Search Results - "Margulies, Elliott H."

A Transcriptomic Atlas of Mouse Neocortical Layers by Belgard, T. Grant, Marques, Ana C., Oliver, Peter L., Abaan, Hatice Ozel, Sirey, Tamara M., Hoerder-Suabedissen, Anna, García-Moreno, Fernando, Molnár, Zoltán, Margulies, Elliott H., Ponting, Chris P.

“…In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement is likely to contribute to…”
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A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree by Eberle, Michael A, Fritzilas, Epameinondas, Krusche, Peter, Källberg, Morten, Moore, Benjamin L, Bekritsky, Mitchell A, Iqbal, Zamin, Chuang, Han-Yu, Humphray, Sean J, Halpern, Aaron L, Kruglyak, Semyon, Margulies, Elliott H, McVean, Gil, Bentley, David R

“…Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of…”
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Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms by Raczy, Come, Petrovski, Roman, Saunders, Christopher T, Chorny, Ilya, Kruglyak, Semyon, Margulies, Elliott H, Chuang, Han-Yu, Källberg, Morten, Kumar, Swathi A, Liao, Arnold, Little, Kristina M, Strömberg, Michael P, Tanner, Stephen W

“…An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant…”
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High-Resolution Mapping and Characterization of Open Chromatin across the Genome by Boyle, Alan P., Davis, Sean, Shulha, Hennady P., Meltzer, Paul, Margulies, Elliott H., Weng, Zhiping, Furey, Terrence S., Crawford, Gregory E.

“…Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers,…”
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Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler by Zerbino, Daniel R, McEwen, Gayle K, Margulies, Elliott H, Birney, Ewan

“…Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in…”
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Accurate and comprehensive sequencing of personal genomes by Ajay, Subramanian S, Parker, Stephen C J, Abaan, Hatice Ozel, Fajardo, Karin V Fuentes, Margulies, Elliott H

“…As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to…”
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Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites by Hogart, Amber, Lichtenberg, Jens, Ajay, Subramanian S, Anderson, Stacie, Margulies, Elliott H, Bodine, David M

“…DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse…”
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Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing by Teer, Jamie K, Bonnycastle, Lori L, Chines, Peter S, Hansen, Nancy F, Aoyama, Natsuyo, Swift, Amy J, Abaan, Hatice Ozel, Albert, Thomas J, Margulies, Elliott H, Green, Eric D, Collins, Francis S, Mullikin, James C, Biesecker, Leslie G

“…Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods…”
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Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors by Belgard, T. Grant, Montiel, Juan F., Wang, Wei Zhi, García-Moreno, Fernando, Margulies, Elliott H., Ponting, Chris P., Molnár, Zoltán

“…The thorniest problem in comparative neurobiology is the identification of the particular brain region of birds and reptiles that corresponds to the mammalian…”
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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation by Pilon, Andre M., Ajay, Subramanian S., Kumar, Swathi Ashok, Steiner, Laurie A., Cherukuri, Praveen F., Wincovitch, Stephen, Anderson, Stacie M., Mullikin, James C., Gallagher, Patrick G., Hardison, Ross C., Margulies, Elliott H., Bodine, David M.

“…Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by…”
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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection by Shibata, Yoichiro, Sheffield, Nathan C, Fedrigo, Olivier, Babbitt, Courtney C, Wortham, Matthew, Tewari, Alok K, London, Darin, Song, Lingyun, Lee, Bum-Kyu, Iyer, Vishwanath R, Parker, Stephen C J, Margulies, Elliott H, Wray, Gregory A, Furey, Terrence S, Crawford, Gregory E

“…Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding…”
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Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS) by Crawford, Gregory E, Holt, Ingeborg E, Whittle, James, Webb, Bryn D, Tai, Denise, Davis, Sean, Margulies, Elliott H, Chen, YiDong, Bernat, John A, Ginsburg, David, Zhou, Daixing, Luo, Shujun, Vasicek, Thomas J, Daly, Mark J, Wolfsberg, Tyra G, Collins, Francis S

“…A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I…”
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Large-Scale Sequencing of the CD33-Related Siglec Gene Cluster in Five Mammalian Species Reveals Rapid Evolution by Multiple Mechanisms by Angata, Takashi, Margulies, Elliott H., Green, Eric D., Varki, Ajit, Goodman, Morris

“…Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs…”
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Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements by Nikolaev, Sergey I, Montoya-Burgos, Juan I, Popadin, Konstantin, Parand, Leila, Margulies, Elliott H, Antonarakis, Stylianos E

“…A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans…”
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Somatic Mutations in MAP3K5 Attenuate Its Proapoptotic Function in Melanoma through Increased Binding to Thioredoxin by Prickett, Todd D., Zerlanko, Brad, Gartner, Jared J., Parker, Stephen C.J., Dutton-Regester, Ken, Lin, Jimmy C., Teer, Jamie K., Wei, Xiaomu, Jiang, Jiji, NISC Comparative Sequencing Program, Chen, Guo, Davies, Michael A., Gershenwald, Jeffrey E., Robinson, William, Robinson, Steven, Hayward, Nicholas K., Rosenberg, Steven A., Margulies, Elliott H., Samuels, Yardena

“…Patients with advanced metastatic melanoma have poor prognosis and the genetics underlying its pathogenesis are poorly understood. High-throughput sequencing…”
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Early history of mammals is elucidated with the ENCODE multiple species sequencing data by Nikolaev, Sergey, Montoya-Burgos, Juan I, Margulies, Elliott H, Rougemont, Jacques, Nyffeler, Bruno, Antonarakis, Stylianos E

“…Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using…”
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An Initial Strategy for the Systematic Identification of Functional Elements in the Human Genome by Low-Redundancy Comparative Sequencing by Margulies, Elliott H., Vinson, Jade P., NISC Comparative Sequencing Program, Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., Green, Eric D., Lander, Eric S., Mullikin, James C., Clamp, Michele

“…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…”
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Sequencing studies in human genetics: design and interpretation by Goldstein, David B., Allen, Andrew, Keebler, Jonathan, Margulies, Elliott H., Petrou, Steven, Petrovski, Slavé, Sunyaev, Shamil

“…Key Points The interpretation of next-generation sequencing data is technically and conceptually much more challenging than the data used in genome-wide…”
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Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes by Parker, Stephen C J, Gartner, Jared, Cardenas-Navia, Isabel, Wei, Xiaomu, Ozel Abaan, Hatice, Ajay, Subramanian S, Hansen, Nancy F, Song, Lingyun, Bhanot, Umesh K, Killian, J Keith, Gindin, Yevgeniy, Walker, Robert L, Meltzer, Paul S, Mullikin, James C, Furey, Terrence S, Crawford, Gregory E, Rosenberg, Steven A, Samuels, Yardena, Margulies, Elliott H

“…Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the…”
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A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data by Goldfeder, Rachel L, Parker, Stephen C J, Ajay, Subramanian S, Ozel Abaan, Hatice, Margulies, Elliott H

“…The ability to generate whole genome data is rapidly becoming commoditized. For example, a mammalian sized genome (∼3Gb) can now be sequenced using…”
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