Search

Your search keyword '"Shoresh, Noam"' showing total 255 results
Start Over Author "Shoresh, Noam"
255 results on '"Shoresh, Noam"'

1. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Author

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Cortez Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, J, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Bernstein, Bradley, and Guigó, Roderic

Subjects
ENCODE, GTEx, allele-specific activity, eQTLs, functional epigenomes, functional genomics, genome annotations, personal genome, predictive models, structural variants, tissue specificity, transformer model, Epigenome, Quantitative Trait Loci, Genome-Wide Association Study, Genomics, Phenotype, Polymorphism, Single Nucleotide
Abstract

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

Published
2023

2. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author

Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.

Published
2022

4. Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author

Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Vaccine Related (AIDS), Prevention, Immunization, Vaccine Related, HIV/AIDS, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Chromatin, DNA, DNA Footprinting, DNA Methylation, DNA Replication Timing, Databases, Genetic, Deoxyribonuclease I, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Mice, Transgenic, Molecular Sequence Annotation, RNA-Binding Proteins, Registries, Regulatory Sequences, Nucleic Acid, Transcription, Genetic, Transposases, ENCODE Project Consortium, General Science & Technology
Abstract

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Published
2020

5. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Author

ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
ENCODE Project Consortium, Chromatin, Animals, Mice, Transgenic, Humans, Mice, Deoxyribonuclease I, Transposases, RNA-Binding Proteins, Histones, DNA, Registries, DNA Footprinting, Genomics, DNA Methylation, DNA Replication Timing, Transcription, Genetic, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Databases, Genetic, Molecular Sequence Annotation, Human Genome, HIV/AIDS, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Published
2020

6. “Multiplexed screen identifies aPseudomonas aeruginosa-specific small molecule targeting the outer membrane protein OprH and its interaction with LPS”

Author

Poulsen, Bradley E., primary, Warrier, Thulasi, additional, Barkho, Sulyman, additional, Bagnall, Josephine, additional, Romano, Keith P., additional, White, Tiantian, additional, Yu, Xiao, additional, Kawate, Tomohiko, additional, Nguyen, Phuong H., additional, Raines, Kyra, additional, Ferrara, Kristina, additional, Golas, Aaron, additional, Fitzgerald, Michael, additional, Boeszoermenyi, Andras, additional, Kaushik, Virendar, additional, Serrano-Wu, Michael, additional, Shoresh, Noam, additional, and Hung, Deborah T., additional

Published
2024
Full Text
View/download PDF

9. Genetic and epigenetic fine mapping of causal autoimmune disease variants

Author

Farh, Kyle Kai-How, Marson, Alexander, Zhu, Jiang, Kleinewietfeld, Markus, Housley, William J, Beik, Samantha, Shoresh, Noam, Whitton, Holly, Ryan, Russell JH, Shishkin, Alexander A, Hatan, Meital, Carrasco-Alfonso, Marlene J, Mayer, Dita, Luckey, C John, Patsopoulos, Nikolaos A, De Jager, Philip L, Kuchroo, Vijay K, Epstein, Charles B, Daly, Mark J, Hafler, David A, and Bernstein, Bradley E

Subjects
Immunization, Human Genome, Vaccine Related, Autoimmune Disease, Genetics, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Inflammatory and immune system, Autoimmune Diseases, Base Sequence, Chromatin, Consensus Sequence, Enhancer Elements, Genetic, Epigenesis, Genetic, Epigenomics, Genome-Wide Association Study, Humans, Nucleotide Motifs, Organ Specificity, Polymorphism, Single Nucleotide, T-Lymphocytes, Transcription Factors, General Science & Technology
Abstract

Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated CD4(+) T-cell subsets, regulatory T cells, CD8(+) T cells, B cells, and monocytes. We find that ∼90% of causal variants are non-coding, with ∼60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10-20% directly alter recognizable transcription factor binding motifs. Rather, most non-coding risk variants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models.

Published
2015

10. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination

Author

Bhattacharyya, Roby P., Bandyopadhyay, Nirmalya, Ma, Peijun, Son, Sophie S., Liu, Jamin, He, Lorrie L., Wu, Lidan, Khafizov, Rustem, Boykin, Rich, Cerqueira, Gustavo C., Pironti, Alejandro, Rudy, Robert F., Patel, Milesh M., Yang, Rui, Skerry, Jennifer, Nazarian, Elizabeth, Musser, Kimberly A., Taylor, Jill, Pierce, Virginia M., Earl, Ashlee M., Cosimi, Lisa A., Shoresh, Noam, Beechem, Joseph, Livny, Jonathan, and Hung, Deborah T.

