10.1371/journal.pgen.1003553

NSAIDs Modulate Clonal Evolution in Barrett's Esophagus
Cited by: 60
Author(s): Rumen Kostadinov, Mary K. Kuhner, Xiaohong Li, Carissa A. Sanchez, Patricia C. Galipeau, Thomas G. Paulson, Cassandra L. Sather, Amitabh Srivastava, Robert D. Odze, Patricia L. Blount, Thomas L. Vaughan, Brian J. Reid, Carlo C. Maley
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1005001

Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells
Cited by: 71
Author(s): Fujun Qin, Zhenguo Song, Mihaela Babiceanu, Yansu Song, Loryn Facemire, Ritambhara Singh, Mazhar Adli, Hui Li
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1000875

Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System
Cited by: 68
Author(s): Ana M. Tomljenovic-Berube, David T. Mulder, Matthew D. Whiteside, Fiona S. L. Brinkman, Brian K. Coombes
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pgen.1007003

Genomics-enabled analysis of the emergent disease cotton bacterial blight
Cited by: 36
Author(s): Anne Z. Phillips, Jeffrey C. Berry, Mark C. Wilson, Anupama Vijayaraghavan, Jillian Burke, Jason Bunn, Tom Allen, Terry A. Wheeler, Rebecca Bart
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0007184

Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples
Cited by: 10
Author(s): Uma S. Kamaraj, Jun Tan, Ong Xin Mei, Louise Pan, Tanu Chawla, Anna Uehara, Lin‐Fa Wang, Eng Eong Ooi, Duane J. Gubler, Hasitha Tissera, Lee Ching Ng, Annelies Wilder‐Smith, Paola Flórez de Sessions, Timothy Barkham, Danielle E. Anderson, October M. Sessions
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pntd.0008148

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing
Cited by: 12
Author(s): Jingkai Ji, Bin Li, Jingzhong Li, Wangmu Danzeng, Jiandong Li, Yongqiang Zhao, Gezhen Qiangba, Qingda Zhang, Nibu Renzhen, Zhuoga Basang, Changlin Jia, Gongsang Quzhen, Jinmin Ma, Yicong Wang, Fang Chen, Hong Zhou, Huasang, Jiefang Yin, Jiandan Xie, Na Pei, Huimin Cai, Huayan Jiang, Huanming Yang, Jian Wang, Asan, Xiumin Han, Junhua Li, Weijun Chen, Dong Yang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0151412

Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding
Cited by: 13
Author(s): Rico Schwarz, Dirk Tänzler, Christian Ihling, Andrea Sinz
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0220374

Molecular identification of the phosphate transporter family 1 (PHT1) genes and their expression profiles in response to phosphorus deprivation and other abiotic stresses in Brassica napus
Cited by: 30
Author(s): Li Yu, Xue Wang, Hao Zhang, Sheliang Wang, Xiangsheng Ye, Lei Shi, Fangsen Xu, Guangda Ding
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0074513

Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM
Cited by: 46
Author(s): Yun E. Wang, Georgi K. Marinov, B Wold, David C. Chan
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0180323

Seasonal differences in the testicular transcriptome profile of free-living European beavers (Castor fiber L.) determined by the RNA-Seq method
Cited by: 12
Author(s): Iwona Bogacka, Łukasz Paukszto, J Jastrzebski, Joanna Czerwińśka, Katarzyna Chojnowska, Barbara Kamińska, Aleksandra Kurzyńska, Nina Smolińska, Zygmunt Giżejewski, Tadeusz Kamiński
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0199192

Genome-wide identification and classification of MYB superfamily genes in peach
Cited by: 41
Author(s): Chunhua Zhang, Ruijuan Ma, Jianlan Xu, Juan Yan, Lei Guo, Juan Song, Ruchao Feng, Mingliang Yu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0076376

Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i
Cited by: 72
Author(s): Jimmy H. Saw, Michael C. Schatz, Mark V. Brown, Dennis D. Kunkel, Jamie S. Foster, H. Shick, Stephanie Christensen, Shaobin Hou, Xuehua Wan, Stuart P. Donachie
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0234411

Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L.
Cited by: 5
Author(s): Shuai Shen, Fangfang Sun, Meichen Zhu, Si Chen, Mingwei Guan, Rui Chen, Fang Tang, Nengwen Yin, Xinhua Xu, Zhongjie Tang, Jiana Li, Kun Lu, Cunmin Qu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0101419

Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus
Cited by: 49
Author(s): Grant A. Hill-Cawthorne, Lyndsey O. Hudson, Moataz Abd El Ghany, Olaf Piepenburg, Mridul Nair, Andrew Dodgson, Matthew S. Forrest, Taane G. Clark, Arnab Pain
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0223441

Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content
Cited by: 14
Author(s): Saminathan Subburaj, Kayoun Lee, Yongsam Jeon, Luhua Tu, Gilwoo Son, SuBok Choi, Yong-Pyo Lim, Cecilia McGregor, Geung–Joo Lee
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0057281

Quantitative Genetic Analysis of Retinal Degeneration in the Blind Cavefish Astyanax mexicanus
Cited by: 78
Author(s): Kelly E. O’Quin, Masato Yoshizawa, Pooja Doshi, William R. Jeffery
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0065953

Unbiased Approach for Virus Detection in Skin Lesions
Cited by: 55
Author(s): Davit Bzhalava, Hanna Katarina Lilith Johansson, Johanna Ekström, Helena Faust, Birgitta Moller, Carina Eklund, Peter Nordin, Bo Stenquist, John Paoli, Bengt Persson, Ola Forslund, Joakim Dillner
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0079704

Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151
Cited by: 35
Author(s): Mario L. Arrieta-Ortiz, Luis M. Rodríguez-R, Álvaro L. Pérez‐Quintero, Lucie Poulin, Ana Cristina Díaz, Nathalia Arias Rojas, César Trujillo, Mariana Restrepo Benavides, Rebecca Bart, Jens Boch, Tristan Boureau, Armelle Darrasse, Perrine David, Thomas Dugé de Bernonville, Paula Fontanilla, Lionel Gagnevin, Fabien Guérin, Marie‐Agnès Jacques, Emmanuelle Lauber, Pierre Lefeuvre, César A. Medina, Edgar M. Medina, Nathaly Montenegro, Alejandra Muñoz-Bodnar, Laurent Noël, Juan F. Ortiz Quiñones, Daniela Osorio, Carolina E. Pardo, Prabhu B. Patil, Stéphane Poussier, Olivier Pruvost, Isabelle Robène-Soustrade, Robert P. Ryan, Javier F. Tabima, Oscar G. Urrego Morales, Christian Vernière, Sébastien Carrère, Valérie Verdier, Boris Szurek, Silvia Restrepo, Camilo López, Ralf Koebnik, Adriana Bernal
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0157524

Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon
Cited by: 29
Author(s): Sathishkumar Natarajan, Hoy‐Taek Kim, Senthil Kumar Thamilarasan, Karpagam Veerappan, Jong-In Park, Ill–Sup Nou
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0186721

Genome-wide analysis of structural variants reveals genetic differences in Chinese pigs
Cited by: 7
Author(s): Ruifei Yang, Shuai Fang, Jing Wang, Chunyuan Zhang, Ran Zhang, Di Liu, Yiqiang Zhao, Xiaoxiang Hu, Ning Li
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0027354

Molecular Basis of Virulence in Staphylococcus aureus Mastitis
Cited by: 70
Author(s): Caroline Le Maréchal, Núbia Seyffert, Julien Jardin, David Hernández, Gwenaël Jan, Lucie Rault, Vasco Azevedo, Patrice François, Jacques Schrenzel, Maarten van de Guchte, Sergine Even, Nadejda Berkova, Richard Thiéry, J. Ross Fitzgerald, Eric Vautor, Yves Le Loir
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0164535

ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data
Cited by: 18
Author(s): Fatemeh Vafaee, James R. Krycer, Xiuquan Ma, Timur Burykin, David E. James, Zdenka Kuncic
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0129318

