pypi: genome | Projects | Ecosyste.ms: Papers

10.7554/eLife.39380

Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Cited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-017-1942-z

A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa
Cited by: 17
Author(s): Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs
Software Mentions: 7
Published: almost 7 years ago

10.1016/j.cell.2016.10.026

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Cited by: 527
Author(s): Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Yan Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice Mann, José Marı́a Fernández, Sophia Rowlston, Steven P. Wilder, Samantha Farrow, Xiaojian Shao, John Lambourne, Adriana Redensek, Cornelis A. Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren A. Cheung, Olivier Delaneau, Emmanouil T. Dermitzakis, Heather Elding, Irina Colgiu, Frederik Otzen Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva M. Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T. Maurano, John A. Morris, Véra Pancaldi, Farzin Pourfarzad, Karola Rehnström, Augusto Rendon, Thomas S. Risch, Nilofar Sharifi, Simon Maguire, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E. Antonarakis, Laura Clarke, Marie–Laure Yaspo, Stephan Beck, Roderic Guigó, Daniel Rico, Joost H.A. Martens, Willem H. Ouwehand, Taco W. Kuijpers, Dirk S. Paul, Hendrik G. Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Software Mentions: 7
Published: about 8 years ago

10.1186/1471-2105-15-167

PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Cited by: 4
Author(s): Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh
Software Mentions: 6
Published: over 10 years ago

10.7554/eLife.35788

A promoter interaction map for cardiovascular disease genetics
Cited by: 111
Author(s): Lindsey Montefiori, Débora R. Sobreira, Noboru Jo Sakabe, Ivy Aneas, Amelia C Joslin, Grace Hansen, Grazyna Bozek, Ivan P. Moskowitz, Elizabeth M. McNally, Marcelo A. Nóbrega
Software Mentions: 5
Published: over 6 years ago

10.1186/s13601-016-0105-z

Cow’s milk allergy in Dutch children: an epigenetic pilot survey
Cited by: 36
Author(s): Nicole C. M. Petrus, Peter Henneman, Andrea Venema, Adri N. Mul, Femke van Sinderen, Martin A. Haagmans, Olaf R.F. Mook, Raoul C. M. Hennekam, A. B. Sprikkelman, Marcel M.A.M. Mannens
Software Mentions: 5
Published: over 8 years ago

10.1186/s42523-020-00038-4

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution
Cited by: 23
Author(s): Yuliaxis Ramayo-Caldas, Francesc X. Prenafeta-Boldú, Laura M. Zingaretti, Olga González‐Rodríguez, Antoni Dalmau, Raquel Quintanilla, María Ballester
Software Mentions: 5
Published: over 4 years ago

10.26508/lsa.201900318

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
Cited by: 11
Author(s): Junaid Akhtar, Piyush More, Steffen Albrecht, Fédérico Marini, Walter Kaiser, Apurva Kulkarni, Leszek Wojnowski, Jean-Fred Fontaine, Miguel A. Andrade‐Navarro, Marion Silies, Christian Berger
Software Mentions: 5
Published: over 5 years ago

10.1093/molbev/msab078

Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia
Cited by: 21
Author(s): Laura Buggiotti, Andrey A. Yurchenko, N. A. Yudin, Christy J. Vander Jagt, Nadezhda V. Vorobieva, Mariya A. Kusliy, S. Vasiliev, Andrey N. Rodionov, O. I. Boronetskaya, N. A. Zinovieva, Alexander S. Graphodatsky, Hans D. Daetwyler, Denis M. Larkin
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: about 4 years ago

10.1111/1751-7915.13871

Strain diversity of plant‐associated <i>Lactiplantibacillus plantarum</i>
Cited by: 15
Author(s): Alice Yu, Elissa A. Goldman, Jason T. Brooks, Benjamin L. Golomb, Irene S. Yim, Velitchka Gotcheva, Angel Angelov, Eun Bae Kim, Maria L. Marco
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.24751.2

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity
Cited by: 9
Author(s): Evan Bolyen, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, Jason W. Sahl, Andrew Sanchez, Chris Holdgraf, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew R. McKay, Anthony Simard, David M. Engelthaler, Michael Worobey, Paul Keim, J. Gregory Caporaso
Software Mentions: 4
Published: about 4 years ago

10.1186/s13062-015-0071-8

Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-5605-5

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens
Cited by: 20
Author(s): Andrei A. Kudinov, Natalia V. Dementieva, О.В. Митрофанова, Olga I. Stanishevskaya, Е.С. Федорова, Tatiana A. Larkina, Arina I Mishina, Kirill Plemyashov, Darren K. Griffin, Michael N Romanov
Software Mentions: 4
Published: over 5 years ago

10.1186/s12711-019-0490-6

Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs
Cited by: 20
Author(s): Yuliaxis Ramayo-Caldas, Emilio Mármol-Sánchez, María Ballester, Juan Pablo Sánchez, Rayner González-Prendes, Marcel Amills, Raquel Quintanilla
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2229-12-197

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni
Cited by: 19
Author(s): Vibha Mandhan, Jagdeep Kaur, Kashmir Singh
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.ppat.1008402

Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II
Cited by: 30
Author(s): Ming Li, Christopher B. Ball, Geoffrey S Collins, Qiaolin Hu, Donal S. Luse, David H. Price, Jeffery L. Meier
Software Mentions: 3
Published: over 4 years ago

10.1128/AEM.01741-18

Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate
Cited by: 5
Author(s): Clara Pliego, José Ignacio Crespo-Gómez, Adrián Pintado, Isabel Pérez‐Martínez, Antonio de Vicente, Francisco M. Cazorla, Cayo Ramos
Software Mentions: 3
Published: almost 6 years ago