Published
2019
Full Text
View/download PDF

11. Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

Author

Cejas, Paloma, Drier, Yotam, Dreijerink, Koen M. A., Brosens, Lodewijk A. A., Deshpande, Vikram, Epstein, Charles B., Conemans, Elfi B., Morsink, Folkert H. M., Graham, Mindy K., Valk, Gerlof D., Vriens, Menno R., Castillo, Carlos Fernandez-del, Ferrone, Cristina R., Adar, Tomer, Bowden, Michaela, Whitton, Holly J., Da Silva, Annacarolina, Font-Tello, Alba, Long, Henry W., Gaskell, Elizabeth, Shoresh, Noam, Heaphy, Christopher M., Sicinska, Ewa, Kulke, Matthew H., Chung, Daniel C., Bernstein, Bradley E., and Shivdasani, Ramesh A.

Published
2019
Full Text
View/download PDF

12. Comparative analysis of metazoan chromatin organization

Author

Ho, Joshua WK, Jung, Youngsook L, Liu, Tao, Alver, Burak H, Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y, Appert, Alex, Parker, Stephen CJ, Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C, Bishop, Eric, Egelhofer, Thea A, Hu, Sheng'en Shawn, Alekseyenko, Artyom A, Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A, Bowman, Sarah K, Chen, Q Brent, Chen, Ron A-J, Day, Daniel S, Dong, Yan, Dose, Andrea C, Duan, Xikun, Epstein, Charles B, Ercan, Sevinc, Feingold, Elise A, Ferrari, Francesco, Garrigues, Jacob M, Gehlenborg, Nils, Good, Peter J, Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M, Jeffers, Tess E, Kharchenko, Peter V, Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V, Kumar, Nischay, Langley, Sasha A, Larschan, Erica N, Latorre, Isabel, Libbrecht, Maxwell W, Lin, Xueqiu, Park, Richard, Pazin, Michael J, Pham, Hoang N, Plachetka, Annette, Qin, Bo, Schwartz, Yuri B, Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M, Xue, Huiling, Kingston, Robert E, Kim, Ju Han, Bernstein, Bradley E, Dernburg, Abby F, Pirrotta, Vincenzo, Kuroda, Mitzi I, Noble, William S, Tullius, Thomas D, Kellis, Manolis, MacAlpine, David M, Strome, Susan, Elgin, Sarah CR, Liu, Xiaole Shirley, Lieb, Jason D, Ahringer, Julie, Karpen, Gary H, and Park, Peter J

Subjects
Biochemistry and Cell Biology, Biological Sciences, Immunization, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Caenorhabditis elegans, Cell Line, Centromere, Chromatin, Chromatin Assembly and Disassembly, DNA Replication, Drosophila melanogaster, Enhancer Elements, Genetic, Epigenesis, Genetic, Heterochromatin, Histones, Humans, Molecular Sequence Annotation, Nuclear Lamina, Nucleosomes, Promoter Regions, Genetic, Species Specificity, General Science & Technology
Abstract

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.

Published
2014

13. Light hadron spectroscopy in quenched QCD with overlap fermions

Author

Babich, Ronald, Berruto, Federico, Garron, Nicolas, Hoelbling, Christian, Howard, Joseph, Lellouch, Laurent, Rebbi, Claudio, and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

A simulation of quenched QCD with the overlap Dirac operator has been carried out using 100 Wilson gauge configurations at beta = 6 on an 18^3 x 64 lattice and at beta = 5.85 on a 14^3 x 48 lattice. Here we present results for meson masses, meson final state "wave functions," decay constants, and other observables, as well as details on our algorithmic and data analysis techniques. We also summarize results for baryon masses and quark and diquark propagators in the Landau gauge., Comment: 11 pages, 17 figures. Combined contribution by C.R. and R.B. to Lattice 2005 (Hadron spectrum and quark masses), Trinity College, Dublin, 25-30 July 2005

Published
2005

14. Light hadron and diquark spectroscopy in quenched QCD with overlap quarks on a large lattice

Author

Babich, Ronald, Berruto, Federico, Garron, Nicolas, Hoelbling, Christian, Howard, Joseph, Lellouch, Laurent, Rebbi, Claudio, and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

A simulation of quenched QCD with the overlap Dirac operator has been completed using 100 Wilson gauge configurations at beta = 6 on an 18^3 x 64 lattice and at beta = 5.85 on a 14^3 x 48 lattice, both in Landau gauge. We present results for light meson and baryon masses, meson final state "wave functions," and other observables, as well as some details on the numerical techniques that were used. Our results indicate that scaling violations, if any, are small. We also present an analysis of diquark correlations using the quark propagators generated in our simulation., Comment: 28 LaTeX pages, 41 figures, v2: minor updates, version published in JHEP

