pypi: bwa | Projects | Ecosyste.ms: Papers

10.3389/fonc.2020.00302

CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma
Cited by: 7
Author(s): Robyn T. Sussman, Jo Lynne Rokita, Kevin Huang, Pichai Raman, Komal S. Rathi, Daniel Martı́nez, Kristopher R. Bosse, Maria Lane, Lori S. Hart, Tricia R. Bhatti, Bruce Pawel, John M. Maris
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00876

Chromosome Genome Assembly of the Leopard Coral Grouper (Plectropomus leopardus) With Nanopore and Hi-C Sequencing Data
Cited by: 4
Author(s): Yongbo Wang, Xintian Wen, Xinhui Zhang, Shuyuan Fu, Jinye Liu, Wei Tan, Ming Luo, Longlong Liu, Hai Huang, Xinxin You, Jian Luo, Fuxiao Chen
Software Mentions: 3
Published: about 4 years ago

10.1016/j.molcel.2017.01.030

Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways
Cited by: 33
Author(s): Jérôme Jullien, Munender Vodnala, Vincent Pasque, Mami Oikawa, Kazuaki Miyamoto, George E. Allen, Sarah-Anne David, Vincent Brochard, Stan Wang, Charles R. Bradshaw, Haruhiko Koseki, Vittorio Sartorelli, Nathalie Beaujean, J. B. Gurdon
Software Mentions: 3
Published: over 7 years ago

10.1186/s40478-018-0584-3

Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration
Cited by: 64
Author(s): Tuan Leng Tay, Sagar, Jana Dautzenberg, Dominic Grün, Marco Prinz
Software Mentions: 3
Published: about 6 years ago

10.1128/mSphere.00164-20

Accumulation of Antibiotic Resistance Genes in Carbapenem-Resistant Acinetobacter baumannii Isolates Belonging to Lineage 2, Global Clone 1, from Outbreaks in 2012–2013 at a Tehran Burns Hospital
Cited by: 21
Author(s): Masoumeh Douraghi, Johanna J. Kenyon, Parisa Aris, Mahla Asadian, Sedighe Ghourchian, Mohammad Hamidian
Software Mentions: 3
Published: over 4 years ago

10.1128/mBio.01399-18

Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification
Cited by: 76
Author(s): Giovanni Bussotti, Evi Gouzelou, Mariana Côrtes Boité, Ihcene Kherachi Djenad, Zoubir Harrat, Naouel Eddaikra, Jeremy C. Mottram, Μαρία Αντωνίου, Vasiliki Christodoulou, Aymen Bali, Fatma Z. Guerfali, Dhafer Laouini, M. Shahid Mukhtar, Franck Dumetz, Jean‐Claude Dujardin, Despina Smirlis, Pierre Lechat, Pascale Pescher, Adil El Hamouchi, Meryem Lemrani, Carmen Chicharro, Ivonne Pamela Llanes-Acevedo, Laura Botana, Israel Cruz, Javier Moreno, Fakhri Jeddi, Abdul Karim, A. Bouratbine, Elisa Cupolillo, Gérald F. Späth
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.stemcr.2021.02.017

Inaccessible LCG Promoters Act as Safeguards to Restrict T Cell Development to Appropriate Notch Signaling Environments
Cited by: 0
Author(s): Suzanne Furuyama, Qian Wu, Barbara Varnum‐Finney, Richard Sandstrom, Wouter Meuleman, J Stamatoyannopoulos, Irwin D. Bernstein
Software Mentions: 3
Published: over 3 years ago

10.1186/s13100-017-0086-z

Considerations and complications of mapping small RNA high-throughput data to transposable elements
Cited by: 9
Author(s): Alexandros Bousios, Brandon S. Gaut, Nikos Darzentas
Software Mentions: 3
Published: almost 8 years ago

