Zobrazeno 1 - 10
of 26
pro vyhledávání: '"Siddarth Selvaraj"'
Autor:
William W. Greenwald, He Li, Paola Benaglio, David Jakubosky, Hiroko Matsui, Anthony Schmitt, Siddarth Selvaraj, Matteo D’Antonio, Agnieszka D’Antonio-Chronowska, Erin N. Smith, Kelly A. Frazer
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-17 (2019)
It is currently unclear how quantitative changes in chromatin loop propensity contribute to differential gene regulation. Here, the authors use phased Hi-C, RNA-seq, and ChIP-seq to show that subtle changes in loop propensity associate with different
Externí odkaz:
https://doaj.org/article/f72b1213a233451aa67b2d6cb89c60be
Autor:
Jay Ghurye, Arang Rhie, Brian P Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M Phillippy, Sergey Koren
Publikováno v:
PLoS Computational Biology, Vol 15, Iss 8, p e1007273 (2019)
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scal
Externí odkaz:
https://doaj.org/article/4e2720458e9042768bc79a2b45168547
Autor:
Yan Li, Chloe M Rivera, Haruhiko Ishii, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Jesse R Dixon, Bing Ren
Publikováno v:
PLoS ONE, Vol 9, Iss 12, p e114485 (2014)
The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency fact
Externí odkaz:
https://doaj.org/article/0e24ffcf8509483e901078173ca87330
Autor:
Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S Liu
Publikováno v:
PLoS Computational Biology, Vol 9, Iss 1, p e1002893 (2013)
Knowledge of spatial chromosomal organizations is critical for the study of transcriptional regulation and other nuclear processes in the cell. Recently, chromosome conformation capture (3C) based technologies, such as Hi-C and TCC, have been develop
Externí odkaz:
https://doaj.org/article/49f3dcf30380453396e825d5a6d73f0a
Autor:
Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim
Publikováno v:
Nature, 592, 737-746
Nature
Rhie, A, McCarthy, S A, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, B J, Chaisson, M, Gedman, G L, Cantin, L J, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, S C, Lama, T M, Grutzner, F, Warren, W C, Balakrishnan, C N, Burt, D, George, J M, Biegler, M T, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, A F, Franchini, P, Detrich, H W, Svardal, H, Wagner, M, Naylor, G J P, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, B T, Pesout, T, Houck, M, Misuraca, A, Kingan, S B, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, R E, Putnam, N H, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, R E, Guan, D, London, S E, Clayton, D F, Mello, C V, Friedrich, S R, Lovell, P V, Osipova, E, Al-Ajli, F O, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, R S, Makova, K D, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, B P, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, R H S, Crawford, A J, Gilbert, M T P, Zhang, G, Venkatesh, B, Murphy, R W, Koepfli, K-P, Shapiro, B, Johnson, W E, Di Palma, F, Marques-Bonet, T, Teeling, E C, Warnow, T, Graves, J M, Ryder, O A, Haussler, D, O’Brien, S J, Korlach, J, Lewin, H A, Howe, K, Myers, E W, Durbin, R, Phillippy, A M & Jarvis, E D 2021, ' Towards complete and error-free genome assemblies of all vertebrate species ', Nature, vol. 592, no. 7856, pp. 737-746 . https://doi.org/10.1038/s41586-021-03451-0
Natureevents directory, 592(7856):737-746
Digital.CSIC. Repositorio Institucional del CSIC
instname
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
Nature, 592, 7856, pp. 737-746
Nature
Rhie, A, McCarthy, S A, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, B J, Chaisson, M, Gedman, G L, Cantin, L J, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, S C, Lama, T M, Grutzner, F, Warren, W C, Balakrishnan, C N, Burt, D, George, J M, Biegler, M T, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, A F, Franchini, P, Detrich, H W, Svardal, H, Wagner, M, Naylor, G J P, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, B T, Pesout, T, Houck, M, Misuraca, A, Kingan, S B, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, R E, Putnam, N H, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, R E, Guan, D, London, S E, Clayton, D F, Mello, C V, Friedrich, S R, Lovell, P V, Osipova, E, Al-Ajli, F O, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, R S, Makova, K D, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, B P, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, R H S, Crawford, A J, Gilbert, M T P, Zhang, G, Venkatesh, B, Murphy, R W, Koepfli, K-P, Shapiro, B, Johnson, W E, Di Palma, F, Marques-Bonet, T, Teeling, E C, Warnow, T, Graves, J M, Ryder, O A, Haussler, D, O’Brien, S J, Korlach, J, Lewin, H A, Howe, K, Myers, E W, Durbin, R, Phillippy, A M & Jarvis, E D 2021, ' Towards complete and error-free genome assemblies of all vertebrate species ', Nature, vol. 592, no. 7856, pp. 737-746 . https://doi.org/10.1038/s41586-021-03451-0
Natureevents directory, 592(7856):737-746
Digital.CSIC. Repositorio Institucional del CSIC
instname
