Large-Scale Multiple Alignment (2008)
Michael Brudno, Chuong B. Do, Gregory M. Cooper, Michael F. Kim, Eugene Davydov, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Analysis ofP/--3[ Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2008)
Ge Liu Nis, Eric D. Green, Evan E. Eichler
aterial is available online at www.genome.org.] Initial studie ofprimate gemat variation weR base largeW onindire1 eire1H obtaine from DNA hybridization kineG ics(Sible and Ahlquist 1984; Powe1...
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets (2008)
Prasad, Arjun B., Allard, Marc W., Green, Eric D.
The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among...
Regulatory divergence modifies limb length between mammals (2008)
Cretekos, Chris J., Wang, Ying, Green, Eric D., Martin, James F., Rasweiler, John J., ...
Natural selection acts on variation within populations, resulting in modified organ morphology, physiology, and ultimately the formation of new species. Although variation in orthologous proteins can...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Hurle, Belen, Swanson, Willie, Green, Eric D.
The initial comparison of the human and chimpanzee genome sequences revealed 16 genomic regions with an unusually high density of rapidly evolving genes. One such region is the whey acidic protein...
Jabba, Sairam V, Oelke, Alisha, Singh, Ruchira, Maganti, Rajanikanth J, Fleming, Sherry, Wall, Susan M, ...
Abstract Background Pendred syndrome, an autosomal-recessive disorder characterized by deafness and goiter, is caused by a mutation of SLC26A4 , which codes for the anion exchanger pendrin. We...
Recurrent duplication-driven transposition of DNA during hominoid evolution. (2006)
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Antonellis, Anthony, Bennett, William R., Menheniott, Trevelyan R., Prasad, Arjun B., Lee-Lin, Shih-Queen, ...
The transcription factor SOX10 is mutated in the human neurocristopathy Waardenburg–Shah syndrome (WS4), which is characterized by enteric aganglionosis and pigmentation defects. SOX10 directly...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Progressive proximal expansion of the primate X chromosome centromere. (2005)
Schueler, Mary G., Dunn, John M., Bird, Christine P., Ross, Mark T., Viggiano, Luigi, ...
Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the...
Distribution and intensity of constraint in mammalian genomic sequence (2005)
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Phenotypic spectrum of disorders associated with glycyl-tRNA synthetase mutations (2005)
Sivakumar, Kumaraswamy, Kyriakides, Theodoros, Puls, Imke, Nicholson, Garth A., Funalot, Benoît, Antonellis, Anthony, ...
We describe clinical, electrophysiological, histopathological and molecular features of a unique disease caused by mutations in the glycyl-tRNA synthetase (GARS) gene. Sixty patients from five...
Grice, Elizabeth A., Rochelle, Erin S., Green, Eric D., Chakravarti, Aravinda, McCallion, Andrew S.
Evolutionary sequence conservation is now a relatively common approach for the prediction of functional DNA sequences. However, the fraction of conserved non-coding sequences with regulatory...
Distribution and intensity of constraint in mammalian genomic sequence (2005)
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Wangemann, Philine, Itza, Erin M, Albrecht, Beatrice, Wu, Tao, Jabba, Sairam V, Maganti, Rajanikanth J, ...
Abstract Background Pendred syndrome, a common autosomal-recessive disorder characterized by congenital deafness and goiter, is caused by mutations of SLC26A4, which codes for pendrin. We...
Piontkivska, Helen, Zhang, Yi, Green, Eric D, Elnitski, Laura
Abstract Background The elastin gene (ELN) is implicated as a factor in both supravalvular aortic stenosis (SVAS) and Williams Beuren Syndrome (WBS), two diseases involving pronounced complications...
Bmc Genomics, Yi Zhang, Eric D Green, Nisc Comparative, Sequencing Program, ...
Background: The elastin gene (ELN) is implicated as a factor in both supravalvular aortic stenosis (SVAS) and Williams Beuren Syndrome (WBS), two diseases involving pronounced complications in mental...
Scherer, Stephen W., Green, Eric D.
Human chromosome 7 is arguably amongst the most comprehensively characterized segments of the human genome. By microscopic examination, it belongs to the medium-sized group C submetacentric class,...
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner (2004)
Blanchette, Mathieu, Kent, W. James, Riemer, Cathy, Elnitski, Laura, Smit, Arian F.A., Roskin, Krishna M., ...
