bioconductor: GenomicRanges | Projects

10.1016/j.devcel.2020.09.002

Combinatorial Action of Temporally Segregated Transcription Factors
Cited by: 38
Author(s): Julien Charest, Thomas Daniele, Jingkui Wang, Aleksandr Bykov, Ariane Mandlbauer, Mila Asparuhova, Josef Röhsner, Paula Gutiérrez-Pérez, Luisa Cochella
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-020-6662-5

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Cited by: 12
Author(s): Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yoshihisa Yamashita, Shuichi Naito, Atsushi Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima, Hitoshi Onouchi
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0104355

Copy Number Variation in Thai Population
Cited by: 25
Author(s): Bhoom Suktitipat, Chaiwat Naktang, Wuttichai Mhuantong, Tularak Thitima, Paramita Artiwet, Pasomsap Ekawat, Wallaya Jongjaroenprasert, Suthat Fuchareon, Surakameth Mahasirimongkol, Wasun Chantratita, Boonsit Yimwadsana, Varodom Charoensawan, Natini Jinawath
Software Mentions: 4
Published: over 10 years ago

10.1038/s42003-020-01516-w

miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1
Cited by: 17
Author(s): Mitsuo Kato, Maryam Abdollahi, Ragadeepthi Tunduguru, Walter Tsark, Zhuo Chen, Xiwei Wu, Jinhui Wang, Zhen Bouman Chen, Feng‐Mao Lin, Linda Lanting, Mei Wang, Janice M. Huss, Patrick T. Fueger, David C. Chan, Rama Natarajan
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-79552-z

Host mitochondrial transcriptome response to SARS-CoV-2 in multiple cell models and clinical samples
Cited by: 45
Author(s): Brendan Miller, Ana R. Silverstein, Melanie Flores, Kevin Cao, Hiroshi Kumagai, Hemal H. Mehta, Kelvin Yen, Su Jeong Kim, Pinchas Cohen
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2019.00269

Does Prenatal Stress Shape Postnatal Resilience? – An Epigenome-Wide Study on Violence and Mental Health in Humans
Cited by: 50
Author(s): Fernanda Serpeloni, Karl M. Radtke, Tobias Hecker, Johanna Sill, Vanja Vukojević, Simone Gonçalves de Assis, Maggie Schauer, Thomas Elbert, Daniel Nätt
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0094164

From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis
Cited by: 4
Author(s): Sebastian Weiterer, Florian Uhle, Sabin Bhuju, Michael Jarek, Markus A. Weigand, Marek Bartkuhn
Software Mentions: 4
Published: over 10 years ago

10.1097/MIB.0000000000001131

Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: over 7 years ago

10.1007/s00401-017-1773-z

Comprehensive molecular characterisation of epilepsy-associated glioneuronal tumours
Cited by: 50
Author(s): T. J. Stone, Angus Keeley, Alex Virasami, William Harkness, Martin Tisdall, Elisa Izquierdo, Alice Gutteridge, Tony Brooks, Mark Kristiansen, Jane Chalker, Lisa Wilkhu, William Mifsud, John Apps, Maria Thom, Michael Hubank, Tim Forshew, J. Helen Cross, Darren Hargrave, Jonathan Ham, Thomas S. Jacques
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0108424

CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems
Cited by: 156
Author(s): Lihua Julie Zhu, Benjamin Holmes, Neil Aronin, Michael Brodsky
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.ppat.1005702

Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody
Cited by: 72
Author(s): Ningli Chai, Lee R. Swem, Mike Reichelt, Haiyin Chen-Harris, Luis Elizabeth, Summer Park, Ashley E. Fouts, P.J. Lupardus, Thomas D. Wu, Olga Li, Jacqueline McBride, Michael C. Lawrence, Min Xu, Man‐Wah Tan
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.ppat.1008154

Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model
Cited by: 10
Author(s): Lorenz M. Loyola, Vasudevan Achuthan, Kathryn Gilroy, Gillian Borland, Anna Kilbey, Nancy MacKay, Margaret Bell, Jodie Hay, Sriram Aiyer, Dylan Fingerman, Rodrigo A. Villanueva, Ewan R. Cameron, Christine A. Kozak, Alan Engelman, James C. Neil, Monica J. Roth
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-016-1158-7

