bioconductor: ggbio | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.3389/fimmu.2020.565730

Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Cited by: 22
Author(s): Marco Antônio M. Pretti, Rômulo Gonçalves Galvani, Gustavo Fioravanti Vieira, Adriana Bonomo, Martín Bonamino, Mariana Boroni
Software Mentions: 17
Published: almost 4 years ago

10.1186/s13059-020-02233-7

tidybulk: an R tidy framework for modular transcriptomic data analysis
Cited by: 22
Author(s): Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle, Anthony T. Papenfuss
Software Mentions: 13
Published: almost 4 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: over 4 years ago

10.1186/gb-2012-13-8-r77

ggbio: an R package for extending the grammar of graphics for genomic data
Cited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago

10.1186/s12859-019-2706-8

svist4get: a simple visualization tool for genomic tracks from sequencing experiments
Cited by: 32
Author(s): Artyom A. Egorov, Ekaterina Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
Software Mentions: 11
Published: over 5 years ago

10.12688/f1000research.17976.2

TFutils: Data structures for transcription factor bioinformatics
Cited by: 2
Author(s): Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin A. Raby, Vincent J. Carey
Software Mentions: 10
Published: over 5 years ago

10.1186/s12859-019-2797-2

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Cited by: 19
Author(s): Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell
Software Mentions: 10
Published: over 5 years ago

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: about 9 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: about 6 years ago

10.7717/peerj-cs.251

<i>RIdeogram</i>: drawing SVG graphics to visualize and map genome-wide data on the idiograms
Cited by: 221
Author(s): Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12859-016-1051-4

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics
Cited by: 17
Author(s): Zuguang Gu, Roland Eils, Matthias Schlesner
Software Mentions: 8
Published: over 8 years ago

10.1186/s13104-019-4473-z

RepViz: a replicate-driven R tool for visualizing genomic regions
Cited by: 0
Author(s): Thomas Faux, Kalle T. Rytkönen, Asta Laiho, Laura L. Elo
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-017-09064-w

Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching
Cited by: 27
Author(s): Douglas C. Wu, Alan M. Lambowitz
Software Mentions: 8
Published: over 7 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: almost 6 years ago

10.1093/bioinformatics/btx346

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
Cited by: 451
Author(s): Bernat Gel, Eduard Serra
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-015-0568-2

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Cited by: 95
Author(s): Tiphaine Martin, İdil Yet, Pei-Chien Tsai, Jordana T. Bell
Software Mentions: 7
Published: over 9 years ago

10.1186/s13059-018-1582-2

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Cited by: 77
Author(s): Anna R. Poetsch, Simon J. Boulton, Nicholas M. Luscombe
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2164-15-480

Detection of copy number variations and their effects in Chinese bulls
Cited by: 50
Author(s): Liangzhi Zhang, Shangang Jia, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou, Chunlei Zhang, Xin Zhao, Hong Chen
Software Mentions: 7
Published: over 10 years ago

10.1186/s12859-019-2610-2

BPG: Seamless, automated and interactive visualization of scientific data
Cited by: 55
Author(s): Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Davina Mak, Felix Lam, Marco A. Albuquerque, Yaoguo Wu, Esther Jung, Maud H.W. Starmans, Michelle Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang, Emilie Lalonde, Syed Haider, Nicole A. Simone, Dorota H. Sendorek, Kenneth C. Chu, Nathalie C. Moon, Natalie S. Fox, Michal R. Grzadkowski, Nicholas J. Harding, Clement Fung, Amanda R. Murdoch, Kathleen E. Houlahan, Jianxin Wang, David R. Garcia, Richard de Borja, Ren Sun, Xihui Lin, Gregory M. Chen, Aileen Lu, Yu-Jia Shiah, Amin Zia, Ryan Kearns, Paul C. Boutros
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12859-020-3434-9

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Cited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: over 4 years ago

10.1038/srep34220

Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Cited by: 99
Author(s): Christian Trolle, Morten Muhlig Nielsen, Anne Skakkebæk, Philippe Lamy, Søren Vang, Jakob Hedegaard, Iver Nordentoft, Torben F. Ørntoft, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 6
Published: about 8 years ago