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane
Cited by: 81
Author(s): Lucas Mitsuo Taniguti, Patrícia Dayane Carvalho Schaker, Juliana Benevenuto, Leila Priscila Peters, Gabriela Ferreira Carvalho, Aristides Palhares, Maria Carolina Quecine, Filipe R. S. Nunes, Maria Carolina Pezzo Kmit, Alvan Wai, Georg Hausner, Karen S. Aitken, Paul J. Berkman, James A. Fraser, Paula Moolhuijzen, Luiz Lehmann Coutinho, Silvana Creste, Maria Lúcia Carneiro Vieira, João Paulo Kitajima, Cláudia Barros Monteiro-Vitorello
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0051687

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata
Cited by: 66
Author(s): Stephen H. Kazakoff, Michael Imelfort, David Edwards, Jasper J. Koehorst, Bandana Biswas, Jacqueline Batley, Paul T. Scott, Peter M. Gresshoff
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0161499

Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi
Cited by: 5
Author(s): Brian P. Anton, Gregory P Harhay, Timothy P. L. Smith, Jochen Blom, Richard J. Roberts
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0083012

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing
Cited by: 66
Author(s): Taane G. Clark, Kim Mallard, Francesc Español i Coll, Mark D. Preston, Samuel Assefa, David Harris, Sam Ogwang, Francis Mumbowa, Bruce Kirenga, Denise M O’Sullivan, Alphonse Okwera, Kathleen D. Eisenach, Moses Joloba, Stephen D. Bentley, Jerrold J. Ellner, Julian Parkhill, Edward C. Jones-López, Ruth McNerney
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0190352

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis
Cited by: 38
Author(s): Luis Eduardo Martínez Villegas, Thaís Bonifácio Campolina, Nilton R. Barnabe, Alessandra S Orfanó, Bárbara Aparecida Chaves, Douglas E. Norris, Paulo Pimenta, Nágila Francinete Costa Secundino
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0094924

Analysis of Molecular Cytogenetic Alteration in Rhabdomyosarcoma by Array Comparative Genomic Hybridization
Cited by: 19
Author(s): Chunxia Liu, Dongliang Li, Jinfang Jiang, Jianming Hu, Wei Zhang, Yunzhao Chen, Xiaobin Cui, Qi Yan, Hong Zou, Wenjie Zhang, Feng Li
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0112998

Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice
Cited by: 34
Author(s): Nadja Korotkova, Lars Nauheimer, Hasmik Ter-Voskanyan, Martin Allgaier, Thomas Borsch
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0074432

Next-Generation Sequence Analysis of Cancer Xenograft Models
Cited by: 32
Author(s): Fernando Rossello, Richard W. Tothill, Kara Britt, Kieren D. Marini, Jeanette Falzon, David M. Thomas, Craig D. Peacock, Luigi Marchionni, Jason Li, Samara Bennett, Erwin Tantoso, Tracey Brown, Philip Wai Hong Chan, Luciano G. Martelotto, D. Neil Watkins
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0069476

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes
Cited by: 43
Author(s): Guozheng Liu, Dandan Cao, Shuangshuang Li, Aiguo Su, Jianing Geng, Corrinne E. Grover, Songnian Hu, Jinping Hua
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0071952

Microbial Life in a Fjord: Metagenomic Analysis of a Microbial Mat in Chilean Patagonia
Cited by: 14
Author(s): Juan A. Ugalde, María José Gallardo, Camila Belmar, Práxedes Muñoz, Nathaly Ruiz‐Tagle, Sandra Ferrada-Fuentes, Claudia Espinoza, Eric E. Allen, Víctor A. Gallardo
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0177553

Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species
Cited by: 10
Author(s): Zhiqiang Wu, Cuihua Gu, Luke R. Tembrock, Dong Zhang, Song Ge
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0075072

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes
Cited by: 133
Author(s): Bishwo N. Adhikari, John Hamilton, Marcelo M. Zerillo, Ned Tisserat, C. André Lévesque, C. Robin Buell
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0188682