10.3390/microorganisms9051022

Genomics and Virulence of Klebsiella pneumoniae Kpnu95 ST1412 Harboring a Novel Incf Plasmid Encoding Blactx-M-15 and Qnrs1 Causing Community Urinary Tract Infection
Cited by: 3
Author(s): Ayala Gancz, Kira Kondratyeva, Dorit Cohen-Eli, Shiri Navon-Venezia
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-86612-5

Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells
Cited by: 4
Author(s): Olivier B. Bakker, Aarón D. Ramírez-Sánchez, Z Borek, Nigel Klein, Yang Li, Rutger Modderman, Yvonne Kooy–Winkelaar, Marie K. Johannesen, Filomena Matarese, Joost H.A. Martens, Vinod Kumar, Jeroen van Bergen, Shuo‐Wang Qiao, Knut E.A. Lundin, Ludvig M. Sollid, Frits Koning, Cisca Wijmenga, Sebo Withoff, Iris Jonkers
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.02359-20

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways
Cited by: 26
Author(s): Miglė Gabrielaite, Helle Krogh Johansen, Søren Molin, Finn C. Nielsen, Rasmus Lykke Marvig
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-59407-3

MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella
Cited by: 15
Author(s): Krishnendu Mukherjee, Daniel Amsel, Miriam Kalsy, André Billion, Ulrich Dobrindt, Andreas Vilcinskas
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-3679-5

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
Cited by: 21
Author(s): William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson, Weizhong Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s40168-021-01064-3

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Cited by: 465
Author(s): Chang Liu, Meng‐Xuan Du, Rexiding Abuduaini, Haiying Yu, Dan‐Hua Li, Yujing Wang, Nan Zhou, Min-Zhi Jiang, Ping Niu, Shanshan Han, Hong-He Chen, Wenyu Shi, Linhuan Wu, Yu‐Hua Xin, Juncai Ma, Yu‐Guang Zhou, Cheng‐Ying Jiang, Hongwei Liu, Shuang‐Jiang Liu
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-53802-1

Oral microbiome diversity in chimpanzees from Gombe National Park
Cited by: 14
Author(s): Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne E. Pusey, Anne C. Stone
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-31304-w

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation
Cited by: 70
Author(s): Andrey A. Yurchenko, Hans D. Daetwyler, N. A. Yudin, Robert D. Schnabel, Christy J. Vander Jagt, В. А. Солошенко, Bulat Lhasaranov, Ruslan Popov, Taylor Jf, Denis M. Larkin
Software Mentions: 3
Published: about 6 years ago

10.1002/evl3.8

Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius
Cited by: 54
Author(s): Ann-Marie Oppold, Markus Pfenninger
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-49467-5

The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone
Cited by: 18
Author(s): Swaine L. Chen, Ying Ding, Anucha Apisarnthanarak, Shirin Kalimuddin, Sophia Archuleta, Sharifah Faridah Syed Omar, Partha Pratim De, Tse Hsien Koh, Kean Lee Chew, Nadia Atiya, Nuntra Suwantarat, Rukumani Devi Velayuthan, Joshua Wong, David C. Lye
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0194-3

The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies
Cited by: 30
Author(s): Baohua Chen, Zhixiong Zhou, Qiaozhen Ke, Yidi Wu, Haili Bai, Fei Pu, Peng Xu
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-08563-0

Patterns of transcriptional parallelism and variation in the developing olfactory system of Drosophila species
Cited by: 7
Author(s): Jia-Wern Pan, Qingyun Li, Scott Barish, Sumie Okuwa, Shuaiguo Zhao, Charles Soeder, Matthew Kanke, Corbin D. Jones, Pelin Volkan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-50805-w

Identification of somatic alterations in lipoma using whole exome sequencing
Cited by: 4
Author(s): Deepika Kanojia, Pushkar Dakle, Anand Mayakonda, Rajeev Parameswaran, Mark E. Puhaindran, Victor Kwan Min Lee, Vikas Madan, Phillip Koeffler
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pntd.0001512