DISMISS: detection of stranded methylation in MeDIP-Seq data
Cited by: 6
Author(s): Umar Niazi, Kathrin K. Geyer, Martin Vickers, Karl F. Hoffmann, Martin Swain
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2156-15-24

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk
Cited by: 21
Author(s): Samuel G. Younkin, Robert B. Scharpf, Holger Schwender, Margaret M. Parker, Alan F. Scott, Mary L. Marazita, Terri H. Beaty, Ingo Ruczinski
Software Mentions: 4
Published: almost 11 years ago

10.12688/f1000research.51143.1

periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
Cited by: 5
Author(s): Jacques Serizay, Julie Ahringer
Software Mentions: 4
Published: over 3 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

10.1186/s13059-019-1706-3

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C
Cited by: 25
Author(s): Yousra Ben Zouari, Anne Molitor, Natalia Sikorska, Véra Pancaldi, Tom Sexton
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-73307-6

Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Cited by: 6
Author(s): Hiro Takahashi, Shido Miyaki, Hitoshi Onouchi, Taichiro Motomura, Nobuo Idesako, Atsushi Takahashi, Masataka Murase, Shuichi Fukuyoshi, Toshinori Endo, Kenji Satou, Shuichi Naito, Motoyuki Itoh
Software Mentions: 4
Published: about 4 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/s13148-021-01161-y

Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes
Cited by: 12
Author(s): Lyndsey E. Shorey‐Kendrick, Cindy T. McEvoy, Shannon M. O’Sullivan, Kristin Milner, Brittany Vuylsteke, Robert S. Tepper, David M. Haas, Byung Park, Lina Gao, Annette Vu, Cynthia D. Morris, Eliot R. Spindel
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-020-02249-z

N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease
Cited by: 112
Author(s): Andrew M Shafik, Feiran Zhang, Zhiqin Guo, Qing Dai, Kinga Pajdzik, Yangping Li, Yunhee Kang, Bing Yao, Hao Wu, Chuan He, Emily G. Allen, Ranhui Duan, Peng Jin
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers12082003

Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer
Cited by: 5
Author(s): Elsa Arbajian, Mattias Aine, Anna Karlsson, Johan Vallon‐Christersson, Hans Brunnström, Josef Davidsson, Sofie Mohlin, Maria Planck, Johan Staaf
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1006091

Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
Cited by: 1
Author(s): R. Buckley, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-39633-0

Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
Cited by: 24
Author(s): Marco Cavalli, Nicholas Baltzer, Husen M. Umer, Jan Grau, Ioana Lemnian, Gang Pan, Ola Wallerman, Rapolas Spalinskas, Pelin Sahlén, Ivo Große, Jan Komorowski, Claes Wadelius
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-018-0235-8

The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a
Cited by: 23
Author(s): Alexey V. Pindyurin, Artem A. Ilyin, Anton V. Ivankin, Mikhail V. Tselebrovsky, Valentina V. Nenasheva, Elena A. Mikhaleva, Ludo Pagie, Bas van Steensel, Yuri Y. Shevelyov
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0143193

Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome
Cited by: 10
Author(s): Elena Hilario, Lorna Barron, Cecilia Deng, Paul M. Datson, Nihal De Silva, Marcus Davy, Roy Storey
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0198201

Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae
Cited by: 13
Author(s): Henrik U. Stotz, Pascoe J. Harvey, Parham Haddadi, Alla Mashanova, Andreas Kukol, Nicholas J. Larkan, M. Hossein Borhan, Bruce D.L. Fitt
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0128969

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
Cited by: 29
Author(s): Ben Dorshorst, Corneliu Hénégar, Xiaoping Liao, Markus Sällman Almén, Carl-Johan Rubin, Shosuke Ito, Kazumasa Wakamatsu, Paul Stothard, Brian Van Doormaal, Graham Plastow, Gregory S. Barsh, Leif Andersson
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0091041

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion
Cited by: 70
Author(s): Heesun Shin, Casey P. Shannon, Nick Fishbane, Jian Ruan, Mi Zhou, Robert Balshaw, J. Wilson-McManus, Raymond T. Ng, Bruce M. McManus, Scott J. Tebbutt
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1008370