We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) builds a...
Reconstructing large regions of an ancestral mammalian genome in silico (2004)
Blanchette, Mathieu, Green, Eric D., Miller, Webb, Haussler, David
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral...
An intermediate grade of finished genomic sequence suitable for comparative analyses (2004)
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
An intermediate grade of finished genomic sequence suitable for comparative analyses (2004)
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Pericentromeric Duplications in the Laboratory Mouse (2003)
Thomas, James W., Schueler, Mary G., Summers, Tyrone J., Blakesley, Robert W., McDowell, Jennifer C., Thomas, Pamela J., ...
Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of...
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences (2003)
Schwartz, Scott, Elnitski, Laura, Li, Mei, Weirauch, Matt, Riemer, Cathy, Smit, Arian, ...
Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server,...
Identification and Characterization of Multi-Species Conserved Sequences (2003)
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (2003)
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes (2003)
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (2003)
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Sequence-Ready Clone Contig Maps in Multiple Species (2002)
James W. Thomas, Arjun B. Prasad, Tyrone J. Summers, Jacquelyn R. Idol, ...
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Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species (2002)
Thomas, James W., Prasad, Arjun B., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V.B., Idol, Jacquelyn R., ...
Retention of pendrin in the endoplasmic reticulum is a major mechanism for Pendred syndrome (2002)
Rotman-Pikielny, Pnina, Hirschberg, Koret, Maruvada, Padma, Suzuki, Koichi, Royaux, Ines E., Green, Eric D., ...
Pendred syndrome is a major cause of congenital deafness, goiter and defective iodide organification. Mutations in the transmembrane protein, pendrin, cause diminished export of iodide from thyroid...
Pericentromeric Duplications in the Laboratory Mouse (2002)
Thomas, James W., Schueler, Mary G., Summers, Tyrone J., Blakesley, Robert W., McDowell, Jennifer C., Thomas, Pamela J., ...
Systematic sequencing of cDNA clones using the transposon Tn5 (2002)
Shevchenko, Yuriy, Bouffard, Gerard G., Butterfield, Yaron S. N., Blakesley, Robert W., Hartley, James L., Young, Alice C., ...
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the...
DeSilva, Udaya, Elnitski, Laura, Idol, Jacquelyn R., Doyle, Johannah L., Gan, Weiniu, Thomas, James W., ...
Everett, Lorraine A., Belyantseva, Inna A., Noben-Trauth, Konrad, Cantos, Raquel, Chen, Amy, Thakkar, Sneha I., ...
Following the positional cloning of PDS, the gene mutated in the deafness/goitre disorder Pendred syndrome (PS), numerous studies have focused on defining the role of PDS in deafness and PS as...
Jamison, D. Curtis, Thomas, James W., Green, Eric D.
Motivation: The construction of physical maps based on bacterial clones [e.g. bacterial artificial chromosomes (BACs)] is valuable for a number of molecular genetics applications, including the...
Touchman, Jeffrey W., Anikster, Yair, Dietrich, Nicole L., Maduro, Valerie V. Braden, McDowell, Geraldine, Shotelersuk, Vorasuk, ...
Thomas, James W., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V. Braden, Idol, Jacquelyn R., Mastrian, Stephen D., ...
Comparative Mapping of the Region of Human Chromosome 7 Deleted in Williams Syndrome (1999)
DeSilva, Udaya, Massa, Hillary, Trask, Barbara J., Green, Eric D.
An Effective Approach for Analyzing "Prefinished" Genomic Sequence Data (1999)
Kuehl, Peter M., Weisemann, Jane M., Touchman, Jeffrey W., Green, Eric D., Boguski, Mark S.
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
High Throughput Fingerprint Analysis of Large-Insert Clones (1997)
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
Bouffard, Gerard G., Idol, Jacquelyn R., Braden, Valerie V., Iyer, Leslie M., Cunningham, Aimee F., Weintraub, Lauren A., ...
Green, Eric D., Ldol, Jacquelyn R., Mohr-Tldwell, Rose M., Braden, Valerie V., Peluso, Dale C., Fulton, Robert S., ...
An Important goal of the human genome project is to assemble fully integrated physical, genetic and cytogenetic maps for each human chromosome. Towards that end, we have isolated yeast artificial...
Maraia, Richard J., Sasaki-Tozawa, Noriko, Driscoll, Claire T., Green, Eric D., Darlington, Gretchen J.