10.1186/s12864-017-4364-4

Pronounced strain-specific chemosensory receptor gene expression in the mouse vomeronasal organ
Cited by: 16
Author(s): Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, Chong Yu
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-020-78288-0

Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral blood
Cited by: 19
Author(s): Andrea Hanel, Antonio Neme, Marjo Malinen, Emmi Hämäläinen, Henna-Riikka Malmberg, Stéphane Etheve, Tomi‐Pekka Tuomainen, Jyrki K. Virtanen, Igor Bendik, Carsten Carlberg
Software Mentions: 5
Published: almost 4 years ago

10.1093/hmg/ddv203

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans
Cited by: 65
Author(s): Ali Amin Al Olama, Tokhir Dadaev, Dennis J. Hazelett, Qiuyan Li, Daniel Leongamornlert, Ed Saunders, Sarah H. Stephens, Clara Cieza-Borrella, Ian Whitmore, Sara Benlloch Garcia, Graham G. Giles, Melissa C. Southey, Liesel M. FitzGerald, Henrik Grönberg, Fredrik Wiklund, Markus Aly, Brian E. Henderson, Fredrick Schumacher, Christopher A. Haiman, Johanna Schleutker, Tiina Wahlfors, Teuvo L.J. Tammela, Børge G. Nordestgaard, Tim Key, Ruth C. Travis, David E. Neal, Jenny Donovan, Freddie C. Hamdy, Paul D.P. Pharoah, Nora Pashayan, Kay‐Tee Khaw, Janet L. Stanford, Stephen N. Thibodeau, Shannon K. McDonnell, Daniel J. Schaid, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S. Kibel, Cezary Cybulski, Dominika Wokołorczyk, Wojciech Kluźniak, Lisa A. Cannon‐Albright, Hermann Brenner, Katja Butterbach, Volker Arndt, Jong Y. Park, Thomas A. Sellers, Hui‐Yi Lin, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Judith A. Clements, Amanda B. Spurdle, Manuel R. Teixeira, Paula Paulo, Sofia Maia, Hardev Pandha, Agnieszka Michael, Andrzej M. Kierzek, Koveela Govindasami, Michelle Guy, Artitaya Lophatonanon, Kenneth Muir, Ana Viñuela, Andrew Anand Brown, Cogs-Cruk Gwas-Ellipse Initiative, Mathew Freedman, David V. Conti, Douglas F. Easton, Gerhard A. Coetzee, Rosalind Eeles, Zsofia Kote‐Jarai
Software Mentions: 5
Published: over 9 years ago

10.1186/s10020-020-00253-4

Genomic imbalances in the placenta are associated with poor fetal growth
Cited by: 13
Author(s): Giulia Gobbo, Yue Yin, Sanaa Choufani, Emma Butcher, John Wei, Evica Rajcan‐Separovic, Hayley Bos, Peter von Dadelszen, Rosanna Weksberg, Wendy P. Robinson, Ryan K. C. Yuen
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0123609

Mapsnp: An R Package to Plot a Genomic Map for Single Nucleotide Polymorphisms
Cited by: 5
Author(s): Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Cheng Zhang, Guoqiang Wang, Yin Yao Shugart
Software Mentions: 5
Published: over 9 years ago