Environmental and epigenetic regulation of Rider retrotransposons in tomato
Cited by: 49
Author(s): Matthias Benoit, Hajk-Georg Drost, Marco Catoni, Quentin Gouil, Sara López-Gomollón, David C. Baulcombe, Jerzy Paszkowski
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-13-229

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities
Cited by: 9
Author(s): Fahim Mohammad, Robert M. Flight, Benjamin J. Harrison, Jeffrey C. Petruska, Eric C. Rouchka
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pgen.1009252

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program
Cited by: 4
Author(s): Rajalakshmi Srinivasan, Adhish Walvekar, Zeenat Rashida, Aswin Sai Narain Seshasayee, Sunil Laxman
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2017.00335

CD103+ CD8 T Cells in the Toxoplasma-Infected Brain Exhibit a Tissue-Resident Memory Transcriptional Profile
Cited by: 45
Author(s): Tyler Landrith, Suhas Sureshchandra, Andrea Rivera, Jessica Jang, Maham Rais, Meera G. Nair, Ilhem Messaoudi, Emma H. Wilson
Software Mentions: 3
Published: over 7 years ago

10.1002/1878-0261.12168

Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma‐initiating cells
Cited by: 21
Author(s): Rola Dali, Federica Verginelli, Albéna Pramatarova, Robert Sladek, Stefano Stifani
Software Mentions: 3
Published: over 6 years ago

10.1093/molbev/msz105

Altered Localization of Hybrid Incompatibility Proteins in Drosophila
Cited by: 8
Author(s): Jacob C. Cooper, A. Lukacs, Shelley Reich, Tamás Schauer, Axel Imhof, Nitin Phadnis
Software Mentions: 3
Published: over 5 years ago

10.1186/s13100-021-00241-3

The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis
Cited by: 6
Author(s): Mahboubeh Rostami, Martina Bradić
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8122007

Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair
Cited by: 7
Author(s): Eleftherios Kontizas, Spyros Tastsoglou, Timokratis Karamitros, Yiannis Karayiannis, Panagoula Κollia, Artemis G. Hatzigeorgiou, Dionyssios N. Sgouras
Software Mentions: 3
Published: almost 4 years ago

10.1186/gb-2014-15-6-r86

IVT-seq reveals extreme bias in RNA sequencing
Cited by: 135
Author(s): Nicholas F. Lahens, İbrahim Halil Kavaklı, Ray Zhang, Katharina E. Hayer, Michael B. Black, Hannah Dueck, Angel Pizarro, Junhyong Kim, Rafael A. Irizarry, Russell S. Thomas, Gregory R. Grant, John B. Hogenesch
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13059-014-0472-5

Dynamic evolution of clonal epialleles revealed by methclone
Cited by: 60
Author(s): Sheng Li, Francine E. Garrett-Bakelman, Alexander E. Perl, Selina M. Luger, Chao Zhang, Bik To, Ian D. Lewis, Anna L. Brown, Richard J. D’Andrea, M. Elizabeth Ross, Ross L. Levine, Martin Carroll, Ari Melnick, Christopher E. Mason
Software Mentions: 3
Published: about 10 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

10.1186/s13059-014-0567-z

The draft genome of Primula veris yields insights into the molecular basis of heterostyly
Cited by: 90
Author(s): Michael Nowak, Giancarlo Russo, Ralph Schlapbach, Cuong Nguyen Huu, Michael Lenhard, Elena Conti
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-015-0857-0

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells
Cited by: 53
Author(s): Geert Geeven, Yun Zhu, Byung Ju Kim, Boris Bartholdy, Seung Min Yang, Todd S. Macfarlan, Wesley D. Gifford, Samuel L. Pfaff, Marjon J.A.M. Verstegen, Hugo Borges Pinto, Marit W. Vermunt, Menno P. Creyghton, Patrick J. Wijchers, J Stamatoyannopoulos, Arthur I. Skoultchi, Wouter de Laat
Software Mentions: 3
Published: almost 9 years ago

10.1093/bioinformatics/btv335

FourCSeq: analysis of 4C sequencing data
Cited by: 85
Author(s): Felix A. Klein, Tibor Pakozdi, Simon Anders, Yad Ghavi-Helm, Eileen E. M. Furlong, Wolfgang Huber
Software Mentions: 3
Published: over 9 years ago