Genome-wide recombination rate variation in a recombination map of cotton
Cited by: 21
Author(s): Chao Shen, Ximei Li, Ruiting Zhang, Zhenhua Lin
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0173064

Multimodal MR-imaging reveals large-scale structural and functional connectivity changes in profound early blindness
Cited by: 39
Author(s): Corinna M. Bauer, Gabriella V. Hirsch, Lauren Zajac, Bang‐Bon Koo, Olivier Collignon, Lotfi B. Merabet
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0233813

Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations
Cited by: 12
Author(s): William T. Molin, Eric Patterson, Christopher Saski
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2020.00565

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops
Cited by: 9
Author(s): Weilong Kong, Tong Sun, Chenhao Zhang, Yalin Qiang, Yangsheng Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00788

Comprehensive Analysis of Respiratory Burst Oxidase Homologs (Rboh) Gene Family and Function of GbRboh5/18 on Verticillium Wilt Resistance in Gossypium barbadense
Cited by: 18
Author(s): Ying Chang, Bo Li, Qian Shi, Rui Geng, Shuaipeng Geng, Jinlei Liu, Yuanyuan Zhang, Yingfan Cai
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2020.00044

The Cytochrome P450 Monooxygenase Inventory of Grapevine (Vitis vinifera L.): Genome-Wide Identification, Evolutionary Characterization and Expression Analysis
Cited by: 28
Author(s): Songtao Jiu, Yan Xu, Jiyuan Wang, Lei Wang, Xunju Liu, Wanxia Sun, Irfan Ali Sabir, Chao Ma, Wenping Xu, Shiping Wang, Muhammad Abdullah, Caixi Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2018.03163

VH1-69 Utilizing Antibodies Are Capable of Mediating Non-neutralizing Fc-Mediated Effector Functions Against the Transmitted/Founder gp120
Cited by: 11
Author(s): S Abigail Smith, Samantha L. Burton, William Kilembe, Shabir Lakhi, Etienne Karita, Matt A. Price, Susan Allen, Cynthia A. Derdeyn
Software Mentions: 2
Published: almost 8 years ago

10.3389/fimmu.2021.587440

Transcriptome and Differential Methylation Integration Analysis Identified Important Differential Methylation Annotation Genes and Functional Epigenetic Modules Related to Vitiligo
Cited by: 11
Author(s): Yihuan Pu, Xuenuo Chen, Yangmei Chen, Lingzhao Zhang, Jiayi Chen, Yujie Zhang, Xinyi Shao
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2016.00301

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments
Cited by: 45
Author(s): Alexander Crits-Christoph, Courtney K. Robinson, Bing Ma, Jacques Ravel, Jacek Wierzchos, Carmen Ascaso, Octavio Artieda, Virginia Souza-Egipsy, María Cristina Casero, Jocelyne DiRuggiero
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2016.00573

Genomic and Secondary Metabolite Analyses of Streptomyces sp. 2AW Provide Insight into the Evolution of the Cycloheximide Pathway
Cited by: 16
Author(s): Elizabeth R. Stulberg, Gabriel L. Lozano, Jesse B. Morin, Hyunjun Park, Ezra Baraban, Christine Mlot, Christopher Heffelfinger, Gillian M. Phillips, Jason S. Rush, Andrew J. Phillips, Nichole A. Broderick, Michael G. Thomas, Eric V. Stabb, Jo Handelsman
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2021.662966

Effects of Gallic Acid on Fermentation Parameters, Protein Fraction, and Bacterial Community of Whole Plant Soybean Silage
Cited by: 19
Author(s): Cheng Wang, Mingyang Zheng, Shuo Wu, Xuan Zhou, Xiaoyang Chen, Liangfa Ge, Qing Zhang
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.01291

Disentangling the Drivers of Diversity and Distribution of Fungal Community Composition in Wastewater Treatment Plants Across Spatial Scales
Cited by: 33
Author(s): Haihan Zhang, Ji Feng, Shengnan Chen, Baoqin Li, Raju Sekar, Zhenfang Zhao, Jingyu Jia, Yue Wang, Peng-Liang Kang
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.00079