Ro ribonucleoproteins (RNP) constitute a class of evolutionary conserved small cytoplasmic (sc) RNPs whose functions are unknown. In human cells four distinctive scRNAs designated hY1, hY3, hY4 and...
Fluorescence in situ hybridization of YAC clones after Alu-PCR amplification (1992)
Lengauer, Christoph, Green, Eric D., Cremer, Thomas
Alu-PCR protocols were optimized for the generation of human DNA probes from yeast strains containing yeast artificial chromosomes (YACs) with human inserts between 100 and 800 kb in size. The...
Lengauer, Christoph, Riethman, Harold C., Speicher, Michael R., Taniwaki, Masafumi, Konecki, David, Green, Eric D., ...
A human yeast artificial chromosome (YAC) library was screened by polymerase chain reaction with oligonucleotide primers defined for DNA sequences of the BCR gene and the protooncogenes c-raf-1,...
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
Liang, Hong, Fairman, Jeff, Claxton, David F., Nowell, Peter C., Green, Eric D., Nagarajan, Lalitha
Complete or partial deletions of the long arm of chromosome 7 (7q- and -7) are nonrandom abnormalities seen in primary and therapy-induced myelodysplasia (MDS) and acute myelogenous leukemia (AML)....
Everett, Lorraine A., Morsli, Hakim, Wu, Doris K., Green, Eric D.
Pendred’s syndrome is an autosomal-recessive disorder characterized by deafness and goiter. After our recent identification of the human gene mutated in Pendred’s syndrome (PDS), we sought to...
Royaux, Ines E., Wall, Susan M., Karniski, Lawrence P., Everett, Lorraine A., Suzuki, Koichi, Knepper, Mark A., ...
Pendrin is an anion transporter encoded by the PDS/Pds gene. In humans, mutations in PDS cause the genetic disorder Pendred syndrome, which is associated with deafness and goiter. Previous studies...
Systematic sequencing of cDNA clones using the transposon Tn5
Shevchenko, Yuriy, Bouffard, Gerard G., Butterfield, Yaron S. N., Blakesley, Robert W., Hartley, James L., Young, Alice C., ...
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the...
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
Schwartz, Scott, Elnitski, Laura, Li, Mei, Weirauch, Matt, Riemer, Cathy, Smit, Arian, ...
Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server,...
Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
Thomas, James W., Prasad, Arjun B., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V.B., Idol, Jacquelyn R., ...
Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
An Effective Approach for Analyzing “Prefinished” Genomic Sequence Data
Kuehl, Peter M., Weisemann, Jane M., Touchman, Jeffrey W., Green, Eric D., Boguski, Mark S.
Ongoing efforts to sequence the human genome are already generating large amounts of data, with substantial increases anticipated over the next few years. In most cases, a shotgun sequencing strategy...
The CMT2D Locus: Refined Genetic Position and Construction of a Bacterial Clone-Based Physical Map
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
Charcot-Marie-Tooth (CMT) disease is a progressive neuropathy of the peripheral nervous system, typically characterized by muscle weakness of the distal limbs. CMT is noted for its genetic...
Comparative Mapping of the Region of Human Chromosome 7 Deleted in Williams Syndrome
DeSilva, Udaya, Massa, Hillary, Trask, Barbara J., Green, Eric D.
Williams syndrome (WS) is a complex developmental disorder resulting from the deletion of a large (∼1.5–2 Mb) segment of human chromosome 7q11.23. Physical mapping studies have revealed that this...
Touchman, Jeffrey W., Anikster, Yair, Dietrich, Nicole L., Maduro, Valerie V. Braden, McDowell, Geraldine, Shotelersuk, Vorasuk, ...
Nephropathic cystinosis is an autosomal recessive disorder caused by the defective transport of cystine out of lysosomes. Recently, the causative gene (CTNS) was identified and presumed to encode an...
Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7
Thomas, James W., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V. Braden, Idol, Jacquelyn R., Mastrian, Stephen D., ...
The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse...
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
Crawford, Gregory E., Holt, Ingeborg E., Mullikin, James C., Tai, Denise, Green, Eric D., Wolfsberg, Tyra G., ...
Analysis of the human genome sequence has identified ≈25,000–30,000 protein-coding genes, but little is known about how most of these are regulated. Mapping DNase I hypersensitive (HS) sites has...