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing
Cited by: 85
Author(s): Adriano C. Coelho, Sébastien Boisvert, Avinaba Mukherjee, Philippe Leprohon, Jacques Corbeil, Marc Ouellette
Software Mentions: 3
Published: almost 13 years ago

10.1111/eva.13086

Population genomic data in spider mites point to a role for local adaptation in shaping range shifts
Cited by: 11
Author(s): Lei Chen, Jing‐Tao Sun, Peng‐Yu Jin, Ary A. Hoffmann, Xiao‐Li Bing, Dian‐Shu Zhao, Xiao‐Feng Xue, Xiao‐Yue Hong
Software Mentions: 3
Published: about 4 years ago

10.1111/eva.13231

Leveraging genomics to understand threats to migratory birds
Cited by: 4
Author(s): Brenda Larison, Alec R. Lindsay, Christen M. Bossu, Michael D. Sorenson, Jonas Kaplan, David C. Evers, James D. Paruk, Jeffrey M. DaCosta, Thomas B. Smith, Kristen Ruegg
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pmed.1002136

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine
Cited by: 25
Author(s): Gerald Goh, RM Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock‐Ah Im, Sung‐Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil L. Spector, Thomas Yau, Mehdi Afrit, Slim Ben Ahmed, Stephen Johnston, Neil Gibson, Martina Uttenreuther-Fischer, Javier Herrero, Charles Swanton
Software Mentions: 3
Published: almost 8 years ago

10.3389/fphys.2015.00286

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution
Cited by: 30
Author(s): Anita Tripathi, Kavita Goswami, Neeti Sanan-Mishra
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.03533-20

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1009138

Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
Cited by: 28
Author(s): Caoimhe E. O’Brien, João Oliveira-Pacheco, Eoin Ó Cinnéide, Max A. B. Haase, Chris Todd Hittinger, Thomas R. Rogers, Óscar Zaragoza, Ursula Bond, Geraldine Butler
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1005406

Tempo and Mode of Transposable Element Activity in Drosophila
Cited by: 97
Author(s): Robert Kofler, Viola Nolte, Christian Schlötterer
Software Mentions: 3
Published: over 9 years ago

10.1098/rspb.2021.0177

Genotype by environment interactions in coral bleaching
Cited by: 27
Author(s): Crawford Drury, Diego Lirman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008476

Past and ongoing adaptation of human cytomegalovirus to its host
Cited by: 18
Author(s): Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell’Oste, Chiara Pontremoli, Chiara Vantaggiato, Diego Forni, Mario Clerici, Santo Landolfo, Manuela Sironi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41438-021-00551-w

A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China
Cited by: 15
Author(s): Jihua Wang, Shiqiang Xu, Mei Yu, Shuang Cai, Yan Gu, Minyang Sun, Zhiyao Liang, Yong Xiao, Muqing Zhang, Shan Yang
Software Mentions: 3
Published: over 3 years ago

10.3390/insects10070209

Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation
Cited by: 3
Author(s): Erin Rebecca Thompson, Jason Baumsteiger, Ryan I. Hill
Software Mentions: 3
Published: over 5 years ago

10.1098/rspb.2020.3169

Conservation and turnover of miRNAs and their highly complementary targets in early branching animals
Cited by: 5
Author(s): Daniela Praher, Bob Zimmermann, Rohit Dnyansagar, David J. Miller, Aurélie Moya, Vengamanaidu Modepalli, Arie Fridrich, Daniel Sher, Lene Friis-Møller, Per Sundberg, Sylvain Forêt, Regan Ashby, Yehu Moran, Ulrich Technau
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006550

Mutation Accumulation in an Asexual Relative of Arabidopsis
Cited by: 52
Author(s): John T Lovell, R. Williamson, Stephen I. Wright, John McKay, Timothy F. Sharbel
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-15-1107