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle
Cited by: 32
Author(s): Trestan Pillonel, Claire Bertelli, Gilbert Greub
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2019.00504

Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems
Cited by: 25
Author(s): Hanna Koch, Heike M. Freese, Richard L. Hahnke, Meinhard Simon, Matthias Wietz
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.568457

The Effect of Xylooligosaccharide, Xylan, and Whole Wheat Bran on the Human Gut Bacteria
Cited by: 8
Author(s): Miao Chen, Shujun Liu, Khandaker Md Sharif Uddin Imam, Lichao Sun, Yulu Wang, Tianyi Gu, Bin Wen, Fengjiao Xin
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2019.02792

Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae
Cited by: 31
Author(s): Xiong Zhang, Bo Liu, Fen Zou, Danyu Shen, Zhiyuan Yin, Rongbo Wang, Feng He, Yuanchao Wang, Brett M. Tyler, Wei Fan, Wanqiang Qian, Daolong Dou
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2016.00248

Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island
Cited by: 23
Author(s): Eduard Fadeev, Fabio De Pascale, Alessandro Vezzi, Sariel Hübner, Dikla Aharonovich, Daniel Sher
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2020.00445

Microbiota Succession and Chemical Composition Involved in the Radish Fermentation Process in Different Containers
Cited by: 14
Author(s): Lei Liu, Xiao She, Xing Chen, Qian Yang, Yufei Tao, Yalin Li, Shuyu Guo, Wenliang Xiang, Guorong Liu, Yu Rao
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.01520

Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism
Cited by: 30
Author(s): Yuanchan Luo, Yuejuan Cheng, Jincui Yi, Zhijun Zhang, Qian Luo, Daojing Zhang, Yuanguang Li
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2019.02506

Changes in the Carbon Metabolism of Escherichia coli During the Evolution of Doxycycline Resistance
Cited by: 15
Author(s): Yiwen Yang, Jiandui Mi, Jiadi Liang, Xindi Liao, Baohua Ma, Yongde Zou, Yan Wang, Jiankun Liang, Yinbao Wu
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2019.01786

Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus
Cited by: 12
Author(s): Lei Sun, Yuhua Fu, Yang Yang, Xinxin Wang, Weijie Cui, Dan Li, Xiaohui Yuan, Zhiwu Zhang, Yongping Fu, Li Yu
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2019.01579

The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities
Cited by: 5
Author(s): Chaoyun Chen, Ruiqiao He, Zhangyu Cheng, Maozhen Han, Yuguo Zha, Pengshuo Yang, Qi Yao, Hao Zhou, Chunrong Zhong, Kang Ning
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00058

Exploring K2G30 Genome: A High Bacterial Cellulose Producing Strain in Glucose and Mannitol Based Media
Cited by: 43
Author(s): Maria Gullo, Salvatore La China, Giulio Petroni, Simona Di Gregorio, Paolo Giudici
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.00540

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass
Cited by: 34
Author(s): Aoife Joyce, Umer Zeeshan Ijaz, Corine Nzeteu, Aoife Vaughan, Sally L. Shirran, Catherine H. Botting, Christopher Quince, Vincent O’Flaherty, Florence Abram
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2021.630841

Preventive Effects of Bacillus licheniformis on Heat Stroke in Rats by Sustaining Intestinal Barrier Function and Modulating Gut Microbiota
Cited by: 13
Author(s): Lei Li, Man Wang, Ji-Kuai Chen, Zhuoran Xu, Shaokang Wang, Xinyu Xia, Dong Liu, Sheng Wang, Chaoyu Xie, Jianghong Wu, Jinfeng Li, Jiqianzhu Zhang, Meitang Wang, Jian Zhu, Changquan Ling, Shuogui Xu
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.01248