10.18632/oncotarget.12818

Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21
Cited by: 32
Author(s): Yosr Hamdi, Penny Soucy, Véronique Adoue, Kyriaki Michailidou, Sander Canisius, Audrey Lemaçon, Arnaud Droit, Irene L. Andrulis, Hoda Anton‐Culver, Volker Arndt, Caroline Baynes, Carl Blomqvist, Natalia Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne‐Lise Børresen‐Dale, Judith S. Brand, Hiltrud Brauch, Hermann Brenner, Annegien Broeks, Barbara Burwinkel, Jenny Chang–Claude, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Hatef Darabi, Joe Dennis, Peter Devilee, Thilo Dörk, Isabel dos‐Santos‐Silva, Mikael Eriksson, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García‐Closas, Graham G. Giles, Mark S. Goldberg, Anna González‐Neira, Grethe Irene Grenaker-Alnæs, Pascal Guénel, Lothar Haeberle, Christopher A. Haiman, Ute Hamann, Emily Hallberg, Maartje J. Hooning, John L. Hopper, Anna Jakubowska, Michael E. Jones, Maria Kabisch, Vesa Kataja, Diether Lambrechts, Loı̈c Le Marchand, Annika Lindblom, Jan Lubiński, Arto Mannermaa, Mel Maranian, Sara Margolin, Frederik Marmé, Roger L. Milne, Susan L. Neuhausen, Heli Nevanlinna, Patrick Neven, Curtis Olswold, Julian Peto, Dijana Plaseska‐Karanfilska, Katri Pylkäs, Paolo Radice, Anja Rudolph, Elinor J. Sawyer, Marjanka K. Schmidt, Xiao‐Ou Shu, Melissa C. Southey, Anthony Swerdlow, Rob A.E.M. Tollenaar, Ian Tomlinson, Diana Torres, Thérèse Truong, Celine M. Vachon, Ans M.W. van den Ouweland, Qin Wang, Robert Winqvist, _ kConFab, Aocs Investigators, Wei Zheng, Javier Benı́tez, Georgia Chenevix-Trench, Alison M. Dunning, Paul D.P. Pharoah, Vessela N. Kristensen, Per Hall, Douglas F. Easton, Tomi Pastinen, Silje Nord, Jacques Simard
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2105-14-244

RCircos: an R package for Circos 2D track plots
Cited by: 425
Author(s): Hongen Zhang, Paul S. Meltzer, Sean Davis
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2105-15-198

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-021-07417-4

Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae
Cited by: 3
Author(s): Klavdija Pačnik, Mojca Ogrizović, Matthias Diepold, Tobias Eisenberg, Mia Žganjar, Gašper Žun, Beti Kužnik, Cene Gostinčar, Tomaž Curk, Uroš Petrovič, Klaus Natter
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13058-016-0718-0