Published
2005
Full Text
View/download PDF

15. Chiral Perturbation Theory for Staggered Sea Quarks and Ginsparg-Wilson Valence Quarks

Author

Baer, Oliver, Bernard, Claude, Rupak, Gautam, and Shoresh, Noam

Subjects
High Energy Physics - Lattice, Nuclear Theory
Abstract

We study lattice QCD with staggered sea and Ginsparg-Wilson valence quarks. The Symanzik effective action for this mixed lattice theory, including the lattice spacing contributions of O(a^2), is derived. Using this effective theory we construct the leading order chiral Lagrangian. The masses and decay constants of pseudoscalars containing two Ginsparg-Wilson valence quarks are computed at one loop order., Comment: 38 pages, 5 figures, LaTeX2e; references added and typos corrected

Published
2005
Full Text
View/download PDF

16. Electroweak penguins and SUSY K^0-\bar K^0 mixing with Neuberger quarks

Author

Berruto, Federico, Garron, Nicolas, Hoelbling, Christian, Howard, Joseph, Lellouch, Laurent, Necco, Silvia, Rebbi, Claudio, and Shoresh, Noam

Subjects
High Energy Physics - Lattice, High Energy Physics - Phenomenology
Abstract

We present results for Delta I=3/2 and Delta S=2 matrix elements relevant for CP violation in K->Pi Pi decays and for the K_S-K_L mass difference in the standard model and beyond. They were obtained with Neuberger fermions on quenched gauge configurations generated with the Wilson plaquette action at beta=6.0 on an 18^3x64 lattice., Comment: 4 LaTeX pages (espcrc2.sty), 6 figures. Combined contributions by J.H., L.L. and C.R. at Lattice2004(weak), Fermilab, June 21-26, 2004

Published
2004
Full Text
View/download PDF

17. Light hadron spectra and wave functions in quenched QCD with overlap quarks on a large lattice

Author

Berruto, Federico, Garron, Nicolas, Hoelbling, Christian, Howard, Joseph, Lellouch, Laurent, Necco, Silvia, Rebbi, Claudio, and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

A simulation of quenched QCD with the overlap Dirac operator has been completed using 100 Wilson gauge configurations at beta=6 on an 18^3x64 lattice. We present results for meson and baryon masses, meson final state "wave functions'' and other observables., Comment: 5 LaTeX pages (espcrc2.sty), 13 figures. Combined contributions by J.H., L.L. and C.R. at Lattice2004(spectrum), Fermilab, June 21-26, 2004

Published
2004
Full Text
View/download PDF

18. Preliminary results from a simulation of quenched QCD with overlap fermions on a large lattice

Author

Berruto, Federico, Garron, Nicolas, Hoelbling, Christian, Lellouch, Laurent, Rebbi, Claudio, and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

We simulate quenched QCD with the overlap Dirac operator. We work with the Wilson gauge action at beta=6 on an 18^3x64 lattice. We calculate quark propagators for a single source point and quark mass ranging from am_q=0.03 to 0.75. We present here preliminary results based on the propagators for 60 gauge field configurations., Comment: Lattice2003(chiral); 9 latex pages (espcrc2.sty), 13 figures. Based on talks given by C.H., L.L. and C.R. at 21st International Symposium on Lattice Field Theory (Lattice 2003), Tsubuka, Japan, 15-19 July 2003. Repitition in references corrected and one reference added

Published
2003
Full Text
View/download PDF

19. Chiral perturbation theory at O(a^2) for lattice QCD

Author

Baer, Oliver, Rupak, Gautam, and Shoresh, Noam

Subjects
High Energy Physics - Lattice, Nuclear Theory
Abstract

We construct the chiral effective Lagrangian for two lattice theories: one with Wilson fermions and the other with Wilson sea fermions and Ginsparg-Wilson valence fermions. For each of these theories we construct the Symanzik action through order $a^2$. The chiral Lagrangian is then derived, including terms of order $a^2$, which have not been calculated before. We find that there are only few new terms at this order. Corrections to existing coefficients in the continuum chiral Lagrangian are proportional to $a^2$, and appear in the Lagrangian at order $a^2 p^2$ or higher. Similarly, O(4) symmetry breaking terms enter the Symanzik action at order $a^2$, but contribute to the chiral Lagrangian at order $a^2 p^4$ or higher. We calculate the light meson masses in chiral perturbation theory for both lattice theories. At next-to-leading order, we find that there are no order $a^2$ corrections to the valence-valence meson mass in the mixed theory due to the enhanced chiral symmetry of the valence sector., Comment: 25 pages, LaTeX2e; references added