10.1093/bioinformatics/btv612

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Cited by: 315
Author(s): Nathan C. Sheffield, Christoph Bock
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-019-1854-5

Assessment of computational methods for the analysis of single-cell ATAC-seq data
Cited by: 197
Author(s): Huidong Chen, Caleb A. Lareau, Tommaso Andreani, Michael Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade‐Navarro, Jason D. Buenrostro, Luca Pinello
Software Mentions: 3
Published: about 5 years ago

10.1186/s12881-017-0399-2

Whole-exome sequencing and digital PCR identified a novel compound heterozygous mutation in the NPHP1 gene in a case of Joubert syndrome and related disorders
Cited by: 7
Author(s): Shingo Koyama, Hidenori Sato, Manabu Wada, Toru Kawanami, Mitsuru Emi, Takeshi Kato
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-017-3586-9

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP
Cited by: 31
Author(s): Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R. Wright, Conrad Smith, Rolf Backofen, Romy Wecko, Daniel A. Keim, Siegfried Scherer
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-020-00724-7

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
Cited by: 14
Author(s): Justyna A. Wierzbińska, Réka Tóth, Naveed Ishaque, Karsten Rippe, Jan‐Philipp Mallm, Lara Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert, John C. Byrd, Christopher C. Oakes, Christoph Plass, Daniel B. Lipka
Software Mentions: 3
Published: over 4 years ago

10.1038/s41438-019-0169-8

A QTL associated with leaf trichome traits has a major influence on the abundance of the predatory mite Typhlodromus pyri in a hybrid grapevine population
Cited by: 13
Author(s): Paola Barba, Rebecca L. Loughner, Karen Wentworth, Jan P. Nyrop, Gregory M. Loeb, Bruce I. Reisch
Software Mentions: 3
Published: over 5 years ago

10.1038/s41438-021-00572-5

Tissue and regional expression patterns of dicistronic tRNA–mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants
Cited by: 4
Author(s): Pastor Jullian Fabres, Lakshay Anand, Na Sai, Stephen Pederson, Fei Zheng, Alexander A. Stewart, Benjamin Clements, Edwin R. Lampugnani, James Breen, Matthew Gilliham, Penny J. Tricker, Carlos M. Rodríguez López, Rakesh David
Software Mentions: 3
Published: over 3 years ago

10.1074/jbc.RA120.016009

Human genetic variants disrupt RGS14 nuclear shuttling and regulation of LTP in hippocampal neurons
Cited by: 9
Author(s): Katherine E. Squires, Kyle J. Gerber, Matthew Tillman, Daniel Lustberg, Carolina Montañez-Miranda, Mei Zhao, Suneela Ramineni, Christopher D. Scharer, Ramendra N. Saha, Shu Fang, Jeanne L. Schroeder, Eric A. Ortlund, David Weinshenker, Serena M. Dudek, John R. Hepler
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms21186700

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations
Cited by: 13
Author(s): Aleksandra Skalska, Christoph Stritt, Michele Wyler, H. Williams, Martin Vickers, Jungong Han, Metin Tuna, Gülsemin Savaş Tuna, Karolina Susek, Martin Swain, Rafał Wóycicki, Saurabh Chaudhary, Fiona Corke, John H. Doonan, Anne Roulin, Robert Hasterok, Luis A. J. Mur
Software Mentions: 3
Published: about 4 years ago

10.1126/sciadv.aax0396

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans
Cited by: 55
Author(s): Luís R. Saraiva, Fernando Riveros-Mckay, Massimo Mezzavilla, Eman H. AbouMoussa, Charles J. Arayata, Mélanie Makhlouf, Casey Trimmer, Ximena Ibarra-Soria, Mona Khan, Laura Van Gerven, Mark Jorissen, Matthew Gibbs, Ciaran O’Flynn, Scott J. McGrane, Peter Mombaerts, John C. Marioni, Joel D. Mainland, Darren W. Logan
Software Mentions: 3
Published: over 5 years ago

10.1038/srep28396

Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Cited by: 42
Author(s): Eva D’haene, Eva Jacobs, Pieter-Jan Volders, Tim De Meyer, Björn Menten, Sarah Vergult
Software Mentions: 3
Published: over 8 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