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
Cited by: 30
Author(s): Chenjie Zeng, Xingyi Guo, Jirong Long, Karoline Kuchenbaecker, Arnaud Droit, Kyriaki Michailidou, Maya Ghoussaini, Siddhartha Kar, Adam N. Freeman, John L. Hopper, Roger L. Milne, Manjeet K. Bolla, Qin Wang, Joe Dennis, Simona Agata, Shahana Ahmed, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton‐Culver, Natalia Antonenkova, Aðalgeir Arason, Volker Arndt, Banu K. Arun, Brita Arver, François Bertucci, Daniel Barrowdale, Caroline Baynes, Alicia Beeghly–Fadiel, Javier Benı́tez, Marina Bermisheva, Carl Blomqvist, William J. Blot, Natalia Bogdanova, Stig E. Bojesen, Bernardo Bonanni, Anne Lise Børresen-Dale, Judith S. Brand, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Annegien Broeks, Thomas Brüning, Barbara Burwinkel, Saundra S. Buys, Qiuyin Cai, Trinidad Caldés, Ian Campbell, Jane Carpenter, Jenny Chang‐Claude, Ji Yeob Choi, Kathleen Claes, Christine L. Clarke, Angela Cox, Simon S. Cross, Kamila Czene, Mary B. Daly, Miguel de la Hoya, Kim De Leeneer, Peter Devilee, Orland Díez, Susan M. Domchek, Michele M. Doody, Cecilia M. Dorfling, Thilo Dörk, Isabel dos‐Santos‐Silva, Martine Dumont, Miriam Dwek, Bernd Dworniczak, Kathleen M. Egan, Ursula Eilber, Zakaria Einbeigi, Bent Ejlertsen, Steve Ellis, Debra Frost, Fiona Lalloo, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Michael Friedlander, Eitan Friedman, Gaetana Gambino, Yu Tang Gao, Judy E. Garber, Montserrat García‐Closas, Andrea Gehrig, Francesca Damiola, Fabienne Lesueur, Sylvie Mazoyer, Dominique Stoppa‐Lyonnet, Graham G. Giles, Andrew K. Godwin, David E. Goldgar, Anna González‐Neira, Mark H. Greene, Pascal Guénel, Lothar Haeberle, Christopher A. Haiman, Emily Hallberg, Ute Hamann, Thomas V.O. Hansen, Steven N. Hart, Jaana M. Hartikainen, Mikael Hartman, Norhashimah Hassan, Sue Healey, Frans B.L. Hogervorst, Senno Verhoef, Carolyn B. Hendricks, Peter Hillemanns, Antoinette Hollestelle, Peter J. Hulick, David J. Hunter, Evgeny N. Imyanitov, Claudine Isaacs, Hidemi Ito, Anna Jakubowska, Ramūnas Janavičius, Katarzyna Jaworska–Bieniek, Uffe Birk Jensen, Esther M. John, Charles Joly Beauparlant, Michael E. Jones, Maria Kabisch, Daehee Kang, Beth Y. Karlan, Saila Kauppila, Michael J. Kerin, Sofia Khan, Э. К. Хуснутдинова, Julia A. Knight, Irene Konstantopoulou, Peter Kraft, Ava Kwong, Yael Laitman, Diether Lambrechts, Conxi Lázaro, Loı̈c Le Marchand, Chuen Neng Lee, Min Hyuk Lee, Jenny Lester, Jingmei Li, Annelie Liljegren, Annika Lindblom, Artitaya Lophatananon, Jan Lubiński, L. Phuong, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Frederik Marmé, Keitaro Matsuo, Lesley McGuffog, Alfons Meindl, Florence Ménégaux, Marco Montagna, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Polly A. Newcomb, Silje Nord, Robert L. Nussbaum, Kenneth Offit, Edith Olàh, Olufunmilayo I. Olopade, Curtis Olswold, Ana Osorio, Laura Papi, Tjoung Won Park-Simon, Ylva Paulsson-Karlsson, Stéphanie Peeters, Bernard Peissel, Paolo Peterlongo, Julian Peto, Georg Pfeiler, Catherine M. Phelan, Nadège Presneau, Paolo Radice, Nazneen Rahman, Susan J. Ramus, Muhammad Usman Rashid, Gad Rennert, Kerstin Rhiem, Anja Rudolph, Ritu Salani, Suleeporn Sangrajrang, Elinor J. Sawyer, Marjanka K. Schmidt, Rita K. Schmutzler, Minouk J. Schoemaker, Peter Schürmann, Caroline Seynaeve, Chen Shen, Martha J. Shrubsole, Xiao Ou Shu, Alice J. Sigurdson, Christian F. Singer, Susan L. Slager, Penny Soucy, Melissa C. Southey, Doris Steinemann, Anthony Swerdlow, Csilla I. Szabo, Sandrine Tchatchou, Manuel R. Teixeira, Soo Hwang Teo, Mary Beth Terry, Daniel C. Tessier, Àlex Teulé, Mads Thomassen, Laima Tihomirova, Marc Tischkowitz, Amanda E. Toland, Nadine Tung, Clare Turnbull, Ans M.W. van den Ouweland, Elizabeth J. van Rensburg, David ven den Berg, Joseph Vijai, Shan Wang-Gohrke, Jeffrey N. Weitzel, Alice S. Whittemore, Robert Winqvist, Tien Yin Wong, Anna H. Wu, Drakoulis Yannoukakos, Jyh Cherng Yu, Paul D.P. Pharoah, Per Hall, Georgia Chenevix-Trench, Alison M. Dunning, Jacques Simard, Fergus J. Couch, Antonis C. Antoniou, Douglas F. Easton, Zheng Wang
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0129350

Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection
Cited by: 0
Author(s): Thadeous J. Kacmarczyk, Caitlin Bourque, Xihui Zhang, Yanwen Jiang, Yariv Houvras, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 9 years ago