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
Cited by: 60
Author(s): Nicholas B. Justice, Anders Norman, Christopher T. Brown, Anil K. Singh, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 3
Published: almost 11 years ago

10.1007/s00401-019-01976-3

Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
Cited by: 33
Author(s): Rita Cacace, Bavo Heeman, Sara Van Mossevelde, Arne De Roeck, Julie Hoogmartens, Peter De Rijk, Helena Gossye, Kristof De Vos, Wouter De Coster, Mojca Stražišar, Greet De Baets, Joost Schymkowitz, Frédéric Rousseau, Nathalie Geerts, Tim De Pooter, Karin Peeters, Anne Sieben, Jean‐Jacques Martin, Sebastiaan Engelborghs, Eric Salmon, Patrick Santens, Rik Vandenberghe, Patrick Cras, Peter Paul De Deyn, John C. van Swieten, Cornelia M. van Duijn, Julie van der Zee, Kristel Sleegers, Christine Van Broeckhoven
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa121

Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix
Cited by: 5
Author(s): Justin Bedő, Leon Di Stefano, Anthony T. Papenfuss
Software Mentions: 3
Published: about 4 years ago

10.1186/s41065-017-0027-3

Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology
Cited by: 13
Author(s): Bing Zeng, Haidong Yan, Xinchun Liu, Wenjing Zang, Ailing Zhang, Sifan Zhou, Linkai Huang, Jinping Liu
Software Mentions: 3
Published: over 7 years ago

10.1073/pnas.2003724117

Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles
Cited by: 28
Author(s): Asier Ullate-Agote, Ingrid Burgelin, Adrien Debry, Carine Langrez, Florent Montange, Rodrigue Peraldi, Jean Daraspe, Henrik Kaessmann, Michel C. Milinkovitch, Athanasia C. Tzika
Software Mentions: 3
Published: about 4 years ago

10.1186/s13073-020-00814-6

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition
Cited by: 69
Author(s): Stefan E. Heiden, Nils–Olaf Hübner, Jürgen A. Bohnert, Claus–Dieter Heidecke, Axel Krämer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker, Katharina Schaufler
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12915-021-01041-0

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence
Cited by: 13
Author(s): Zhaoen Yang, Xiaoyang Ge, Weinan Li, Yang Jin, Lisen Liu, Wei Hu, Fuyan Liu, Yanli Chen, Shaoliang Peng
Software Mentions: 3
Published: over 3 years ago

10.1099/mgen.0.000221

Identification of novel adenovirus genotype 90 in children from Bangladesh
Cited by: 9
Author(s): Charlotte J. Houldcroft, Mathew A. Beale, Abu Sayeed, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Software Mentions: 3
Published: about 6 years ago

10.1186/s13073-014-0090-6

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Cited by: 816
Author(s): Michael Inouye, Harriet Dashnow, Lesley Raven, Mark B. Schultz, Bernard J. Pope, Takehiro Tomita, Justin Zobel, Kathryn E. Holt
Software Mentions: 3
Published: about 10 years ago

10.1002/ece3.2466

Dealing with paralogy in <scp>RAD</scp> seq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
Cited by: 26
Author(s): Cindy Verdu, Erwan Guichoux, Samuel Quevauvillers, Olivier De Thier, Yec’han Laizet, Adline Delcamp, Frédéric Gévaudant, Arnaud Monty, Annabel J. Porté, Philippe Lejeune, Ludivine Lassois, Stéphanie Mariette
Software Mentions: 3
Published: about 8 years ago

10.1099/mgen.0.000388

Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland
Cited by: 25
Author(s): Joseph Crispell, Sophie Cassidy, Kevin Kenny, Guy McGrath, Susan Warde, H. S. Cameron, Gianluigi Rossi, Teresa MacWhite, Piran White, Samantha Lycett, Rowland R. Kao, John Moriarty, Stephen V. Gordon
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008673