10.1002/1878-0261.12101

β-Catenin in desmoid-type fibromatosis: deep insights into the role of T41A and S45F mutations on protein structure and gene expression
Cited by: 27
Author(s): Chiara Colombo, Antonino Belfiore, Nicholas Paielli, Loris De Cecco, Silvana Canevari, Erik Laurini, Maurizio Fermeglia, Sabrina Pricl, Paolo Verderio, Stefano Bottelli, Marco Fiore, Silvia Stacchiotti, Elena Palassini, Alessandro Gronchi, Silvana Pilotti, Francesco Perrone
Software Mentions: 3
Published: about 7 years ago

10.1111/pbi.12988

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process
Cited by: 81
Author(s): Jianying Li, Maojun Wang, Yajun Li, Qinghua Zhang, Keith Lindsey, Henry Daniell, Shuangxia Jin, Xianlong Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2105-8-349

A cross-species alignment tool (CAT)
Cited by: 4
Author(s): Heng Li, L. Guan, Tao Liu, Yiran Guo, Wei-Mou Zheng, Gane Ka‐Shu Wong, Jun Wang
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pgen.1009689

The native cistrome and sequence motif families of the maize ear
Cited by: 13
Author(s): Savannah D Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jane A Dennis, Jinfeng Zhang, Hank W. Bass
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs
Cited by: 18
Author(s): Abhishek Kumar, Anita Bhandari, Rahul Sinha, Pankaj Goyal, Alessandro Grapputo
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1009133

Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction
Cited by: 4
Author(s): Emily J. Parnell, Timothy J. Parnell, Chao Yan, Lu Bai, David J. Stillman
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-11-382

Integration and visualization of systems biology data in context of the genome
Cited by: 35
Author(s): J. Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S. Baliga
Software Mentions: 2
Published: over 14 years ago

10.1038/s42003-020-01497-w

Fine-mapping and cell-specific enrichment at corneal resistance factor loci prioritize candidate causal regulatory variants
Cited by: 7
Author(s): Xinyi Jiang, Nefeli Dellepiane, Erola Pairo-Castineira, Thibaud Boutin, Yatendra Kumar, Wendy A. Bickmore, Véronique Vitart
Software Mentions: 2
Published: almost 4 years ago

10.1093/hmg/ddy121

Genome-wide association study identifies nine novel loci for 2D:4D finger ratio, a putative retrospective biomarker of testosterone exposure in utero
Cited by: 36
Author(s): Nicole M. Warrington, Enisa Shevroja, Gibran Hemani, Pirro G. Hysi, Yunxuan Jiang, Adam Auton, Cindy G. Boer, Massimo Mangino, Carol A. Wang, John P. Kemp, George McMahon, Carolina Medina‐Gomez, Martha Hickey, Katerina Trajanoska, Dieter Wolke, M. Arfan Ikram, Grant W. Montgomery, Janine F. Felix, Margaret J. Wright, David A. Mackey, Vincent W.V. Jaddoe, Nicholas G. Martin, Joyce Y. Tung, George Davey Smith, Craig E. Pennell, Tim D. Spector, Joyce B. J. van Meurs, Fernando Rivadeneira, Sarah E. Medland, David M. Evans
Software Mentions: 2
Published: over 6 years ago

10.3389/fpsyt.2018.00743

Childhood Adversity Is Associated With Increased KITLG Methylation in Healthy Individuals but Not in Bipolar Disorder Patients
Cited by: 9
Author(s): Yujie He, Christiaan H. Vinkers, Lotte C Houtepen, Lot de Witte, Marco P. Boks
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.51317

Reversible promoter methylation determines fluctuating expression of acute phase proteins
Cited by: 13
Author(s): Shichao Zhang, Mingyu Wang, Jun-Rui Feng, Yue Chang, Shang‐Rong Ji, Yi Wu
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01292-19

Coding-Complete Sequences of Barley Virus G Isolates from Australia, Obtained from a 34-Year-Old and a 1-Year-Old Sample
Cited by: 3
Author(s): Narelle Nancarrow, Solomon Maina, Linda Zheng, Mohammad Aftab, Angela Freeman, Wycliff M. Kinoti, Brendan Rodoni, Piotr Trębicki
Software Mentions: 1
Published: about 5 years ago

10.1128/MRA.00971-20

Draft Genome Sequences of Five Paenibacillus Species of Dairy Origin
Cited by: 0
Author(s): Abimbola Olaniyi Olajide, Shu Chen, Gisèle LaPointe
Software Mentions: 1
Published: about 4 years ago

10.3390/v12050544

Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01
Cited by: 6
Author(s): Cindy M. Spruit, Anu Wicklund, Xing Wan, Mikael Skurnik, Maria I. Pajunen
Software Mentions: 1
Published: over 4 years ago

10.3390/v13040583

Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses
Cited by: 13
Author(s): Solomon Maina, Linda Zheng, Brendan Rodoni
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.0030131

Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network
Cited by: 461
Author(s): Reut Shalgi, Daniel S. Lieber, Moshe Oren, Yitzhak Pilpel
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0058815

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data
Cited by: 109
Author(s): Emma M. Quinn, Paul Cormican, Elaine Kenny, Matthew Hill, Richard Anney, Michael Gill, Aiden Corvin, Derek W. Morris
Software Mentions: 1
Published: over 11 years ago

10.1128/genomeA.00340-17

First Genome Sequences of Dengue Virus Strains Isolated during the First DENV-4 Outbreak in São Paulo, Brazil
Cited by: 1
Author(s): Ayda Susana Ortiz-Báez, Danielle Ferreira Silva, Daniel Ferreira, Paolo Marinho de Andrade Zanotto
Software Mentions: 1
Published: over 7 years ago

Ecosyste.ms: Papers

Projects: pypi: genome

Papers Mentioning genome 36