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Blanchette, Mathieu, Kent, W. James, Riemer, Cathy, Elnitski, Laura, Smit, Arian F.A., Roskin, Krishna M., ...
We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) builds a...
Identification and Characterization of Multi-Species Conserved Sequences
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
Pericentromeric Duplications in the Laboratory Mouse
Thomas, James W., Schueler, Mary G., Summers, Tyrone J., Blakesley, Robert W., McDowell, Jennifer C., Thomas, Pamela J., ...
Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of...
Wangemann, Philine, Itza, Erin M, Albrecht, Beatrice, Wu, Tao, Jabba, Sairam V, Maganti, Rajanikanth J, ...
Angata, Takashi, Margulies, Elliott H., Green, Eric D., Varki, Ajit
Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs (CD33rSiglecs) are a subgroup with as-yet-unknown...
An intermediate grade of finished genomic sequence suitable for comparative analyses
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
Reconstructing large regions of an ancestral mammalian genome in silico
Blanchette, Mathieu, Green, Eric D., Miller, Webb, Haussler, David
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Kashuk, Carl S., Stone, Eric A., Grice, Elizabeth A., Portnoy, Matthew E., Green, Eric D., Sidow, Arend, ...
The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic...
Distribution and intensity of constraint in mammalian genomic sequence
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Progressive proximal expansion of the primate X chromosome centromere
Schueler, Mary G., Dunn, John M., Bird, Christine P., Ross, Mark T., Viggiano, Luigi, Rocchi, Mariano, ...
Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the...
Lai, Cecilia S. L., Fisher, Simon E., Hurst, Jane A., Levy, Elaine R., Hodgson, Shirley, Fox, Margaret, ...
The KE family is a large three-generation pedigree in which half the members are affected with a severe speech and language disorder that is transmitted as an autosomal dominant monogenic trait. In...
DeSilva, Udaya, Elnitski, Laura, Idol, Jacquelyn R., Doyle, Johannah L., Gan, Weiniu, Thomas, James W., ...
Williams syndrome is a complex developmental disorder that results from the heterozygous deletion of a ∼1.6-Mb segment of human chromosome 7q11.23. These deletions are mediated by large (∼300 kb)...
Gene expression profiles in acute myeloid leukemia with common translocations using SAGE
Lee, Sanggyu, Chen, Jianjun, Zhou, Guolin, Shi, Run Zhang, Bouffard, Gerard G., Kocherginsky, Masha, ...
Identification of the specific cytogenetic abnormality is one of the critical steps for classification of acute myeloblastic leukemia (AML) which influences the selection of appropriate therapy and...
Riazuddin, Saima, Khan, Shaheen N., Ahmed, Zubair M., Ghosh, Manju, Caution, Kyle, Nazli, Sabiha, ...
In seven families, six different mutant alleles of TRIOBP on chromosome 22q13 cosegregate with autosomal recessive nonsyndromic deafness. These alleles include four nonsense (Q297X, R788X, R1068X,...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
Liang, Hong, Fairman, Jeff, Claxton, David F., Nowell, Peter C., Green, Eric D., Nagarajan, Lalitha
Complete or partial deletions of the long arm of chromosome 7 (7q- and -7) are nonrandom abnormalities seen in primary and therapy-induced myelodysplasia (MDS) and acute myelogenous leukemia (AML)....
Everett, Lorraine A., Morsli, Hakim, Wu, Doris K., Green, Eric D.
Pendred’s syndrome is an autosomal-recessive disorder characterized by deafness and goiter. After our recent identification of the human gene mutated in Pendred’s syndrome (PDS), we sought to...
Royaux, Ines E., Wall, Susan M., Karniski, Lawrence P., Everett, Lorraine A., Suzuki, Koichi, Knepper, Mark A., ...
Pendrin is an anion transporter encoded by the PDS/Pds gene. In humans, mutations in PDS cause the genetic disorder Pendred syndrome, which is associated with deafness and goiter. Previous studies...
Systematic sequencing of cDNA clones using the transposon Tn5
Shevchenko, Yuriy, Bouffard, Gerard G., Butterfield, Yaron S. N., Blakesley, Robert W., Hartley, James L., Young, Alice C., ...
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the...
DeSilva, Udaya, Elnitski, Laura, Idol, Jacquelyn R., Doyle, Johannah L., Gan, Weiniu, Thomas, James W., ...