10.3390/cells10061291

Innate and Adaptive Immune Genes Associated with MERS-CoV Infection in Dromedaries
Cited by: 6
Author(s): Sara Lado, Jean P. Elbers, Martin Plášil, Tom Loney, Pia Weidinger, Jeremy V. Camp, Jolanta Kolodziejek, Ján Futas, Dafalla A. Kannan, Pablo Orozco‐terWengel, Petr Hořín, Norbert Nowotny, Pamela A. Burger
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ebiom.2015.07.017

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study
Cited by: 217
Author(s): Helen Ross-Adams, Alastair Lamb, Mark J. Dunning, Silvia Halim, Johan Lindberg, Charles E. Massie, Lars Egevad, Roslin Russell, Antonio Ramos-Montoya, Sarah L. Vowler, Naomi L. Sharma, Jonathan Kay, Hayley C. Whitaker, Jeremy Clark, Rachel Hurst, Vincent Gnanapragasam, Nimish Shah, Anne Y. Warren, Christopher S. Cooper, Andy G. Lynch, Rory Stark, Ian G. Mills, Henrik Grönberg, David E. Neal
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2017.01787

The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae
Cited by: 11
Author(s): Pascal Bartling, Henner Brinkmann, Boyke Bunk, Jörg Overmann, Markus Göker, Jörn Petersen
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.61562

Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans
Cited by: 40
Author(s): Alice V. Easton, Shenghan Gao, Scott P Lawton, Sasisekhar Bennuru, Asis Khan, Eric Dahlstrom, Rita G. Oliveira, Stella Kepha, Stephen F. Porcella, Joanne P. Webster, Roy M. Anderson, Michael E. Grigg, Richard E. Davis, Jianbin Wang, Thomas B. Nutman
Software Mentions: 4
Published: about 4 years ago

10.1021/acssynbio.0c00637

Construction of DNA Tools for Hyperexpression in <i>Marchantia</i> Chloroplasts
Cited by: 8
Author(s): Eftychios Frangedakis, Fernando Guzman Chavez, Marius Rebmann, Kasey Markel, Ying Yu, Artemis Perraki, Sze Wai Tse, Yang Liu, Jenna Rever, Susanna Sauret-Güeto, Bernard Goffinet, Harald Schneider, Jim Haseloff
Software Mentions: 4
Published: over 3 years ago

10.1038/srep32512

Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)
Cited by: 18
Author(s): Hatef Darabi, Jonathan Beesley, Arnaud Droit, Siddhartha Kar, Silje Nord, Mahdi Moradi Marjaneh, Penny Soucy, Kyriaki Michailidou, Maya Ghoussaini, Hanna Fues Wahl, Manjeet K. Bolla, Qin Wang, Joe Dennis, María R. Alonso, Irene L. Andrulis, Hoda Anton‐Culver, Volker Arndt, Matthias W. Beckmann, Javier Benı́tez, Natalia Bogdanova, Stig E. Bojesen, Hiltrud Brauch, Hermann Brenner, Annegien Broeks, Thomas Brüning, Barbara Burwinkel, Jenny Chang–Claude, Ji Yeob Choi, Don Conroy, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Peter Devilee, Thilo Dörk, Douglas F. Easton, Peter A. Fasching, Jonine D. Figueroa, Olivia Fletcher, Henrik Flyger, Eva Galle, Montserrat García‐Closas, Graham G. Giles, Mark S. Goldberg, Anna González‐Neira, Pascal Guénel, Christopher A. Haiman, Emily Hallberg, Ute Hamann, Mikael Hartman, Antoinette Hollestelle, John L. Hopper, Hidemi Ito, Anna Jakubowska, Nichola Johnson, Daehee Kang, Sofia Khan, Veli‐Matti Kosma, Mieke Kriege, Vessela N. Kristensen, Diether Lambrechts, Loı̈c Le Marchand, Soo‐Chin Lee, Annika Lindblom, Artitaya Lophatananon, Jan Lubiński, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Keitaro Matsuo, Rebecca Mayes, James McKay, Alfons Meindl, Roger L. Milne, Kenneth Muir, Susan L. Neuhausen, Heli Nevanlinna, Curtis Olswold, Nick Orr, Paolo Peterlongo, Guillermo Pita, Katri Pylkäs, Anja Rudolph, Suleeporn Sangrajrang, Elinor J. Sawyer, Marjanka K. Schmidt, Rita K. Schmutzler, Caroline Seynaeve, Mitul Shah, Chen‐Yang Shen, Xiao‐Ou Shu, Melissa C. Southey, Daniel O. Stram, Harald Surowy, Anthony Swerdlow, Soo‐Hwang Teo, Daniel C. Tessier, Ian Tomlinson, Diana Torres, Thérèse Truong, Celine M. Vachon, Vincent Denis, Robert Winqvist, Anna H. Wu, Pei-Ei Wu, Cheng Har Yip, Zheng Wang, Paul D.P. Pharoah, Per Hall, Stacey L. Edwards, Jacques Simard, Juliet D. French, Georgia Chenevix-Trench, Alison M. Dunning
Software Mentions: 3
Published: about 8 years ago