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-13-S8-S11

DFI: gene feature discovery in RNA-seq experiments from multiple sources
Cited by: 5
Author(s): Hatice Gülçin Özer, Jeffrey D. Parvin, Kun Huang
Software Mentions: 3
Published: almost 13 years ago

10.1523/JNEUROSCI.1163-18.2018

A Multicomponent Neuronal Response Encodes the Larval Decision to Pupariate upon Amino Acid Starvation
Cited by: 19
Author(s): Siddharth Jayakumar, Shlesha Richhariya, Bipan Kumar Deb, Gaiti Hasan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-45841-5

Etv2 transcriptionally regulates Yes1 and promotes cell proliferation during embryogenesis
Cited by: 12
Author(s): Bhairab N. Singh, Wuming Gong, Satyabrata Das, Joshua W. M. Theisen, Javier Sierra-Pagan, Demetris Yannopoulos, Erik Skie, Pruthvi Shah, Mary G. Garry, Daniel J. Garry
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1583-4

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
Cited by: 44
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Odile Sismeiro, Adrien Villain, Violette Da Cunha, Marie-Elise Caliot, Marie‐Agnès Dillies, Patrick Trieu-Cuot, Philippe Bouloc, Marie‐Frédérique Lartigue, Philippe Glaser
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.11892

Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies
Cited by: 20
Author(s): Andrew J. Colebatch, Leon Di Stefano, Stephen Q. Wong, Ross D. Hannan, Paul Waring, Alexander Dobrovic, Grant A. McArthur, Anthony T. Papenfuss
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-85544-4

Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data
Cited by: 15
Author(s): Christoph Ogris, Yue Hu, Janine Arloth, Nikola S. Müller
Software Mentions: 3
Published: over 3 years ago

10.1038/tp.2015.177

Brain-specific epigenetic markers of schizophrenia
Cited by: 41
Author(s): Leesa Wockner, Charles P. Morris, Ernest P. Noble, Bruce R. Lawford, Vicki Whitehall, Ross McD. Young, Joanne Voisey
Software Mentions: 3
Published: about 9 years ago

10.1128/mBio.01568-20

Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
Cited by: 26
Author(s): Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Software Mentions: 3
Published: about 4 years ago

10.1186/s12885-020-6684-z

Mutational landscape differences between young-onset and older-onset breast cancer patients
Cited by: 9
Author(s): Nicole E. Mealey, Dylan E. O’Sullivan, Joy Pader, Yibing Ruan, Edwin Wang, May Lynn Quan, Darren R. Brenner
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.61406

The kinase PDK1 is critical for promoting T follicular helper cell differentiation
Cited by: 12
Author(s): Zhen Sun, Yingpeng Yao, Menghao You, Jingjing Liu, Wenhui Guo, Zhihong Qi, Zhao Wang, Fang Wang, Weiping Yuan, Shuyang Yu
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.40947

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer
Cited by: 45
Author(s): Anna S Trigos, Richard B. Pearson, Anthony T. Papenfuss, David Goode
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.65331

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast
Cited by: 2
Author(s): Rachael Emily Turner, Paul F. Harrison, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Belinda J. Goldie, Michael See, Amanda L. Peterson, Ralf B. Schittenhelm, David Powell, Darren J. Creek, Bernhard Dichtl, Traude H. Beilharz
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-14-S7-S2

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?
Cited by: 55
Author(s): Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele Calogero
Software Mentions: 3
Published: over 11 years ago

10.7554/eLife.36245

The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis
Cited by: 56
Author(s): Anat Melamed, Hiroko Yaguchi, Michi Miura, Aviva Witkover, Tomas Fitzgerald, Ewan Birney, Charles R. M. Bangham
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-12-200

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration
Cited by: 14
Author(s): Anna Leśniewska, Michał Okoniewski
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.49801

A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization
Cited by: 38
Author(s): Omaya Dudin, Andrej Ondračka, Xavier Grau‐Bové, Arthur Alexander Blørstad Haraldsen, Atsushi Toyoda, Hiroshi Suga, Jon Bråte, Iñaki Ruiz‐Trillo
Software Mentions: 3
Published: about 5 years ago

10.1038/s41421-018-0032-3

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements
Cited by: 36
Author(s): Dang Vinh, Bernhard Strauß, Engin Cukuroglu, Iain C. Macaulay, Keng Boon Wee, Xiaoming Hu, Igor Ruiz de los Mozos, Caroline Lee, Andrew Harrison, Richard J. Butler, Sabine Dietmann, Jernej Ule, John C. Marioni, Christopher W. Smith, Jonathan Göke, M. Azim Surani
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.25552