Williams syndrome is a complex developmental disorder that results from the heterozygous deletion of a ∼1.6-Mb segment of human chromosome 7q11.23. These deletions are mediated by large (∼300 kb)...
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
Schwartz, Scott, Elnitski, Laura, Li, Mei, Weirauch, Matt, Riemer, Cathy, Smit, Arian, ...
Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server,...
Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
Thomas, James W., Prasad, Arjun B., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V.B., Idol, Jacquelyn R., ...
Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
An Effective Approach for Analyzing “Prefinished” Genomic Sequence Data
Kuehl, Peter M., Weisemann, Jane M., Touchman, Jeffrey W., Green, Eric D., Boguski, Mark S.
Ongoing efforts to sequence the human genome are already generating large amounts of data, with substantial increases anticipated over the next few years. In most cases, a shotgun sequencing strategy...
The CMT2D Locus: Refined Genetic Position and Construction of a Bacterial Clone-Based Physical Map
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
Charcot-Marie-Tooth (CMT) disease is a progressive neuropathy of the peripheral nervous system, typically characterized by muscle weakness of the distal limbs. CMT is noted for its genetic...
Comparative Mapping of the Region of Human Chromosome 7 Deleted in Williams Syndrome
DeSilva, Udaya, Massa, Hillary, Trask, Barbara J., Green, Eric D.
Williams syndrome (WS) is a complex developmental disorder resulting from the deletion of a large (∼1.5–2 Mb) segment of human chromosome 7q11.23. Physical mapping studies have revealed that this...
Touchman, Jeffrey W., Anikster, Yair, Dietrich, Nicole L., Maduro, Valerie V. Braden, McDowell, Geraldine, Shotelersuk, Vorasuk, ...
Nephropathic cystinosis is an autosomal recessive disorder caused by the defective transport of cystine out of lysosomes. Recently, the causative gene (CTNS) was identified and presumed to encode an...
Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7
Thomas, James W., Summers, Tyrone J., Lee-Lin, Shih-Queen, Maduro, Valerie V. Braden, Idol, Jacquelyn R., Mastrian, Stephen D., ...
The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse...
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
Crawford, Gregory E., Holt, Ingeborg E., Mullikin, James C., Tai, Denise, Green, Eric D., Wolfsberg, Tyra G., ...
Analysis of the human genome sequence has identified ≈25,000–30,000 protein-coding genes, but little is known about how most of these are regulated. Mapping DNase I hypersensitive (HS) sites has...
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Blanchette, Mathieu, Kent, W. James, Riemer, Cathy, Elnitski, Laura, Smit, Arian F.A., Roskin, Krishna M., ...
We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) builds a...
Identification and Characterization of Multi-Species Conserved Sequences
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
Pericentromeric Duplications in the Laboratory Mouse
Thomas, James W., Schueler, Mary G., Summers, Tyrone J., Blakesley, Robert W., McDowell, Jennifer C., Thomas, Pamela J., ...
Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of...
Wangemann, Philine, Itza, Erin M, Albrecht, Beatrice, Wu, Tao, Jabba, Sairam V, Maganti, Rajanikanth J, ...
Angata, Takashi, Margulies, Elliott H., Green, Eric D., Varki, Ajit
Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs (CD33rSiglecs) are a subgroup with as-yet-unknown...
An intermediate grade of finished genomic sequence suitable for comparative analyses
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
Reconstructing large regions of an ancestral mammalian genome in silico
Blanchette, Mathieu, Green, Eric D., Miller, Webb, Haussler, David
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral...
Margulies, Elliott H., Maduro, Valerie V. B., Thomas, Pamela J., Tomkins, Jeffery P., Amemiya, Chris T., Luo, Meizhong, ...
Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Kashuk, Carl S., Stone, Eric A., Grice, Elizabeth A., Portnoy, Matthew E., Green, Eric D., Sidow, Arend, ...
The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic...
Distribution and intensity of constraint in mammalian genomic sequence
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Antonellis, Anthony, Ellsworth, Rachel E., Sambuughin, Nyamkhishig, Puls, Imke, Abel, Annette, Lee-Lin, Shih-Queen, ...
Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V (dSMA-V) are axonal peripheral neuropathies inherited in an autosomal dominant fashion. Our previous genetic and...