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin
Cited by: 30
Author(s): Yuh Chwen G. Lee, Yuki Ogiyama, Nuno M. C. Martins, Brian J. Beliveau, David Acevedo, Chao-ting Wu, Giacomo Cavalli, Gary H. Karpen
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-15-S7-S2

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree workbench tools
Cited by: 15
Author(s): Cristian Coarfa, Christina S. Pichot, Andrew Jackson, Arpit Tandon, Viren Amin, Sriram Raghuraman, Sameer Paithankar, Adrian V. Lee, Sean E. McGuire, Aleksandar Milosavljevic
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-015-1975-5

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Cited by: 32
Author(s): Elizabeth Hénaff, Luís Zapata, Josep M. Casacuberta, Stephan Ossowski
Software Mentions: 3
Published: about 9 years ago

10.15252/emmm.202011987

Combined targeting of G protein‐coupled receptor and <scp>EGF</scp> receptor signaling overcomes resistance to <scp>PI</scp> 3K pathway inhibitors in <scp>PTEN</scp> ‐null triple negative breast cancer
Cited by: 17
Author(s): Davide Zecchin, Christopher Moore, Fanourios Michailidis, Stuart Horswell, Sareena Rana, Michael Howell, Julian Downward
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-15-262

Exome capture from saliva produces high quality genomic and metagenomic data
Cited by: 35
Author(s): Jeffrey M. Kidd, Thomas J. Sharpton, Dean Bobo, Paul J. Norman, Alicia R. Martin, Meredith L. Carpenter, Martin Sikora, Christopher R. Gignoux, Neda Nemat-Gorgani, Alexandra Adams, Moraima Guadalupe, Xiaosen Guo, Qiang Feng, Yingrui Li, Xiao Liu, Peter Parham, Eileen G. Hoal, Marcus W. Feldman, Katherine S. Pollard, Jeffrey D. Wall, Carlos D. Bustamante, Brenna M. Henn
Software Mentions: 3
Published: over 10 years ago

10.1016/j.dib.2020.105820

Multi-tissue Siberian sturgeon RNA sequencing data
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, Denise Vizziano-Cantonnet
Software Mentions: 3
Published: over 4 years ago

10.1016/j.cub.2021.06.023

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment
Cited by: 21
Author(s): Pere Gelabert, Susanna Sawyer, Anders Bergström, Ashot Margaryan, Thomas C. Collin, Tengiz Meshveliani, Anna Belfer‐Cohen, David Lordkipanidze, Nino Jakeli, Zinovi Matskevich, Guy Bar-Oz, Daniel Fernandes, Olivia Cheronet, Kadir T. Özdoğan, Victoria Oberreiter, Robin N. M. Feeney, Mareike Cordula Stahlschmidt, Pontus Skoglund, Ron Pinhasi
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evv176

Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis
Cited by: 42
Author(s): Amanda M. V. Brown, Dana K. Howe, Sulochana K. Wasala, Amy B. Peetz, Inga A. Zasada, Dee R. Denver
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-021-02456-2

Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index
Cited by: 18
Author(s): Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q. Zhang, Tingting Li
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-019-0476-5

Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring
Cited by: 22
Author(s): Marc A. Beal, Matthew J. Meier, Andrew Williams, Andrea Rowan-Carroll, Rémi Gagné, Sarah Lindsay, Tomas Fitzgerald, Matthew E. Hurles, Francesco Marchetti, Carole L. Yauk
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-06862-x

RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes
Cited by: 12
Author(s): Jeremias N. Brand, R. Axel W. Wiberg, Robert Pjeta, Philip Bertemes, Christian Beisel, Peter Ladurner, Lukas Schärer
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-021-02342-x

nPhase: an accurate and contiguous phasing method for polyploids
Cited by: 14
Author(s): Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
Software Mentions: 3
Published: over 3 years ago

10.1186/s12934-015-0377-3

Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)
Cited by: 102
Author(s): Andrea De La Torre, Aisha Metivier, Frances Chu, Lieve M.L. Laurens, David A. C. Beck, Philip T. Pienkos, Mary E. Lidstrom, Marina G. Kalyuzhnaya
Software Mentions: 3
Published: almost 9 years ago