ERα-mediated cell cycle progression is an important requisite for CDK4/6 inhibitor response in HR+ breast cancer
Cited by: 9
Author(s): Karineh Petrossian, Noriko Kanaya, Chiao Lo, Pei-Yin Hsu, Duc T. Nguyen, Lixin Yang, Lu Yang, Charles Warden, Xiwei Wu, Raju Pillai, Lauren Bernal, Chiun‐Sheng Huang, Laura Kruper, Yuan Yuan, George Somlo, Joanne Mortimer, Shiuan Chen
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-019-0649-6

Genome-wide methylation profiling of Beckwith-Wiedemann syndrome patients without molecular confirmation after routine diagnostics
Cited by: 17
Author(s): Izabela M. Krzyzewska, Mariëlle Alders, Saskia M. Maas, Jet Bliek, Andrea Venema, Peter Henneman, Faisal I. Rezwan, Karin van der Lip, Adri N. Mul, Deborah J G Mackay, Marcel M.A.M. Mannens
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0169249

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
Cited by: 70
Author(s): Benedikt Zacher, Margaux Michel, Björn Schwalb, Patrick Cramer, Achim Tresch, Julien Gagneur
Software Mentions: 3
Published: almost 8 years ago

10.1093/database/baz086

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms
Cited by: 12
Author(s): Jochen T. Bick, Shuqin Zeng, Mark D. Robinson, Susanne E. Ulbrich, Stefan Bauersachs
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1009676

Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome
Cited by: 11
Author(s): Jesse A. Garcia, Kirk E. Lohmueller
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-41067-7

Differential gene expression in response to eCry3.1Ab ingestion in an unselected and eCry3.1Ab-selected western corn rootworm (Diabrotica virgifera virgifera LeConte) population
Cited by: 12
Author(s): Zhichao Zhao, Lisa N. Meihls, Bruce E. Hibbard, Tieming Ji, Christine G. Elsik, Kent S. Shelby
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-020-3536-4

fcScan: a versatile tool to cluster combinations of sites using genomic coordinates
Cited by: 2
Author(s): Abdullah El-Kurdi, Ghiwa Ali Khalil, Georges Khazen, Pierre Khoueiry
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.691997

Phosphoinositide 3-Kinase p110 Delta Differentially Restrains and Directs Naïve Versus Effector CD8+ T Cell Transcriptional Programs
Cited by: 6
Author(s): Laura Spinelli, Julia M. Marchingo, Aneela Nomura, Marcos Damasio, Doreen A. Cantrell
Software Mentions: 2
Published: over 3 years ago

10.1038/srep41748

Genome-wide association study for performance traits in chickens using genotype by sequencing approach
Cited by: 23
Author(s): Fábio Pértille, Gabriel Costa Monteiro Moreira, Ricardo Zanella, José de Ribamar da Silva Nunes, Clarissa Boschiero, Gregorí Alberto Rovadoscki, Gérson Barreto Mourão, Mônica Corrêa Ledur, Luiz Lehmann Coutinho
Software Mentions: 2
Published: almost 8 years ago

10.1007/s00204-017-2060-4

Beyond detoxification: a role for mouse mEH in the hepatic metabolism of endogenous lipids
Cited by: 13
Author(s): Anne Marowsky, Imke Meyer, Kira Erismann-Ebner, Giovanni Pellegrini, Nandkishor Mule, Michael Arand
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-017-3481-4

Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes
Cited by: 34
Author(s): Prashant Singh, Patrick R. van den Berg, Mark D. Long, Angie Vreugdenhil, Laurie Grieshober, Heather M. Ochs‐Balcom, Jianmin Wang, Sylvie Delcambre, Sami Heikkinen, Carsten Carlberg, Moray J. Campbell, Lara E. Sucheston‐Campbell
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2020.00160

Predicting Stage-Specific Recurrent Aberrations From Somatic Copy Number Dataset
Cited by: 2
Author(s): Chaima Aouiche, Bolin Chen, Xuequn Shang
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22094445

Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice
Cited by: 7
Author(s): Hedia Tnani, Dmytro Chebotarov, Ranjita Thapa, John Carlos I. Ignacio, Walter Krystler Israel, Fergie Ann Quilloy, Shalabh Dixit, Endang M. Septiningsih, Tobias Kretzschmar
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-801

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
Cited by: 31
Author(s): Matteo Dell’Acqua, Andrea Zuccolo, Metin Tuna, L. Gianfranceschi, Mario Enrico Pè
Software Mentions: 2
Published: about 10 years ago

10.1093/gigascience/giy039

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm
Cited by: 40
Author(s): Yang Zhou, Erin E. Connor, Derek M. Bickhart, Congjun Li, R.L. Baldwin, Steven G. Schroeder, Benjamin D. Rosen, Liguo Yang, Curtis P. Van Tassell, George E. Liu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0135410

Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation
Cited by: 50
Author(s): Narasimharao Nalabothula, Taha Al-jumaily, Abdallah M. Eteleeb, Robert M. Flight, Xiaorong Shao, Hunter N. B. Moseley, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: about 9 years ago

10.1186/s12916-016-0632-4

Modeling hormonal and inflammatory contributions to preterm and term labor using uterine temporal transcriptomics
Cited by: 54
Author(s): Roberta Migale, David A. MacIntyre, Stefano Cacciatore, Yun Sok Lee, Henrik Hagberg, Bronwen R. Herbert, Mark R. Johnson, Donald Peebles, Simon N. Waddington, Phillip R. Bennett
Software Mentions: 2
Published: over 8 years ago

10.1186/s12920-015-0101-5

Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems
Cited by: 55
Author(s): Pontus Eriksson, Mattias Aine, Srinivas Veerla, Fredrik Liedberg, Gottfrid Sjödahl, Mattias Höglund
Software Mentions: 2
Published: over 9 years ago

10.1186/s13104-015-1404-5

VING: a software for visualization of deep sequencing signals
Cited by: 20
Author(s): Marc Descrimes, Yousra Ben Zouari, Maxime Wéry, Rachel Legendre, Daniel Gautheret, Antonin Morillon
Software Mentions: 2
Published: about 9 years ago

10.1038/s41388-019-0868-5

Gene expression profiles of CMS2-epithelial/canonical colorectal cancers are largely driven by DNA copy number gains
Cited by: 19
Author(s): Kaja Christine Graue Berg, Anita Sveen, Maren Høland, Sharmini Alagaratnam, Marianne Berg, Stine A. Danielsen, Arild Nesbakken, Kjetil Søreide, Ragnhild Lothe
Software Mentions: 2
Published: over 5 years ago

10.1038/s41416-019-0538-y

EZH2 cooperates with E2F1 to stimulate expression of genes involved in adrenocortical carcinoma aggressiveness
Cited by: 20
Author(s): Houda Tabbal, Amandine Septier, M Mathieu, Coralie Drelon, Stéphanie Rodriguez, Cyril Djari, Marie Batisse-Lignier, Igor Tauveron, Jean-Christophe Pointud, Isabelle Sahut‐Barnola, Bruno Ragazzon, Guillaume Assié, Jérôme Bertherat, Anne‐Marie Lefrançois‐Martinez, Antoine Martinez, Pierre Val
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-020-3508-8

Origins and characterization of variants shared between databases of somatic and germline human mutations
Cited by: 10
Author(s): William Meyerson, John Leisman, Fábio C. P. Navarro, Mark Gerstein
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.651604

The Chromatin Accessibility Landscape of Adult Rat
Cited by: 1
Author(s): Yue Yuan, Qiuting Deng, Xiaoyü Wei, Yang Liu, Qing Lan, Yu Jiang, Yeya Yu, Pengcheng Guo, Jiangshan Xu, Yu Sheng Cong, Lei Han, Mengnan Cheng, Peng Wu, Xiao Zhang, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Huanming Yang, Chuanyu Liu, Longqi Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-017-1316-x

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Cited by: 25
Author(s): Dina Hafez, Aslihan Karabacak, Sabrina Krueger, Yi‐Ting Hwang, Li-San Wang, Robert P. Zinzen, Uwe Ohler
Software Mentions: 2
Published: about 7 years ago

Projects: bioconductor: GenomicRanges

Papers Mentioning GenomicRanges 323