Progressive proximal expansion of the primate X chromosome centromere
Schueler, Mary G., Dunn, John M., Bird, Christine P., Ross, Mark T., Viggiano, Luigi, Rocchi, Mariano, ...
Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the...
Lai, Cecilia S. L., Fisher, Simon E., Hurst, Jane A., Levy, Elaine R., Hodgson, Shirley, Fox, Margaret, ...
The KE family is a large three-generation pedigree in which half the members are affected with a severe speech and language disorder that is transmitted as an autosomal dominant monogenic trait. In...
Gene expression profiles in acute myeloid leukemia with common translocations using SAGE
Lee, Sanggyu, Chen, Jianjun, Zhou, Guolin, Shi, Run Zhang, Bouffard, Gerard G., Kocherginsky, Masha, ...
Identification of the specific cytogenetic abnormality is one of the critical steps for classification of acute myeloblastic leukemia (AML) which influences the selection of appropriate therapy and...
Riazuddin, Saima, Khan, Shaheen N., Ahmed, Zubair M., Ghosh, Manju, Caution, Kyle, Nazli, Sabiha, ...
In seven families, six different mutant alleles of TRIOBP on chromosome 22q13 cosegregate with autosomal recessive nonsyndromic deafness. These alleles include four nonsense (Q297X, R788X, R1068X,...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Zenklusen, Jean C, Weintraub, Lauren A, Green, Eric D
Reports of frequent loss of heterozygosity (LOH) of markers on human chromosome 7q in malignant myeloid disorders as well as breast, prostate, ovarian, colon, head and neck, gastric, pancreatic, and...
Macrophage invasion contributes to degeneration of stria vascularis in Pendred syndrome mouse model
Jabba, Sairam V, Oelke, Alisha, Singh, Ruchira, Maganti, Rajanikanth J, Fleming, Sherry, Wall, Susan M, ...
Recurrent duplication-driven transposition of DNA during hominoid evolution
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
Lewanda, Amy Feldman, Green, Eric D., Weissenbach, Jean, Jerald, Heather, Taylor, Eugene, Summar, Marshall L., ...
The locus for Saethre-Chotzen syndrome, a common autosomal dominant disorder of craniosynostosis and digital anomalies, was previously mapped to chromosome 7p between D7S513 and D7S516. We used...
Hurle, Belen, Swanson, Willie, Green, Eric D.
The initial comparison of the human and chimpanzee genome sequences revealed 16 genomic regions with an unusually high density of rapidly evolving genes. One such region is the whey acidic protein...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Regulatory divergence modifies limb length between mammals
Cretekos, Chris J., Wang, Ying, Green, Eric D., Martin, James F., Rasweiler, John J., Behringer, Richard R.
Natural selection acts on variation within populations, resulting in modified organ morphology, physiology, and ultimately the formation of new species. Although variation in orthologous proteins can...
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
Prasad, Arjun B., Allard, Marc W., Green, Eric D.
The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among...
Antonellis, Anthony, Huynh, Jimmy L., Lee-Lin, Shih-Queen, Vinton, Ryan M., Renaud, Gabriel, Loftus, Stacie K., ...
Sox10 is a dynamically regulated transcription factor gene that is essential for the development of neural crest–derived and oligodendroglial populations. Developmental genes often require multiple...
Hardy, Robert W., Green, Eric D., Pikul, Frank J., Silva, David P., Koenig, John W., Scott, Mitchell G.
Dynamic evolution of V1R putative pheromone receptors between Mus musculus and Mus spretus
Kurzweil, Vanessa C, Getman, Mike, Green, Eric D, Lane, Robert P
A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene
Dennis, Megan Y., Paracchini, Silvia, Scerri, Thomas S., Prokunina-Olsson, Ludmila, Knight, Julian C., Wade-Martins, Richard, ...
Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility. The causative variant(s) remains unknown but may modulate gene expression,...
Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event
Rudd, M. Katharine, Endicott, RaeLynn M., Friedman, Cynthia, Walker, Megan, Young, Janet M., Osoegawa, Kazutoyo, ...
Subtelomeres are concentrations of interchromosomal segmental duplications capped by telomeric repeats at the ends of chromosomes. The nature of the segments shared by different sets of human...
Tsipouri, Vicky, Schueler, Mary G, Hu, Sufen, Dutra, Amalia, Pak, Evgenia, Riethman, Harold, ...
Comparative mapping and sequencing was used to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome.