Ecosyste.ms: Papers

10.1186/s12864-015-2096-x

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh
Cited by: 19
Author(s): James Boocock, David Chagné, Tony R. Merriman, Michael A. Black
Software Mentions: 5
Published: about 9 years ago

10.7554/eLife.13546

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity
Cited by: 246
Author(s): Anjar Tri Wibowo, Claude Becker, G. Marconi, Julius Dürr, Jonathan Price, Jörg Hagmann, Ranjith Papareddy, Hadi Putra, Jorge Kageyama, Jörg Becker, Detlef Weigel, José Gutierrez-Marcos
Software Mentions: 5
Published: over 8 years ago

10.1093/hmg/ddv203

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

10.1371/journal.pone.0119198

Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling
Cited by: 47
Author(s): Annapurna Bhattacharjee, Rajesh Ghangal, Rohini Garg, Mukesh Jain
Software Mentions: 5
Published: over 9 years ago

10.1155/2020/3165958

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple
Cited by: 6
Author(s): Qing Liu, Mengnan Chai, Man Zhang, Qing-Yu He, Zhenxia Su, S. V. G. N. Priyadarshani, Liping Liu, Guanxi Dong, Yuan Qin
Software Mentions: 5
Published: over 4 years ago

10.1186/s12915-017-0412-4

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
Cited by: 96
Author(s): Damien J. Lightfoot, David E. Jarvis, Thiruvarangan Ramaraj, R. Lee, Eric N. Jellen, Peter J. Maughan
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-017-03489-z

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli
Cited by: 38
Author(s): Tracy H. Hazen, Jane Michalski, Qingwei Luo, Amol C. Shetty, Sean C. Daugherty, James M. Fleckenstein, David A. Rasko
Software Mentions: 5
Published: over 7 years ago

10.1002/advs.201901672

Comparison of <i>Arachis monticola</i> with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut
Cited by: 38
Author(s): Dongmei Yin, Changmian Ji, Qingxin Song, Wan–Ke Zhang, Xingguo Zhang, Kunkun Zhao, Charles Y. Chen, Chuan Tang Wang, He Guo, Zhe Liang, Xingli Ma, Zhongfeng Li, Yueyi Tang, Yuejun Wang, Ké Li, Longlong Ning, Hui Zhang, Kai Zhao, Xuming Li, Haiyan Yu, Lei Yan, Mingcheng Wang, Liming Ma, Hongkun Zheng, Yijing Zhang, Jinsong Zhang, Wei Hu, Z Jeffrey Chen
Software Mentions: 5
Published: almost 5 years ago

10.1099/mgen.0.000199

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
Cited by: 10
Author(s): Amy C. Fleshman, Kristin Mullins, Jason W. Sahl, Crystal M. Hepp, Nathan C. Nieto, Kristin Wiggins, Heidie Hornstra, Daryl J. Kelly, Teik Chye Chan, Rattanaphone Phetsouvanh, Sabine Dittrich, Phonepasith Panyanivong, Daniel Paris, Paul N. Newton, Allen L. Richards, Talima Pearson
Software Mentions: 5
Published: about 6 years ago

10.1186/s12885-017-3777-4

Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer
Cited by: 28
Author(s): Mingshan Liu, Yang Liu, Jiabo Di, Zhe Su, Hong Yang, Beihai Jiang, Zaozao Wang, Zhen Meng, Fan Bai, Xiangqian Su
Software Mentions: 5
Published: almost 7 years ago

10.1186/s40168-017-0261-y

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Cited by: 127
Author(s): Dorottya Nagy‐Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, M L Eddy, Mady Hornig, W. Ian Lipkin
Software Mentions: 5
Published: over 7 years ago

10.1186/s40168-020-00823-y

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision?
Cited by: 128
Author(s): Tianzhong Jing, Fenghui Qi, Zhiying Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2164-15-537

Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7
Cited by: 6
Author(s): Grit Ebert, Anne Steininger, Robert Weißmann, Vivien Boldt, Allan Lind-Thomsen, Jana Grune, Stefan Badelt, Melanie Heßler, Matthias Peiser, Manuel Hitzler, Lars Riff Jensen, Ines Müller, Hao Hu, Peter F. Arndt, Andreas W. Kuß, Katrin Tebel, Reinhard Ullmann
Software Mentions: 5
Published: over 10 years ago

10.1093/gbe/evab148

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains
Cited by: 2
Author(s): Kun Wu, Zhou‐Hua Cheng, Emily Williams, Nathan T Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dongfeng Liu, Michael Lynch, Hongan Long
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1006017

Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Cited by: 42
Author(s): Kévin Lebrigand, Le He, Nishant Thakur, Marie-Jeanne Arguel, Jolanta Polanowska, Bernard Henrissat, Éric Record, Ghislaine Magdelenat, Valérie Barbe, Sylvain Raffaele, Pascal Barbry, Jonathan J. Ewbank
Software Mentions: 5
Published: over 8 years ago

10.1093/gbe/evx269

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry
Cited by: 53
Author(s): Stephen R. Doyle, Roz Laing, David J. Bartley, Collette Britton, Umer Chaudhry, John S. Gilleard, Nancy Holroyd, Barbara K. Mable, Kirsty Maitland, Alison A. Morrison, Andy Tait, Alan S. Tracey, Matthew Berriman, Eileen Devaney, James A. Cotton, Neil Sargison
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2018.01728

Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions
Cited by: 37
Author(s): Heike Lehnert, Albrecht Serfling, Wolfgang Friedt, Frank Ordon
Software Mentions: 5
Published: almost 6 years ago

10.3390/proteomes6030031

Regional Diversity in the Postsynaptic Proteome of the Mouse Brain
Cited by: 37
Author(s): Marcia Roy, Oksana Sorokina, Colin McLean, Silvia Tapia-González, Javier DeFelipe, J. Douglas Armstrong, Seth G. N. Grant
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-017-1310-3

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation
Cited by: 26
Author(s): Kevin Van Bortle, Douglas H. Phanstiel, M Snyder
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pgen.1005616

Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster
Cited by: 50
Author(s): Sibylle C. Vonesch, David Lamparter, Trudy F. C. Mackay, Sven Bergmann, Ernst Hafen
Software Mentions: 5
Published: almost 9 years ago

10.1093/gigascience/giy086

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Cited by: 17
Author(s): Jang il Sohn, Kyoungwoo Nam, Hyosun Hong, Jun Mo Kim, Dajeong Lim, Kyung Tai Lee, Yoon Jung, Chang Yeon Cho, Namshin Kim, Han Ha Chai, Jin Wu Nam
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2019.01373

Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine
Cited by: 21
Author(s): Elizabeth Demmings, Brigette R. Williams, Cheng‐Ruei Lee, Paola Barba, Shanshan Yang, Chin-Feng Hwang, Bruce I. Reisch, Daniel H. Chitwood, Jason P. Londo
Software Mentions: 5
Published: about 5 years ago

10.3389/fpls.2019.00963

Identification of a Dominant Chlorosis Phenotype Through a Forward Screen of the Triticum turgidum cv. Kronos TILLING Population
Cited by: 17
Author(s): Sophie A Harrington, Nicolás Cobo, Miroslava Karafiátová, Jaroslav Doležel, Philippa Borrill, Cristóbal Uauy
Software Mentions: 5
Published: over 5 years ago

10.1007/s00122-020-03712-y

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding
Cited by: 38
Author(s): Liangliang Gao, Dal Hoe Koo, Philomin Juliana, Trevor W. Rife, Daljit Singh, Cristiano Lemes da Silva, Thomas Lux, Kevin M. Dorn, Marshall Clinesmith, Paula Silva, Xu Wang, Manuel Spannagl, Cécile Monat, Bernd Friebe, Burkhard Steuernagel, Gary J. Muehlbauer, Sean Walkowiak, Curtis Pozniak, Ravi P. Singh, Nils Stein, Martin Mascher, Allan K. Fritz, Jesse Poland
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-020-06784-8

The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste
Cited by: 13
Author(s): Flávia Cristina de Paula Freitas, A. P. Lourenço, Francis Morais Franco Nunes, Alexandre Rossi Paschoal, Fabiano Carlos Pinto de Abreu, Fábio O. Barbin, Luana Bataglia, Carlos Antônio Mendes Cardoso-Júnior, Mário Sérgio Cervoni, Saura R. Silva, Fernanda Dalarmi, Marco Antônio Del Lama, Thiago S. Depintor, Kátia Maria Ferreira, Paula Salles Gória, Michael C. Jaskot, Denyse Cavalcante Lago, Danielle Luna˗Lucena, Lívia Maria Rosatto Moda, Leonardo Penteado Nascimento, Matheus Pedrino, Franciene Rabiço Oliveira, Fernanda C. Sanches, Douglas Elias Santos, Carolina G. Santos, Joseana Vieira, Angel Roberto Barchuk, Klaus Hartfelder, Zilá Luz Paulino Simões, M. M. G. Bitondi, Daniel Guariz Pinheiro
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2017.00367

Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding
Cited by: 14
Author(s): Jan Ištvánek, Jana Dluhošová, Petr Dluhoš, Lenka Pátková, J. Nedĕlník, Jana Řepková
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2164-15-966

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Cited by: 29
Author(s): Johannes A. Hofberger, Beifei Zhou, Haibao Tang, Jonathan D. G. Jones, M. Eric Schranz
Software Mentions: 5
Published: about 10 years ago

10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-14768-0

Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
Cited by: 17
Author(s): Yang Liu, Lingyang Xu, Bo Zhu, Hong Niu, Wengang Zhang, Jianyin Miao, Xiaowen Shi, Ming Zhang, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Li Li, George E. Liu, Junya Li
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-020-03838-2

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference
Cited by: 3
Author(s): Robert J. Moore, Michael Barnathan, Brian Fristensky, Yán Li, Greg Knowles, Paul Gardner-Stephen, Angelo Bueti, Peter Anderson, Jianguang Qin, Andrew S. Ball
Software Mentions: 5
Published: almost 4 years ago

10.7150/thno.55209

<i>Candida albicans</i> disorder is associated with gastric carcinogenesis
Cited by: 48
Author(s): Min Zhong, Yubo Xiong, Jiabao Zhao, Zhi Gao, Jianchao Ma, Zhengxin Wu, Yongxi Song, Xuehui Hong
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-017-15625-w

A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits
Cited by: 49
Author(s): Michał Książkiewicz, Nelson Espinoza N., Huaan Yang, Matthew N. Nelson, Daniel Renshaw, Sandra Rychel, Barbara Ferrari, Maria Carelli, M. Tomaszewska, Stanisław Stawiński, B. Naganowska, B. Wolko, Paolo Annicchiarico
Software Mentions: 5
Published: about 7 years ago

10.3389/fgene.2019.01126

Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation
Cited by: 29
Author(s): Yuan Tian, Haishen Wen, Xin Qi, Xiaoyan Zhang, Shikai Liu, Bingyu Li, Yalong Sun, Jifang Li, Feng He, Wenzhao Yang, Yun Li
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0080822

Bacterial Endosymbiosis in a Chordate Host: Long-Term Co-Evolution and Conservation of Secondary Metabolism
Cited by: 50
Author(s): Jason C. Kwan, Eric W. Schmidt
Software Mentions: 5
Published: almost 11 years ago

10.1111/pbi.13483

The genome of <i>Cleistogenes songorica</i> provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability
Cited by: 18
Author(s): Jiyu Zhang, Fan Wu, Yan Qi, Ulrik P. John, Mingshu Cao, Pao Xu, Zhengshe Zhang, Tiantian Ma, Xifang Zong, Jie Li, Ruijuan Liu, Yufei Zhang, Yufeng Zhao, Gisele Kanzana, Yunyun Lv, Nan Zhang, Germán Spangenberg, Yanrong Wang
Software Mentions: 5
Published: about 4 years ago

10.7717/peerj.6448

The draft genome of strain <i>c</i>Cpun from biting midges confirms insect <i>Cardinium</i> are not a monophyletic group and reveals a novel gene family expansion in a symbiont
Cited by: 10
Author(s): Stefanos Siozios, Jack Pilgrim, Alistair C. Darby, Matthew Baylis, Gregory D. D. Hurst
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2017.00773

The 25–26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes
Cited by: 28
Author(s): Jinbu Jia, Wenqin Lu, Chengcheng Zhong, Ran Zhou, Junjie Xu, Wei Liu, Xiuhong Gou, Qinhu Wang, Junliang Yin, Changwu Xu, Weixing Shan
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2021.691296

Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism
Cited by: 7
Author(s): Katherine Chacón-Vargas, Colin O McCarthy, Dasol Choi, Long Wang, Jae‐Hyuk Yu, John G. Gibbons
Software Mentions: 5
Published: over 3 years ago

10.1111/pbi.12615

A comprehensive draft genome sequence for lupin (<i>Lupinus angustifolius</i>), an emerging health food: insights into plant–microbe interactions and legume evolution
Cited by: 149
Author(s): James K. Hane, Ming Yao, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven B. Cannon, David Edwards, Rhonda C. Foley, Ling Gao, Maria J. Harrison, Wei Huang, Bhavna Hurgobin, Sean Li, Cheng-Wu Liu, Annette McGrath, Grant Morahan, Jeremy D. Murray, James L. Weller, Jianbo Jian, Karam B. Singh
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2020.00062