10.1007/s10549-016-4018-2

Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3
Cited by: 18
Author(s): Yosr Hamdi, Penny Soucy, Karoline B. Kuchenbaeker, Tomi Pastinen, Arnaud Droit, Audrey Lemaçon, Julian Adlard, Kristiina Aittomäki, Irene L. Andrulis, Aðalgeir Arason, Norbert Arnold, Banu K. Arun, Jacopo Azzollini, Anita Bane, Laure Barjhoux, Daniel Barrowdale, Javier Benı́tez, Pascaline Berthet, Marinus J. Blok, Kristie Bobolis, Valérie Bonadona, Bernardo Bonanni, Angela R. Bradbury, Carole Brewer, Benedetto Bruno, Saundra S. Buys, Maria A. Caligo, Jocelyne Chiquette, Wendy K. Chung, Kathleen Claes, Mary B. Daly, Francesca Damiola, Rosemarie Davidson, Miguel de la Hoya, Kim De Leeneer, Orland Díez, Yuan Chun Ding, Riccardo Dolcetti, Susan M. Domchek, Cecilia M. Dorfling, Diana Eccles, Rosalind Eeles, Zakaria Einbeigi, Bent Ejlertsen, Christoph Engel, D. Gareth Evans, Lídia Feliubadaló, Lenka Foretová, Florentia Fostira, William D. Foulkes, George Fountzilas, Eitan Friedman, Debra Frost, Pamela Ganschow, Patricia A. Ganz, Judy E. Garber, Simon A. Gayther, Anne–Marie Gerdes, Gord Glendon, Andrew K. Godwin, David E. Goldgar, Mark H. Greene, Jacek Gronwald, Eric Hahnen, Ute Hamann, Thomas V.O. Hansen, Steven N. Hart, John L. Hays, Frans B.L. Hogervorst, Peter J. Hulick, Evgeny N. Imyanitov, Claudine Isaacs, Louise Izatt, Anna Jakubowska, Paul James, Ramūnas Janavičius, Uffe Birk Jensen, Esther M. John, Joseph Vijai, Walter Just, Katarzyna Kaczmarek, Beth Y. Karlan, C. Marleen Kets, Judy Kirk, Mieke Kriege, Yael Laitman, M Laurent, Conxi Lázaro, Goska Leslie, Jenny Lester, Fabienne Lesueur, Annelie Liljegren, Niklas Loman, Jennifer T. Loud, Siranoush Manoukian, Milena Mariani, Sylvie Mazoyer, Lesley McGuffog, Hanne Meijers-Heijboer, Alfons Meindl, Austin Miller, Marco Montagna, Anna Marie Mulligan, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Robert L. Nussbaum, Edith Olàh, Olufunmilayo I. Olopade, Kai Ren Ong, Jan C. Oosterwijk, Ana Osorio, Laura Papi, Sue Kyung Park, Inge Søkilde Pedersen, Bernard Peissel, Pedro Pérez Segura, Paolo Peterlongo, Catherine M. Phelan, Paolo Radice, Johanna Rantala, Christine Rappaport-Fuerhauser, Gad Rennert, Andrea L. Richardson, Mark E. Robson, Gustavo C. Rodriguez, Matti A. Rookus, Rita K. Schmutzler, Nicolas Sévenet, Payal D. Shah, Christian F. Singer, Thomas P. Slavin, Katie Snape, Johanna Sokolowska, Ida Marie Heeholm Sønderstrup, Melissa C. Southey, Amanda B. Spurdle, Zsofia K. Stadler, Dominique Stoppa‐Lyonnet, Grzegorz Sukiennicki, Christian Sutter, Yen Y. Tan, Muy Kheng Tea, Manuel R. Teixeira, Alexandre Teulé, Soo Hwang Teo, Mary Beth Terry, Mads Thomassen, Laima Tihomirova, Marc Tischkowitz, Silvia Tognazzo, Amanda E. Toland, Nadine Tung, Ans M.W. van den Ouweland, Rob B. van der Luijt, Klaartje van Engelen, Elizabeth J. van Rensburg, Raymonda Varon-Mateeva, Barbara Wappenschmidt, Juul T. Wijnen, Timothy R. Rebbeck, Georgia Chenevix-Trench, Kenneth Offit, Fergus J. Couch, Silje Nord, Douglas F. Easton, Antonis C. Antoniou, Jacques Simard
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0084860

