Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Flavia Villani"'
Publikováno v:
Epigenetics, Vol 18, Iss 1 (2023)
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A
Externí odkaz:
https://doaj.org/article/68768555ee804a4eac247e004c1feffe
Autor:
Nicole Balasco, Gianluca Damaggio, Luciana Esposito, Flavia Villani, Rita Berisio, Vincenza Colonna, Luigi Vitagliano
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
Abstract The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number o
Externí odkaz:
https://doaj.org/article/ed6f49649a2f4946a07c836ce014213c
Autor:
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
Publikováno v:
Nature. 617:312-324
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the
Autor:
Tristan V de Jong, Yanchao Pan, Pasi Rastas, Daniel Munro, Monika Tutaj, Huda Akil, Chris Benner, Apurva S Chitre, William Chow, Vincenza Colonna, Clifton L Dalgard, Wendy M Demos, Peter A Doris, Erik Garrison, Aron Geurts, Hakan M Gunturkun, Victor Guryev, Thibaut Hourlier, Kerstin Howe, Jun Huang, Ted Kalbfleisch, Panjun Kim, Ling Li, Spencer Mahaffey, Fergal J Martin, Pejman Mohammadi, Ayse Bilge Ozel, Oksana Polesskaya, Michal Pravenec, Pjotr Prins, Jonathan Sebat, Jennifer R Smith, Leah C Solberg Woods, Boris Tabakoff, Alan Tracey, Marcela Uliano-Silva, Flavia Villani, Hongyang Wang, Burt M Sharp, Francesca Telese, Zhihua Jiang, Laura Saba, Xusheng Wang, Terence D Murphy, Abraham A Palmer, Anne E Kwitek, Melinda (Mindy) R Dwinell, Robert W Williams, Jun Z Li, Hao Chen
For over a decade, a large research community has relied on a flawed reference assembly of the genome ofRattus norvegicusknown as Rnor_6.0. The seventh assembly of the rat reference genome4mRatBN7.2, based on the inbred Brown Norway rat, corrects num
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::861340d72a1519c031afadb54233c22a
https://doi.org/10.1101/2023.04.13.536694
https://doi.org/10.1101/2023.04.13.536694
Autor:
Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Sven Nahnsen, Zuyu Yang, Mwaniki N. Moses, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins
Publikováno v:
bioRxiv
Pangenome graphs can represent all variation between multiple genomes, but existing methods for constructing them are biased due to reference-guided approaches. In response, we have developed PanGenome Graph Builder (PGGB), a reference-free pipeline
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fb98b2f69c06b54f2279a8a83df36c34
https://europepmc.org/articles/PMC10104075/
https://europepmc.org/articles/PMC10104075/
Autor:
Mikhail O. Maksimov, Cynthia Wu, David G. Ashbrook, Flavia Villani, Vincenza Colonna, Nima Mousavi, Nichole Ma, Lu Lu, Jonathan K. Pritchard, Alon Goren, Robert W. Williams, Abraham A. Palmer, Melissa Gymrek
Publikováno v:
Genome research, vol 33, iss 5
Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1–6bp. We leveraged whole genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map lo
Autor:
Flavia Villani
Short tandem repeats (STRs) are a class of rapidly mutating genetic elements characterized by repeated units of 1 or more nucleotides. We leveraged whole genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family derived from
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::266ff3159154de4cbb56a98e6ed1ad01
https://doi.org/10.1101/2022.03.02.482700
https://doi.org/10.1101/2022.03.02.482700
Autor:
David G. Ashbrook, Hao Chen, Mustafa Hakan Gunturkun, Flavia Villani, Robert W. Williams, Vincenza Colonna
Linked-read whole genome sequencing methods, such as the 10x Chromium, attach a unique molecular barcode to each high molecular weight DNA molecule. The samples are then sequenced using short-read technology. During analysis, sequence reads sharing t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::555e67e68c7e53dcb8d7e82afc2c56dd
https://doi.org/10.1101/2021.11.02.467006
https://doi.org/10.1101/2021.11.02.467006
Autor:
Cecilia Cisar, Vincenza Colonna, Simon Heumos, Emily Kobayashi, Adam M. Novak, Erik Garrison, Glenn Hickey, Flavia Villani, Benedict Paten, Jordan M. Eizenga
Publikováno v:
Bioinformatics (Oxf., Print) 36 (2021): 5139–5144. doi:10.1093/bioinformatics/btaa640
info:cnr-pdr/source/autori:Jordan M Eizenga, Adam M Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison/titolo:Efficient dynamic variation graphs/doi:10.1093%2Fbioinformatics%2Fbtaa640/rivista:Bioinformatics (Oxf., Print)/anno:2021/pagina_da:5139/pagina_a:5144/intervallo_pagine:5139–5144/volume:36
Bioinformatics
Bioinformatics (Oxf., Online) (2020). doi:10.1093/bioinformatics/btaa640
info:cnr-pdr/source/autori:Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E/titolo:Efficient dynamic variation graphs/doi:10.1093%2Fbioinformatics%2Fbtaa640/rivista:Bioinformatics (Oxf., Online)/anno:2020/pagina_da:/pagina_a:/intervallo_pagine:/volume
info:cnr-pdr/source/autori:Jordan M Eizenga, Adam M Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison/titolo:Efficient dynamic variation graphs/doi:10.1093%2Fbioinformatics%2Fbtaa640/rivista:Bioinformatics (Oxf., Print)/anno:2021/pagina_da:5139/pagina_a:5144/intervallo_pagine:5139–5144/volume:36
Bioinformatics
Bioinformatics (Oxf., Online) (2020). doi:10.1093/bioinformatics/btaa640
info:cnr-pdr/source/autori:Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E/titolo:Efficient dynamic variation graphs/doi:10.1093%2Fbioinformatics%2Fbtaa640/rivista:Bioinformatics (Oxf., Online)/anno:2020/pagina_da:/pagina_a:/intervallo_pagine:/volume
Motivation Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9c96e35a0bc2b9fd861bf35e9cf9ba0b
Autor:
Emily Kobayashi, Adam M. Novak, Simon Heumos, Jordan M. Eizenga, Vincenza Colonna, Benedict Paten, Flavia Villani, Glenn Hickey, Cecilia Cisar, Erik Garrison
MotivationPangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pan
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1b9c74c99fb2bb4e6804f48b774c8f80