Fifteen-Year Application of Manure and Chemical Fertilizers Differently Impacts Soil ARGs and Microbial Community Structure
Cited by: 57
Author(s): Fenghua Wang, Wanxue Han, Shuaimin Chen, Wenxu Dong, Mingqiang Qiao, Chunsheng Hu, Binbin Liu
Software Mentions: 5
Published: almost 5 years ago

10.18632/oncotarget.25329

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma
Cited by: 13
Author(s): Toshima Z. Parris, Elisabeth Werner Rönnerman, Hanna Engqvist, Jana Biermann, Katarina Truvé, Szilárd Nemes, Eva Forssell-Aronsson, Giovanni Solinas, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 5
Published: over 6 years ago

10.1111/tpj.14193

Kernel size‐related genes revealed by an integrated<scp>eQTL</scp>analysis during early maize kernel development
Cited by: 30
Author(s): Junling Pang, Junjie Fu, Na Zong, Jing Wang, Dandan Song, Xia Zhang, Cheng He, Ting Fang, Hongwei Zhang, Yanting Fan, Guoying Wang, Jun Zhao
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2019.01491

Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes
Cited by: 26
Author(s): Anisha M. Thanki, Nathan Brown, Andrew Millard, Martha R. J. Clokie
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2021.637832

Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation
Cited by: 3
Author(s): Paula Díez, Martín Pérez‐Andrés, Martin Bøgsted, Mikel Azkargorta, Rodrigo García-Valiente, Rosa Ma Dégano, E Blanco, Sheila Mateos-Gomez, Paloma Bárcena, Santiago Cruz, Rafael Góngora, Félix Elortza, Alicia Landeira-Viñuela, Pablo Juanes-Velasco, Víctor Segura, Raúl Manzano-Román, Júlia Almeida, Karen Dybkær, Alberto Órfão, Manuel Fuentes
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0134880

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine
Cited by: 99
Author(s): Katie E. Hyma, Paola Barba, Minghui Wang, Jason P. Londo, Charlotte B. Acharya, Sharon E. Mitchell, Qi Sun, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1009705

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis
Cited by: 22
Author(s): Masatoshi Nakamoto, Toshitaka Uchino, Eriko Koshimizu, Yudai Kuchiishi, Ryota Sekiguchi, Liu Wang, Ryusuke Sudo, Masato Endo, Yann Guiguen, Manfred Schartl, John H. Postlethwait, Takashi Sakamoto
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-018-23366-7

Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus
Cited by: 25
Author(s): Kayla M. Valdes, Ganesh S. Sundar, Ashton T. Belew, Emrul Islam, Najib M. El-Sayed, Yoann Le Breton, Kevin S. McIver
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.10818

Cytochrome P450 monooxygenase genes in the wild silkworm, <i>Bombyx mandarina</i>
Cited by: 5
Author(s): Linrong Wan, Zhou Anlian, Wen‐Fu Xiao, Bangxing Zou, Yaming Jiang, Jing Xiao, Cao Deng, Youhong Zhang, Mengjia Liu
Software Mentions: 5
Published: almost 4 years ago

10.1007/s10142-018-0639-3

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets
Cited by: 38
Author(s): Sergio Gálvez, Rosa Mérida-García, C. Camino, Philippa Borrill, Michaël Abrouk, Ricardo H. Ramírez-González, Sezgi Biyiklioglu, Francisco Amil-Ruíz, Gabriel Dorado, Hikmet Budak, Victoria González-Dugo, Pablo J. Zarco‐Tejada, R. Appels, Cristóbal Uauy, Pilar Hernández
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-67209-w

Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence
Cited by: 5
Author(s): Jessica A. Goodheart, Geetanjali Minsky, Mira N. Brynjegard-Bialik, Michael S. Drummond, Jacqueline Muñoz, Timothy R. Fallon, Darrin T. Schultz, Jing‐Ke Weng, Elizabeth Torres, Todd H. Oakley
Software Mentions: 5
Published: over 4 years ago

10.3390/cancers12113208

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma
Cited by: 2
Author(s): Daniel A. Rodriguez, Margarita Dorantes Sánchez, Christina L. Decatur, Zélia M. Corrêa, Eden R. Martin, J. William Harbour
Software Mentions: 5
Published: about 4 years ago

10.7717/peerj.3712

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
Cited by: 15
Author(s): Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian
Software Mentions: 5
Published: about 7 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1008566

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Cited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-91684-4