10.1038/s42003-020-01302-8

Network integration and modelling of dynamic drug responses at multi-omics levels
Cited by: 26
Author(s): Nathalie Selevsek, Florian Caiment, Ramona Nudischer, Hans Gmuender, Irina Agarkova, Francis Atkinson, Ivo Bachmann, Vanessa Baier, Gal Barel, Chris Bauer, Stefan Boerno, Nicolas Bosc, Olivia Clayton, Henrik Cordes, Sally J. Deeb, Stefano Gotta, Patrick Guye, Anne Hersey, Fiona Hunter, Laura Kunz, Alex Lewalle, Matthias Lienhard, Jort J. Merken, Jasmine Minguet, Bernardo Lino de Oliveira, Carla Pluess, Ugis Sarkans, Yannick Schrooders, Johannes Schuchhardt, Ines Smit, Christoph Thiel, Bernd Timmermann, Marcha Verheijen, Timo Wittenberger, Witold Wolski, Alexandra Zerck, Stéphane Heymans, Lars Kuepfer, Adrian Roth, Ralph Schlapbach, Steven Niederer, Ralf Herwig, Jos Kleinjans
Software Mentions: 3
Published: about 4 years ago

10.1093/gbe/evx104

Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements
Cited by: 17
Author(s): R. Anderson, Angela Kouris, Christopher H. Seward, Kate M. Campbell, Rachel J. Whitaker
Software Mentions: 3
Published: over 7 years ago

10.1007/s00335-019-09799-z

A high-density genetic map and molecular sex-typing assay for gerbils
Cited by: 7
Author(s): Thomas D. Brekke, S.M. Supriya, Megan G Denver, Angharad Thom, Katherine A. Steele, John F. Mulley
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-2252-3

Construction of relatedness matrices using genotyping-by-sequencing data
Cited by: 104
Author(s): K. G. Dodds, John C. McEwan, Rüdiger Bräuning, R. M. Anderson, Tracey C. van Stijn, Theódór Kristjánsson, Shannon Clarke
Software Mentions: 3
Published: almost 9 years ago

10.1038/s42003-020-01305-5

Focal adhesion ribonucleoprotein complex proteins are major humoral cancer antigens and targets in autoimmune diseases
Cited by: 3
Author(s): Saoko Atsumi, Hiroto Katoh, Daisuke Komura, Itaru Hashimoto, Genta Furuya, Hirotomo Koda, Hiroki Konishi, Ryôhei Suzuki, Asami Yamamoto, Satsuki Yuba, Hiroyuki Abé, Yasushi Rino, Takashi Oshima, Tetsuo Ushiku, Masashi Fukayama, Yasuyuki Seto, Shumpei Ishikawa
Software Mentions: 3
Published: about 4 years ago

10.1186/s13028-018-0415-3

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging
Cited by: 33
Author(s): Marie Lisandra Zepeda Mendoza, Michael Roggenbuck, Karla Manzano Vargas, Lars Hestbjerg Hansen, Søren Brunak, M. Thomas P. Gilbert, Thomas Sicheritz-Pontén
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-021-02305-2

Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction
Cited by: 19
Author(s): Changcai Huang, Guangyu Li, Jiayu Wu, Junbo Liang, Xiaoyue Wang
Software Mentions: 3
Published: over 3 years ago

10.1038/celldisc.2016.10

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing
Cited by: 161
Author(s): Wenqiang Liu, Xiaoyu Liu, Chenfei Wang, Yawei Gao, Rui Gao, Xiaochen Kou, Yanhong Zhao, Jingyi Li, You Wu, Wenchao Xiu, Su Wang, Jie Yin, Wei Liu, Tao Cai, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1007285