Published
2003
Full Text
View/download PDF

21. Chiral perturbation theory for the Wilson lattice action

Author

Rupak, Gautam and Shoresh, Noam

Subjects
High Energy Physics - Lattice, High Energy Physics - Phenomenology, Nuclear Theory
Abstract

We extend chiral perturbation theory to include linear dependence on the lattice spacing $a$ for the Wilson action. The perturbation theory is written as a double expansion in the small quark mass $m_q$ and lattice spacing $a$. We present formulae for the mass and decay constant of a flavor-non-singlet meson in this scheme to order $a$ and $m_q^2$. The extension to the partially quenched theory is also described., Comment: 9 pages LaTeX2e

Published
2002
Full Text
View/download PDF

22. Partially quenched chiral perturbation theory without $\Phi_0$

Author

Sharpe, Stephen and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

This paper completes the argument that lattice simulations of partially quenched QCD can provide quantitative information about QCD itself, with the aid of partially quenched chiral perturbation theory. A barrier to doing this has been the inclusion of $\Phi_0$, the partially quenched generalization of the $\eta'$, in previous calculations in the partially quenched effective theory. This invalidates the low energy perturbative expansion, gives rise to many new unknown parameters, and makes it impossible to reliably calculate the relation between the partially quenched theory and low energy QCD. We show that it is straightforward and natural to formulate partially quenched chiral perturbation theory without $\Phi_0$, and that the resulting theory contains the effective theory for QCD without the $\eta'$. We also show that previous results, obtained including $\Phi_0$, can be reinterpreted as applying to the theory without $\Phi_0$. We contrast the situation with that in the quenched effective theory, where we explain why it is necessary to include $\Phi_0$. We also compare the derivation of chiral perturbation theory in partially quenched QCD with the standard derivation in unquenched QCD. We find that the former cannot be justified as rigorously as the latter, because of the absence of a physical Hilbert space. Finally, we present an encouraging result: unphysical double poles in certain correlation functions in partially quenched chiral perturbation theory can be shown to be a property of the underlying theory, given only the symmetries and some plausible assumptions., Comment: 45 pages, no figures

Published
2001
Full Text
View/download PDF

23. Physical Results from Partially Quenched Simulation

Author

Sharpe, Stephen and Shoresh, Noam

Subjects
High Energy Physics - Lattice
Abstract

We describe how one can use chiral perturbation theory to obtain results for physical quantities, such as quark masses, using partially quenched simulations., Comment: Written version of two talks at DPF 2000. 6 pages, 2 figures

Published
2000
Full Text
View/download PDF

24. Physical Results from Unphysical Simulations

Author

Sharpe, Stephen and Shoresh, Noam

Subjects
High Energy Physics - Lattice, High Energy Physics - Phenomenology
Abstract

We calculate various properties of pseudoscalar mesons in partially quenched QCD using chiral perturbation theory through next-to-leading order. Our results can be used to extrapolate to QCD from partially quenched simulations, as long as the latter use three light dynamical quarks. In other words, one can use unphysical simulations to extract physical quantities - in this case the quark masses, meson decay constants, and the Gasser-Leutwyler parameters L_4-L_8. Our proposal for determining L_7 makes explicit use of an unphysical (yet measurable) effect of partially quenched theories, namely the double-pole that appears in certain two-point correlation functions. Most of our calculations are done for sea quarks having up to three different masses, except for our result for L_7, which is derived for degenerate sea quarks., Comment: 26 pages, 12 figures (discussion on discretization errors at end of sec. IV clarified; minor improvements in presentation; results unchanged)

Published
2000
Full Text
View/download PDF

25. Mapping and analysis of chromatin state dynamics in nine human cell types

Author

Ernst, Jason, Kheradpour, Pouya, Mikkelsen, Tarjei S, Shoresh, Noam, Ward, Lucas D, Epstein, Charles B, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael, Ku, Manching, Durham, Timothy, Kellis, Manolis, and Bernstein, Bradley E

Subjects
Genetics, Biotechnology, Cancer, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Binding Sites, Cell Line, Cell Line, Tumor, Cell Physiological Phenomena, Cells, Cultured, Chromatin, Chromosome Mapping, Gene Expression Regulation, Genome, Human, Hep G2 Cells, Humans, Promoter Regions, Genetic, Reproducibility of Results, Transcription Factors, General Science & Technology
Abstract

Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.