Peptide profiling in cow urine reveals molecular signature of physiology-driven pathways and in-silico predicted bioactive properties
Cited by: 6
Author(s): Rohit Kumar, Syed Azmal Ali, Sumit Kumar Singh, Vanya Bhushan, Jai K. Kaushik, Ashok Kumar Mohanty, Sanjay Kumar
Software Mentions: 5
Published: over 3 years ago

10.1534/g3.115.019166

Genome-Wide Analysis of<i>Drosophila</i>RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
Cited by: 15
Author(s): Yiliang Wei, Shamba S. Mondal, Rima Mouawad, Bartek Wilczyński, R. William Henry, David N. Arnosti
Software Mentions: 5
Published: over 9 years ago

10.3390/ijms20205043

Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.)
Cited by: 18
Author(s): Ge Bai, Da-Hai Yang, Peijian Cao, Huaiying Yao, Yihan Zhang, Xuejun Chen, Bingguang Xiao, Feng Li, Zhenyu Wang, Jun Yang, He Xie
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1006643

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells
Cited by: 102
Author(s): Silva Kasela, Kai Kisand, Liina Tserel, Epp Kaleviste, Anu Remm, Krista Fischer, Tõnu Esko, Harm-Jan Westra, Benjamin P. Fairfax, Seiko Makino, Julian C. Knight, Lude Franke, Andres Metspalu, Pärt Peterson, Lili Milani
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0195461

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome
Cited by: 80
Author(s): Kris A. Christensen, Jong S. Leong, Dionne Sakhrani, Carlo A. Biagi, David R. Minkley, Ruth E. Withler, Eric B. Rondeau, Ben F. Koop, Robert H. Devlin
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-75128-z

Novel genomic targets of valosin-containing protein in protecting pathological cardiac hypertrophy
Cited by: 5
Author(s): Ning Zhou, Xin Chen, Jing Xi, Ben Ma, Christiana Leimena, Shaunrick Stoll, Gangjian Qin, Charles Wang, Hongyu Qiu
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2019.01400

Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms22041811

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes
Cited by: 15
Author(s): Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Software Mentions: 4
Published: almost 4 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: over 6 years ago

10.1111/jpy.13079

Foliose <i>Ulva</i> Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
Cited by: 20
Author(s): Antoine Fort, Marcus McHale, Kévin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
Software Mentions: 4
Published: almost 4 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 4 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 7 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0255822

Evaluation of the severity of nonalcoholic fatty liver disease through analysis of serum exosomal miRNA expression
Cited by: 5
Author(s): Jeong‐An Gim, Soo Min Bang, Young‐Sun Lee, Sun Young Yim, Young Kul Jung, Hayeon Kim, Baek-hui Kim, Ji Hoon Kim, Yeon Seok Seo, Hyung Joon Yim, Jong Eun Yeon, Soon Ho Um, Kwan Soo Byun
Software Mentions: 4
Published: over 3 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
Cited by: 14
Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: about 4 years ago

10.1186/s12951-021-00916-2

Silicon dioxide nanoparticles induced neurobehavioral impairments by disrupting microbiota–gut–brain axis
Cited by: 23
Author(s): Jun Diao, Yinyin Xia, Xuejun Jiang, Jingfu Qiu, Shuqun Cheng, Junhao Su, Xinhao Duan, Min Gao, Xia Qin, Jun Zhang, Jie Fan, Zhen Zou, Chengzhi Chen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 11 years ago

10.3389/fmicb.2021.736411

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Cited by: 2
Author(s): Dong Han, Qiaojuan Yan, Jun Li, Zhengqiang Jiang, Shanchao Yang
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 6 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: almost 4 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.3162

The genomic sequence of<i>Exiguobacterium chiriqhucha</i>str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: about 9 years ago

10.3390/cancers12123738

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients
Cited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-57546-1

Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001
Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: almost 5 years ago

10.3390/genes7040013

Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: over 8 years ago

10.3390/genes9080379

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Cited by: 22
Author(s): George C. diCenzo, Klaudia Dębiec, Jan Krzysztoforski, Witold Uhrynowski, Alessio Mengoni, Camilla Fagorzi, Adrian Górecki, Łukasz Dziewit, Tomasz Bajda, Grzegorz Rzepa, Łukasz Drewniak
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 10 years ago

10.1534/g3.116.037556

Construction of a High-Density American Cranberry (<i>Vaccinium macrocarpon</i>Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
Cited by: 27
Author(s): Brandon Schlautman, Giovanny Covarrubias‐Pazaran, Luis Diaz‐Garcia, Massimo Iorizzo, James J. Polashock, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: over 7 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: over 3 years ago