A Newly Isolated Bacillus subtilis Strain Named WS-1 Inhibited Diarrhea and Death Caused by Pathogenic Escherichia coli in Newborn Piglets
Cited by: 11
Author(s): Yunping Du, Zhichao Xu, Guolian Yu, Wei Liu, Qingfeng Zhou, Dehong Yang, Jie Li, Li Chen, Yun Zhang, Chunyi Xue, Yongchang Cao
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.00126

Genome-Wide Identification and Classification of Soybean C2H2 Zinc Finger Proteins and Their Expression Analysis in Legume-Rhizobium Symbiosis
Cited by: 35
Author(s): Songli Yuan, Xiangyong Li, Rong Li, Lei Wang, Chanjuan Zhang, Limiao Chen, Qingnan Hao, Xiaojuan Zhang, Haifeng Chen, Shan Zhang, Zengling Yang, Shuilian Chen, Dandan Qiu, Danxia Ke, Xinan Zhou
Software Mentions: 2
Published: over 8 years ago

10.1186/gb-2010-11-10-r104

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Cited by: 141
Author(s): Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stéphane Terry, David Z. Chen, Joel Rozowsky, Ashutosh Tewari, Naoki Kitabayashi, Benjamin Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark Gerstein
Software Mentions: 2
Published: about 16 years ago

10.1186/gb-2011-12-10-r103

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Cited by: 176
Author(s): Wigard P. Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S.P. Vermaat, Markus J. van Roosmalen, Stef van Lieshout, Isaäc J Nijman, Wijnand M. Roessingh, Ruben van ‘t Slot, José van de Belt, Victor Guryev, Marco J. Koudijs, Emile E. Voest, Edwin Cuppen
Software Mentions: 2
Published: almost 16 years ago

10.1186/gb-2013-14-11-r129

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2014-15-2-r40

Genome-wide discovery and characterization of maize long non-coding RNAs
Cited by: 385
Author(s): Liang-In Lin, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng‐Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Evans Mulenga, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C.P. Timmermans, Nathan M. Springer, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 13 years ago

10.1186/gb-2013-14-6-r64

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Cited by: 45
Author(s): Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Frédéric Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M. Martis, Klaus Mayer, Abraham B. Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet
Software Mentions: 2
Published: over 13 years ago

10.1186/s13059-014-0415-1

Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops
Cited by: 81
Author(s): Ke Cao, Zhijun Zheng, Lirong Wang, Xin Liu, Guoqiang Zhu, Weichao Fang, Shifeng Cheng, Peng Zeng, Chang Wen Chen, Xinwei Wang, Min Xie, Xiao Bo Zhong, Xiaoli Wang, Pei Zhao, Chao Bian, Yuxia Zhu, Jiahui Zhang, MA Guo-sheng, Chengxuan Chen, Yanjun Li, Fengge Hao, Yong Li, Guodong Huang, Yuxiang Li, Haiyan Li, Jian Guo, Xun Xu, Jun Wang
Software Mentions: 2
Published: over 12 years ago

10.1186/s13059-014-0408-0

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
Cited by: 159
Author(s): Shaoke Lou, Heung‐Man Lee, Hao Qin, Jing‐Woei Li, Zhibo Gao, Xin Liu, Landon L. Chan, Vincent K. Lam, Wing‐Yee So, Ying Wang, Si Lok, Jun Wang, Ronald Cw, Stephen Kwok‐Wing Tsui, Juliana C.N. Chan, Ting-Fung Chan, Kevin Y. Yip
Software Mentions: 2
Published: over 12 years ago

10.1186/s13059-015-0648-7

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
Cited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-015-0849-0

Circlator: automated circularization of genome assemblies using long sequencing reads
Cited by: 715
Author(s): Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-016-0948-6

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
Cited by: 55
Author(s): Alice M. Walsh, John W. Whitaker, Chaohua Huang, Yauheniya Cherkas, S. Lamberth, Carrie Brodmerkel, Mark Curran, Radu Dobrin
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-1080-3

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes
Cited by: 35
Author(s): Anthony J. Studer, James C. Schnable, S. Weissmann, Allison R. Kolbe, Michael R. McKain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-019-1724-1