Published
2011

26. NNLO Calculation of Two-Nucleon Scattering in EFT for a Two Yukawa Toy Model

Author

Rupak, Gautam and Shoresh, Noam

Subjects
Nuclear Theory
Abstract

The effective field theory (EFT) for a toy model of nucleons interacting via a short range and a long range Yukawa potential is presented. The scattering amplitude in the 1S0 channel is calculated up to NNLO using KSW power counting scheme. A particular expansion of the amplitude about the pole at low (imaginary) momentum is used to derive matching conditions for the EFT couplings. In addition, after imposing constraints from a Renormalization Group analysis, there are no new free parameters in the amplitude at NNLO. Comparing the NNLO phase shifts to the full model we show that the EFT expansion is converging., Comment: 24 pages, 11 EPS figures, revtex; typos in formulae corrected; More typos corrected, expressions in appendix added, minor changes in style, graph Fig3(b) replaced

Published
1999
Full Text
View/download PDF

28. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

Author

Hu, Yan, primary, Ma, Sai, additional, Kartha, Vinay K., additional, Duarte, Fabiana M., additional, Horlbeck, Max, additional, Zhang, Ruochi, additional, Shrestha, Rojesh, additional, Labade, Ajay, additional, Kletzien, Heidi, additional, Meliki, Alia, additional, Castillo, Andrew, additional, Durand, Neva, additional, Mattei, Eugenio, additional, Anderson, Lauren J., additional, Tay, Tristan, additional, Earl, Andrew S., additional, Shoresh, Noam, additional, Epstein, Charles B., additional, Wagers, Amy, additional, and Buenrostro, Jason D., additional

Published
2023
Full Text
View/download PDF

31. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Author

Finucane, Hilary K., Reshef, Yakir A., Anttila, Verneri, Slowikowski, Kamil, Gusev, Alexander, Byrnes, Andrea, Gazal, Steven, Loh, Po-Ru, Lareau, Caleb, Shoresh, Noam, Genovese, Giulio, Saunders, Arpiar, Macosko, Evan, Pollack, Samuela, Perry, John R. B., Buenrostro, Jason D., Bernstein, Bradley E., Raychaudhuri, Soumya, McCarroll, Steven, Neale, Benjamin M., and Price, Alkes L.

Published
2018
Full Text
View/download PDF

34. Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA

Author

Bhattacharyya, Roby P., Walker, Mark, Boykin, Rich, Son, Sophie S., Liu, Jamin, Hachey, Austin C., Ma, Peijun, Wu, Lidan, Choi, Kyungyong, Cummins, Kaelyn C., Benson, Maura, Skerry, Jennifer, Ryu, Hyunryul, Wong, Sharon Y., Goldberg, Marcia B., Han, Jongyoon, Pierce, Virginia M., Cosimi, Lisa A., Shoresh, Noam, Livny, Jonathan, Beechem, Joseph, and Hung, Deborah T.

Published
2019
Full Text
View/download PDF

35. At-home Testing and Risk Factors for Acquisition of SARS-CoV-2 Infection in a Major US Metropolitan Area

Author

Woolley, Ann E, primary, Dryden-Peterson, Scott, additional, Kim, Andy, additional, Naz-McLean, Sarah, additional, Kelly, Christina, additional, Laibinis, Hannah H, additional, Bagnall, Josephine, additional, Livny, Jonathan, additional, Ma, Peijun, additional, Orzechowski, Marek, additional, Gomez, James, additional, Shoresh, Noam, additional, Gabriel, Stacey, additional, Hung, Deborah T, additional, and Cosimi, Lisa A, additional

Published
2022
Full Text
View/download PDF

37. Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

Author

Cejas, Paloma, Drier, Yotam, Dreijerink, Koen M. A., Brosens, Lodewijk A. A., Deshpande, Vikram, Epstein, Charles B., Conemans, Elfi B., Morsink, Folkert H. M., Graham, Mindy K., Valk, Gerlof D., Vriens, Menno R., Castillo, Carlos Fernandez-del, Ferrone, Cristina R., Adar, Tomer, Bowden, Michaela, Whitton, Holly J., Da Silva, Annacarolina, Font-Tello, Alba, Long, Henry W., Gaskell, Elizabeth, Shoresh, Noam, Heaphy, Christopher M., Sicinska, Ewa, Kulke, Matthew H., Chung, Daniel C., Bernstein, Bradley E., and Shivdasani, Ramesh A.

Published
2019
Full Text
View/download PDF

38. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author

ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.