Global characterization of copy number variants in epilepsy patients from whole genome sequencing
Cited by: 42
Author(s): Jean Monlong, Simon L. Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M. Andrade, Ron G. Lafrenière, Micheline Gravel, Dan Spiegelman, Alexandre Dionne‐Laporte, Cyrus Boelman, Fadi F. Hamdan, Jacques L. Michaud, Guy A. Rouleau, Berge A. Minassian, Guillaume Bourque, Patrick Cossette
Software Mentions: 3
Published: over 6 years ago

10.1186/s12935-021-02170-w

RNA sequencing analysis reveals the competing endogenous RNAs interplay in resected hepatocellular carcinoma patients who received interferon-alpha therapy
Cited by: 5
Author(s): Yibin Wu, Longrong Wang, Xiaoshuang Wang, Yiming Zhao, Anrong Mao, Ning Zhang, Jiamin Zhou, Qi Pan, Weiping Zhu
Software Mentions: 3
Published: about 3 years ago

10.1016/j.stem.2021.02.005

Development, maturation, and maintenance of human prostate inferred from somatic mutations
Cited by: 25
Author(s): Sebastian Großmann, Yvette Hooks, Laura Wilson, Luiza Moore, Laura P. O’Neill, Iñigo Martincorena, Thierry Voet, Michael R. Stratton, Rakesh Heer, Peter J. Campbell
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006157

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids
Cited by: 86
Author(s): Andreas F. Kautt, Gonzalo Machado‐Schiaffino, Axel Meyer
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0066086

Distinct MicroRNAs Expression Profile in Primary Biliary Cirrhosis and Evaluation of miR 505-3p and miR197-3p as Novel Biomarkers
Cited by: 81
Author(s): Masashi Ninomiya, Yasuteru Kondo, Ryo Funayama, Takeshi Nagashima, Takayuki Kogure, Eiji Kakazu, Osamu Kimura, Yoshiyuki Ueno, Keiko Nakayama, Tooru Shimosegawa
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0182528

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish
Cited by: 29
Author(s): Yunru Chen, Shiyang Zeng, Ruikun Hu, Xiangxiu Wang, Wenyan Huang, Jiangfang Liu, Luying Wang, Guifen Liu, Ying Cao, Yong Zhang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1002714

Confidence-based Somatic Mutation Evaluation and Prioritization
Cited by: 30
Author(s): Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Kneip Christoph, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Uğur Şahin
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pcbi.1007365

Nucleosome positioning sequence patterns as packing or regulatory
Cited by: 3
Author(s): Erinija Pranckevičienė, Sergey Hosid, Nathan Liang, Ilya Ioshikhes
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008562

Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice
Cited by: 20
Author(s): Hui Zhang, Ming Li, Dongli He, Kun Wang, Pingfang Yang
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1007293

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
Cited by: 20
Author(s): Fábio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark Gerstein
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3000838

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions
Cited by: 55
Author(s): Felix L. Wu, Alva I. Strand, Laura A. Cox, Carole Ober, Jeffrey D. Wall, Priya Moorjani, Molly Przeworski
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0081468

Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data
Cited by: 62
Author(s): Yoji Kukita, Junji Uchida, Shigeyuki Oba, Kazumi Nishino, Toru Kumagai, Koki Taniguchi, Takako Okuyama, Fumio Imamura, Kikuya Kato
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0201889

Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing
Cited by: 28
Author(s): B. Larsen, Kyle M. Gardner, Carsten Pedersen, Marian Ørgaard, Zoë Migicovsky, Sean Myles, Torben Bo Toldam‐Andersen
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-016-1056-3

Fitness consequences of polymorphic inversions in the zebra finch genome
Cited by: 41
Author(s): Ulrich Knief, Georg Hemmrich-Stanisak, Michael Wittig, André Franke, Simon C. Griffith, Bart Kempenaers, Wolfgang Forstmeier
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-019-1635-1