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
Nature, 592, 7856, pp. 737-746
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address t
Autor:
David Porubsky, Gulhan Kaya, Ruta Sahasrabudhe, James C. Mullikin, Joel Armstrong, Amy B. Wilfert, Jonathan Wood, Edmund Howe, Ariel Gershman, Amalia Dutra, Jon Matthew Belton, Alexander M. Chang, Karen H. Miga, Valerie A. Schneider, Adam M. Phillippy, Alice Young, Andrey Bzikadze, Tamara A. Potapova, Rosa Ana Risques, Anthony D. Schmitt, Tina A. Graves Lindsay, Gerard G. Bouffard, Nancy F. Hansen, Benedict Paten, Josh Quick, Ira M. Hall, Glennis A. Logsdon, Sergey Koren, Kristof Tigyi, Nadine Holmes, Daniela C. Soto, Beth A. Sullivan, Jeanne Fredrickson, Robert S. Fulton, Siddarth Selvaraj, Milinn Kremitzki, Winston Timp, Nicholas J. Loman, Arang Rhie, Evan E. Eichler, Megan Y. Dennis, Kerstin Howe, Jennifer L. Gerton, Urvashi Surti, Valerie Maduro, Christopher Markovic, Pavel A. Pevzner, Françoise Thibaud-Nissen, William Chow, Shelise Brooks, Evgenia Pak, Matthew Loose, Mitchell R. Vollger
Publikováno v:
Nature, vol 585, iss 7823
Nature
Nature
After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b763e6dc69f68a2c414f6d2d8a9e4a86
https://escholarship.org/uc/item/88w7j3n7
https://escholarship.org/uc/item/88w7j3n7
Autor:
Claudio V. Mello, H. William Detrich, Oliver A. Ryder, George F. Turner, Robert H. S. Kraus, Daryl Eason, Sergey Koren, Stephen J. O'Brien, Ivan Sović, Tandy Warnow, Dave W Burt, Martin Pippel, Mark Diekhans, Jonathan Wood, Sylke Winkler, Joana Damas, Benedict Paten, Shane A. McCarthy, Gregory Gedman, M. Thomas P. Gilbert, David F. Clayton, Erich D. Jarvis, Frank Grützner, Richard E. Green, Andrew J. Crawford, Federica Di Palma, Jason T. Howard, Fergal J. Martin, Brett T. Hannigan, Samantha R. Friedrich, Emma C. Teeling, David Iorns, Woori Kwak, Maximilian Wagner, Iliana Bista, Hiram Clawson, Milan Malinsky, Peter V. Lovell, Gavin J. P. Naylor, Robert S. Harris, Ekaterina Osipova, Sadye Paez, Christopher N. Balakrishnan, Eugene W. Myers, Byrappa Venkatesh, Brian P. Walenz, Warren E. Johnson, Nicholas H. Putnam, Harris A. Lewin, Hannes Svardal, Leanne Haggerty, Andreas F. Kautt, Tomas Marques-Bonet, Luis R Nassar, Maria Simbirsky, Christopher Dunn, William Chow, Marlys L. Houck, Paolo Franchini, Joanna Collins, Jinna Hoffman, Sonja C. Vernes, Alan Tracey, Siddarth Selvaraj, Sarah E. London, Ann C Misuraca, Heebal Kim, Byung June Ko, Trevor Pesout, Françoise Thibaud-Nissen, Jimin George, Jennifer A. Marshall Graves, Arang Rhie, Ying Sims, Mark Wilkinson, Robert W. Murphy, Dengfeng Guan, Axel Meyer, Richard Durbin, Arkarachai Fungtammasan, Sarah Pelan, Lindsey J. Cantin, Erik Garrison, Kerstin Howe, Farooq O. Al-Ajli, Zev N. Kronenberg, Michelle Smith, Paul Flicek, James Torrance, Guojie Zhang, J. H. Kim, Richard Hall, Tanya M. Lama, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Beth Shapiro, Bettina Haase, Andrew Digby, Wesley C. Warren, Alex Hastie, Adam M. Phillippy, Paul Medvedev, Marcela Uliano-Silva, Mark Mooney, Constantina Theofanopoulou, Karen Clark, Chul Hee Lee, Zemin Ning, Olivier Fedrigo, Taylor Edwards, Simona Secomandi, Joyce V. Lee, Jonas Korlach, Patrick Masterson, Jay Ghurye, Jacquelyn Mountcastle, Giulio Formenti, Yang Zhou, Kevin L. Howe, Sarah B. Kingan, Kateryna D. Makova
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1–4. To address thi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ab73960cd65340ab6a1b83ca4de58db9
https://doi.org/10.1101/2020.05.22.110833
https://doi.org/10.1101/2020.05.22.110833
Autor:
Agnieszka D'Antonio-Chronowska, Anthony D. Schmitt, William W. Greenwald, Matteo D’Antonio, Kelly A. Frazer, Paola Benaglio, Hiroko Matsui, Siddarth Selvaraj, He Li, Erin N. Smith, David Jakubosky
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-17 (2019)
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications
Nature communications, vol 10, iss 1
While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate
Autor:
Erin N. Smith, David Jakubosky, Matteo D’Antonio, Paola Benaglio, Kelly A. Frazer, Hiroko Matsui, He Li, Siddarth Selvaraj, Agnieszka D'Antonio-Chronowska, Anthony D. Schmitt, William W. Greenwald
SummaryWhile genetic variation at chromatin loops is relevant for human disease, the relationships between loop strength, genetics, gene expression, and epigenetics are unclear. Here, we quantitatively interrogate this relationship using Hi-C and mol
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::710b2159c01bd89d5accf6804056e391
Autor:
Arang Rhie, Adam M. Phillippy, Brian P. Walenz, Anthony D. Schmitt, Mihai Pop, Jay Ghurye, Sergey Koren, Siddarth Selvaraj
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 15, Iss 8, p e1007273 (2019)
PLoS Computational Biology, Vol 15, Iss 8, p e1007273 (2019)
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::965108da11abc6861159fd83d6b0ca95
https://doi.org/10.1101/261149
https://doi.org/10.1101/261149