Published
2022

39. At-home Testing and Risk Factors for Acquisition of SARS-CoV-2 Infection in a Major US Metropolitan Area

Author

Woolley, Ann E., primary, Dryden-Peterson, Scott, additional, Kim, Andy, additional, Naz-McLean, Sarah, additional, Kelly, Christina, additional, Laibinis, Hannah H., additional, Bagnall, Josephine, additional, Livny, Jonathan, additional, Ma, Peijun, additional, Orzechowski, Marek, additional, Shoresh, Noam, additional, Gabriel, Stacey, additional, Hung, Deborah T., additional, and Cosimi, Lisa A., additional

Published
2022
Full Text
View/download PDF

40. Polyploidy can drive rapid adaptation in yeast

Author

Selmecki, Anna M., Maruvka, Yosef E., Richmond, Phillip A., Guillet, Marie, Shoresh, Noam, Sorenson, Amber L., De, Subhajyoti, Kishony, Roy, Michor, Franziska, Dowell, Robin, and Pellman, David

Subjects
Yeast fungi -- Research, Biological research, Biology, Experimental, Adaptation (Biology) -- Research, Polyploidy -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood (1-4). Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations (2, 5-7). For example, in diverse cell types and organisms, immediately after a whole-genome duplication, newly formed polyploids missegregate chromosomes and undergo genetic instability (8-13). The instability following whole-genome duplications is thought to provide adaptive mutations in microorganisms (13, 14) and can promote tumorigenesis in mammalian cells (11, 15). Polyploidy may also affect adaptation independently of beneficial mutations through ploidy-specific changes in cell physiology (16). Here we perform in vitro evolution experiments to test directly whether polyploidy can accelerate evolutionary adaptation. Compared with haploids and diploids, tetraploids undergo significantly faster adaptation. Mathematical modelling suggests that rapid adaptation of tetraploids is driven by higher rates of beneficial mutations with stronger fitness effects, which is supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provide large fitness gains. We identify several mutations whose beneficial effects are manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation., To determine how polyploidy affects the rate of adaptation, we performed hundreds of independent passaging experiments in a poor carbonsource medium (raffinose, Fig. 1a), comparing isogenic haploid (1N), diploid (2N), [...]

Published
2015

41. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

Author

Fridman, Ofer, Goldberg, Amir, Ronin, Irine, Shoresh, Noam, and Balaban, Nathalie Q.

Subjects
Drug resistance in microorganisms -- Natural history, Drug tolerance -- Natural history, Microbial colonies -- Natural history, Antibiotics -- Dosage and administration, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The great therapeutic achievements of antibiotics have been dramatically undercut by the evolution of bacterial strategies that overcome antibiotic stress (1,2). These strategies fall into two classes. 'Resistance' makes it possible for a microorganism to grow in the constant presence of the antibiotic, provided that the concentration of the antibiotic is not too high. 'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic concentrations, as long as the duration of the treatment is limited. Although both resistance and tolerance are important reasons for the failure of antibiotic treatments (3-6), the evolution of resistance (7-9) is much better understood than that of tolerance. Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. We found that all strains adapted by specific genetic mutations, which became fixed in the evolved populations. By monitoring the phenotypic changes at the population and single-cell levels, we found that the first adaptive change to antibiotic stress was the development of tolerance through a major adjustment in the single-cell lag-time distribution, without a change in resistance. Strikingly, we found that the lag time of bacteria before regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome sequencing of the evolved strains and restoration of the wild-type alleles allowed us to identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag' (tbl). Better understanding of lag-time evolution as a key determinant of the survival of bacterial populations under high antibiotic concentrations could lead to new approaches to impeding the evolution of antibiotic resistance., We exposed batch cultures of the bacterium Escherichia coli to a high concentration of ampicillin (100 µg [ml.sup.-1]), which is 15 times greater than the minimum inhibitory concentration (MIC), in [...]