Modeling double strand break susceptibility to interrogate structural variation in cancer
Cited by: 11
Author(s): Tracy Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto, Colin A. Semple
Software Mentions: 3
Published: almost 6 years ago

10.3390/biology1030575

The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq
Cited by: 34
Author(s): Sébastien Renaut, Christopher J. Grassa, Brook T. Moyers, Nolan C. Kane, Loren H. Rieseberg
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pbio.2002039

Dual role of starvation signaling in promoting growth and recovery
Cited by: 17
Author(s): Yonat Gurvich, Dena Leshkowitz, Naama Barkai
Software Mentions: 3
Published: almost 7 years ago

10.1093/bioinformatics/btu205

ReadXplorer—visualization and analysis of mapped sequences
Cited by: 94
Author(s): Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
Software Mentions: 3
Published: over 10 years ago

10.3390/plants9020268

CRISPR/Cas9-Mediated Mutagenesis of RCO in Cardamine hirsuta
Cited by: 1
Author(s): Claire Lessa Alvim Kamei, Bjorn Pieper, Stefan Laurent, Miltos Tsiantis, Peter Huijser
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0217255

A competence-regulated toxin-antitoxin system in Haemophilus influenzae
Cited by: 3
Author(s): Hailey Findlay Black, Scott Mastromatteo, Sunita Sinha, Rachel Ehrlich, Corey Nislow, Joshua Chang Mell, Rosemary J. Redfield
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0065793

Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing
Cited by: 41
Author(s): Alma Brolund, Oscar Franzén, Öjar Melefors, Karin Tegmark-Wisell, Linus Sandegren
Software Mentions: 3
Published: over 11 years ago

10.1186/s12711-015-0111-y

Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs
Cited by: 32
Author(s): Joaquim Corominas, Jorge Augusto Petroli Marchesi, Anna Puig-Oliveras, Manuel Revilla, Jordi Estellé, E. Alves, Josep María Folch, María Ballester
Software Mentions: 3
Published: over 9 years ago

10.1186/1756-0500-7-864

Comparison of insertion/deletion calling algorithms on human next-generation sequencing data
Cited by: 54
Author(s): Dalia Ghoneim, Jason R. Myers, Emily Tuttle, Alex R. Paciorkowski
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-16-S14-S2

Exact approaches for scaffolding
Cited by: 22
Author(s): Mathias Weller, Annie Château, Rodolphe Giroudeau
Software Mentions: 3
Published: about 9 years ago

10.1186/s13059-015-0696-z

FOXM1 binds directly to non-consensus sequences in the human genome
Cited by: 47
Author(s): Deborah A. Sanders, Michael V. Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-019-1691-6

Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
Cited by: 28
Author(s): Daryl M. Gohl, Alessandro Magli, John Garbe, Aaron Becker, Darrell M. Johnson, Shea Anderson, Benjamin Auch, Bradley Billstein, Elyse Froehling, Shana L. McDevitt, Kenneth B. Beckman
Software Mentions: 3
Published: over 5 years ago

10.1111/eva.13194

Standing genetic variation in laboratory populations of insecticide‐susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance
Cited by: 2
Author(s): David S. Denlinger, Spencer B. Hudson, Nadya S. Keweshan, Zachariah Gompert, Scott A. Bernhardt
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.2209

fluff: exploratory analysis and visualization of high-throughput sequencing data
Cited by: 48
Author(s): Γεώργιος Γεωργίου, Simon J. van Heeringen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-015-0833-4

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Cited by: 33
Author(s): Guillaume Rivière, Christophe Klopp, Ibouniyamine Nabihoudine, Arnaud Huvet, Pierre Boudry, Pascal Favrel
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.8213

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
Cited by: 19
Author(s): Sankar Subramanian, Umayal Ramasamy, David Chen
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0113800

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
Cited by: 44
Author(s): Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, Björn Menten
Software Mentions: 3
Published: almost 10 years ago

Projects: pypi: bwa

Papers Mentioning bwa 989