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud
Cited by: 26
Author(s): Konrad J. Karczewski, Guy Haskin Fernald, Martin Ar, M Snyder, Nicholas P. Tatonetti, Joel T. Dudley
Software Mentions: 3
Published: almost 11 years ago

10.1186/s40001-021-00535-5

Inherited unbalanced reciprocal translocation with 3q duplication and 5p deletion in a foetus revealed by cell-free foetal DNA (cffDNA) testing: a case report
Cited by: 0
Author(s): Taccyanna Mikulski Ali, Emilia Mateu‐Brull, Nuria Balaguer, Camila Gomes Dantas, Haline Risso Borges, Mariana Quintans Guerra de Oliveira, Lorena Rodrigo, Inmaculada Campos‐Galindo, Roser Navarro, Miguel Milán
Software Mentions: 2
Published: over 3 years ago

10.1186/s13029-016-0052-z

A flexible tool to plot a genomic map for single nucleotide polymorphisms
Cited by: 1
Author(s): Fuquan Zhang
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-019-2622-y

Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk
Cited by: 3
Author(s): Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng, Mohammed S. Orloff
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2019.00218

Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen
Cited by: 17
Author(s): Gaurav Sablok, Ali Amiryousefi, Xiaolan He, Jaakko Hyvönen, Péter Poczai
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005947

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Cited by: 91
Author(s): Qiongshi Lu, Ryan L. Powles, Qian Wang, B. Julie He, Hongyu Zhao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-11677-0

Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita
Cited by: 24
Author(s): T. Yamazaki, Kensuke Ichihara, Ritsu Suzuki, Koichiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-016-2693-3

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization
Cited by: 36
Author(s): Andrew S. Fister, Luis C. Mejía, Yufan Zhang, Edward Allen Herre, Siela N. Maximova, Mark J. Guiltinan
Software Mentions: 2
Published: over 8 years ago

10.1038/srep10576

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data
Cited by: 125
Author(s): Qiongshi Lu, Yiming Hu, Jiehuan Sun, Yu‐Wei Cheng, Kei‐Hoi Cheung, Hongyu Zhao
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0242530

Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa
Cited by: 6
Author(s): Hasan Mehraj, Daniel J. Shea, Satoshi Takahashi, Noriaki Miyaji, Ayasha Akter, Motoaki Seki, Elizabeth S. Dennis, Ryo Fujimoto, Kenji Osabe
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.00752

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed
Cited by: 5
Author(s): Favour Oluwapelumi Oyelami, Qi Zhao, Zhong Xu, Zhe Zhang, Hao Sun, Zhenyang Zhang, Peipei Ma, Qishan Wang, Yuchun Pan
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: ggbio

Papers Mentioning ggbio 53