Published
2014

46. Integrative analysis of 111 reference human epigenomes

Author

Consortium, Roadmap Epigenomics, Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Bilenky, Misha, Yen, Angela, Heravi-Moussavi, Alireza, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ziller, Michael J., Whitaker, John W., Ward, Lucas D., Sarkar, Abhishek, Sandstrom, Richard S., Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Harris, Alan R., Epstein, Charles B., Leung, Danny, Hawkins, David R., Hong, Chibo, Mungall, Andrew J., Chuah, Eric, Hansen, Scott R., Bansal, Mukul S., Dixon, Jesse R., Feizi, Soheil, Kim, Ah-Ram, Li, Daofeng, Elliott, GiNell, Neph, Shane J., Polak, Paz, Ray, Pradipta, Siebenthall, Kyle T., Thurman, Robert E., Zhou, Xin, Boyer, Laurie A., De Jager, Philip L., Fisher, Susan J., Li, Wei, McManus, Michael T., Sunyaev, Shamil, Tlsty, Thea D., Wang, Wei, Waterland, Robert A., Costello, Joseph F., Hirst, Martin, Stamatoyannopoulos, John A., Wang, Ting, Amin, Viren, Schultz, Matthew D., Quon, Gerald, Eaton, Matthew L., Pfenning, Andreas, Liu, Melina ClaussnitzerYaping, Coarfa, Cristian, Shoresh, Noam, Gjoneska, Elizabeta, Xie, Wei, Lister, Ryan, Moore, Richard, Tam, Angela, Canfield, Theresa K., Kaul, Rajinder, Sabo, Peter J., Carles, Annaick, Farh, Kai-How, Karlic, Rosa, Kulkarni, Ashwinikumar, Lowdon, Rebecca, Mercer, Tim R., Onuchic, Vitor, Rajagopal, Nisha, Sallari, Richard C., Sinnott-Armstrong, Nicholas A., Stevens, Michael, Wu, Jie, Zhang, Bo, Abdennur, Nezar, Adli, Mazhar, Akerman, Martin, Barrera, Luis, Antosiewicz-Bourget, Jessica, Ballinger, Tracy, Barnes, Michael J., Bates, Daniel, Bell, Robert J. A., Bennett, David A., Bianco, Katherine, Bock, Christoph, Boyle, Patrick, Brinchmann, Jan, Caballero-Campo, Pedro, Camahort, Raymond, Carrasco-Alfonso, Marlene J., Charnecki, Timothy, Chen, Huaming, Chen, Zhao, Cheng, Jeffrey B., Cho, Stephanie, Chu, Andy, Chung, Wen-Yu, Cowan, Chad, Deng, Qixia Athena, Deshpande, Vikram, Diegel, Morgan, Ding, Bo, Durham, Timothy, Echipare, Lorigail, Edsall, Lee, Flowers, David, Genbacev-Krtolica, Olga, Gifford, Casey, Gillespie, Shawn, Giste, Erika, Glass, Ian A., Gnirke, Andreas, Gormley, Matthew, Gu, Hongcang, Gu, Junchen, Hafler, David A., Hangauer, Matthew J., Hariharan, Manoj, Hatan, Meital, Haugen, Eric, He, Yupeng, Heimfeld, Shelly, Herlofsen, Sarah, Hou, Zhonggang, Humbert, Richard, Issner, Robbyn, Jackson, Andrew R., Jia, Haiyang, Jiang, Peng, Johnson, Audra K., Kadlecek, Theresa, Kamoh, Baljit, Kapidzic, Mirhan, Kent, Jim, Kim, Audrey, Kleinewietfeld, Markus, Klugman, Sarit, Krishnan, Jayanth, Kuan, Samantha, Kutyavin, Tanya, Lee, Ah-Young, Lee, Kristen, Li, Jian, Li, Nan, Li, Yan, Ligon, Keith L., Lin, Shin, Lin, Yiing, Liu, Jie, Liu, Yuxuan, Luckey, John C., Ma, Yussanne P., Maire, Cecile, Marson, Alexander, Mattick, John S., Mayo, Michael, McMaster, Michael, Metsky, Hayden, Mikkelsen, Tarjei, Miller, Diane, Miri, Mohammad, Mukame, Eran, Nagarajan, Raman P., Neri, Fidencio, Nery, Joseph, Nguyen, Tung, OʼGeen, Henriette, Paithankar, Sameer, Papayannopoulou, Thalia, Pelizzola, Mattia, Plettner, Patrick, Propson, Nicholas E., Raghuraman, Sriram, Raney, Brian J., Raubitschek, Anthony, Reynolds, Alex P., Richards, Hunter, Riehle, Kevin, Rinaudo, Paolo, Robinson, Joshua F., Rockweiler, Nicole B., Rosen, Evan, Rynes, Eric, Schein, Jacqueline, Sears, Renee, Sejnowski, Terrence, Shafer, Anthony, Shen, Li, Shoemaker, Robert, Sigaroudinia, Mahvash, Slukvin, Igor, Stehling-Sun, Sandra, Stewart, Ron, Subramanian, Sai Lakshmi, Suknuntha, Kran, Swanson, Scott, Tian, Shulan, Tilden, Hannah, Tsai, Linus, Urich, Mark, Vaughn, Ian, Vierstra, Jeff, Vong, Shinny, Wagner, Ulrich, Wang, Hao, Wang, Tao, Wang, Yunfei, Weiss, Arthur, Whitton, Holly, Wildberg, Andre, Witt, Heather, Won, Kyoung-Jae, Xie, Mingchao, Xing, Xiaoyun, Xu, Iris, Xuan, Zhenyu, Ye, Zhen, Yen, Chia-an, Yu, Pengzhi, Zhang, Xian, Zhang, Xiaolan, Zhao, Jianxin, Zhou, Yan, Zhu, Jiang, Zhu, Yun, Ziegler, Steven, Beaudet, Arthur E., Farnham, Peggy J., Haussler, David, Jones, Steven J. M., Marra, Marco A., Thomson, James A., Tsai, Li-Huei, Zhang, Michael Q., Chadwick, Lisa H., Bernstein, Bradley E., Ecker, Joseph R., Meissner, Alexander, Milosavljevic, Aleksandar, Ren, Bing, and Kellis, Manolis

Published
2015
Full Text
View/download PDF

47. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
Full Text
View/download PDF

48. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Author

Rozowsky, Joel, primary, Drenkow, Jorg, additional, Yang, Yucheng T, additional, Gursoy, Gamze, additional, Galeev, Timur, additional, Borsari, Beatrice, additional, Epstein, Charles B, additional, Xiong, Kun, additional, Xu, Jinrui, additional, Gao, Jiahao, additional, Yu, Keyang, additional, Berthel, Ana, additional, Chen, Zhanlin, additional, Navarro, Fabio, additional, Liu, Jason, additional, Sun, Maxwell S, additional, Wright, James, additional, Chang, Justin, additional, Cameron, Christopher JF, additional, Shoresh, Noam, additional, Gaskell, Elizabeth, additional, Adrian, Jessika, additional, Aganezov, Sergey, additional, Aguet, François, additional, Balderrama-Gutierrez, Gabriela, additional, Banskota, Samridhi, additional, Corona, Guillermo Barreto, additional, Chee, Sora, additional, Chhetri, Surya B, additional, Cortez Martins, Gabriel Conte, additional, Danyko, Cassidy, additional, Davis, Carrie A, additional, Farid, Daniel, additional, Farrell, Nina P, additional, Gabdank, Idan, additional, Gofin, Yoel, additional, Gorkin, David U, additional, Gu, Mengting, additional, Hecht, Vivian, additional, Hitz, Benjamin C, additional, Issner, Robbyn, additional, Kirsche, Melanie, additional, Kong, Xiangmeng, additional, Lam, Bonita R, additional, Li, Shantao, additional, Li, Bian, additional, Li, Tianxiao, additional, Li, Xiqi, additional, Lin, Khine Zin, additional, Luo, Ruibang, additional, Mackiewicz, Mark, additional, Moore, Jill E, additional, Mudge, Jonathan, additional, Nelson, Nicholas, additional, Nusbaum, Chad, additional, Popov, Ioann, additional, Pratt, Henry E, additional, Qiu, Yunjiang, additional, Ramakrishnan, Srividya, additional, Raymond, Joe, additional, Salichos, Leonidas, additional, Scavelli, Alexandra, additional, Schreiber, Jacob M, additional, Sedlazeck, Fritz J, additional, See, Lei Hoon, additional, Sherman, Rachel M, additional, Shi, Xu, additional, Shi, Minyi, additional, Sloan, Cricket Alicia, additional, Strattan, J Seth, additional, Tan, Zhen, additional, Tanaka, Forrest Y, additional, Vlasova, Anna, additional, Wang, Jun, additional, Werner, Jonathan, additional, Williams, Brian, additional, Xu, Min, additional, Yan, Chengfei, additional, Yu, Lu, additional, Zaleski, Christopher, additional, Zhang, Jing, additional, Ardlie, Kristin, additional, Cherry, J Michael, additional, Mendenhall, Eric M, additional, Noble, William S, additional, Weng, Zhiping, additional, Levine, Morgan E, additional, Dobin, Alexander, additional, Wold, Barbara, additional, Mortazavi, Ali, additional, Ren, Bing, additional, Gillis, Jesse, additional, Myers, Richard M, additional, Snyder, Michael P, additional, Choudhary, Jyoti, additional, Milosavljevic, Aleksandar, additional, Schatz, Michael C, additional, Guigó, Roderic, additional, Bernstein, Bradley E, additional, Gingeras, Thomas R, additional, and Gerstein, Mark, additional

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results