Genomics and data science: an application within an umbrella
Cited by: 42
Author(s): Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Software Mentions: 2
Published: over 7 years ago

10.1093/gbe/evu003

Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain
Cited by: 12
Author(s): David J. Krause, Xavier Didelot, Hinsby Cadillo‐Quiroz, Rachel J. Whitaker
Software Mentions: 2
Published: almost 13 years ago

10.1093/gbe/evx041

Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins
Cited by: 22
Author(s): Daniel Straub, Stephan Wenkel
Software Mentions: 2
Published: over 9 years ago

10.1093/gbe/evy036

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa
Cited by: 33
Author(s): Germain Chevignon, Bret M. Boyd, Jayce W. Brandt, Kerry M. Oliver, Michael R. Strand
Software Mentions: 2
Published: over 8 years ago

10.1093/gbe/evz072

Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship
Cited by: 20
Author(s): Trestan Pillonel, Claire Bertelli, Sébastien Aeby, Marie de Barsy, Nicolas Jacquier, Carole Kebbi-Beghdadi, Linda Mueller, Manon Vouga, Gilbert Greub
Software Mentions: 2
Published: over 7 years ago

10.1186/s13073-014-0088-0

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity
Cited by: 90
Author(s): Barbara Hrdličková, Vinod Kumar, Kartiek Kanduri, Daria V. Zhernakova, Subhash Tripathi, Juha Karjalainen, Riikka Lund, Yang Li, Ubaid Ullah, Rutger Modderman, Wayel H. Abdulahad, Harri Lähdesmäki, Lude Franke, Riitta Lahesmaa, Cisca Wijmenga, Sebo Withoff
Software Mentions: 2
Published: almost 12 years ago

10.1186/2047-217X-3-1

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
Cited by: 67
Author(s): Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster, Andrew Stubbs
Software Mentions: 2
Published: over 12 years ago

10.1093/gigascience/giy046

Chromosome-scale assembly of the Monopterus genome
Cited by: 28
Author(s): Xueya Zhao, Majing Luo, Zhigang Li, Zhong Pei, Yang Cheng, Fengling Lai, Xin Wang, Min Jiang, Mingzhou Bai, Yulan Yang, Hanhua Cheng, Rongjia Zhou
Software Mentions: 2
Published: over 8 years ago

10.1093/gigascience/giz108

High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
Cited by: 35
Author(s): Andreas J. Stroehlein, Pasi K. Korhonen, Teik Min Chong, Yan Lue Lim, Kok‐Gan Chan, Bonnie L. Webster, David Rollinson, Paul J. Brindley, Robin B. Gasser, Neil D. Young
Software Mentions: 2
Published: about 7 years ago

10.1093/gigascience/giaa065

Galactic Circos: User-friendly Circos plots within the Galaxy platform
Cited by: 26
Author(s): Helena Rasche, Saskia Hiltemann
Software Mentions: 2
Published: over 6 years ago

10.1093/gigascience/giaa069

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
Cited by: 5
Author(s): Morteza Roodgar, Afshin Babveyh, Linh P. Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, Mohan Avula, Lihua Jiang, Ruiqi Jian, Ho-Yong Lee, Giltae Song, Hassan Chaı̈b, Irving Weissman, Serafim Batzoglou, Susan Holmes, David Glenn Smith, Joseph L. Mankowski, Stefan Prost, M Snyder
Software Mentions: 2
Published: over 6 years ago

10.1038/s41437-020-00365-x

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population
Cited by: 24
Author(s): Yanhua Zhang, Yuzhe Wang, Yiyi Li, Jun Wu, Xinlei Wang, Cheng Bian, Yadong Tian, Guirong Sun, Ruili Han, Xiaojun Liu, Ruirui Jiang, Yanbin Wang, Guoxi Li, Wenting Li, Xiaoxiang Hu, Xin Kang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-020-0308-2

A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination
Cited by: 4
Author(s): Thomas M. Davis, Yayuan Yang, Lise L. Mahoney, Daniel C. Frailey
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-021-00565-4

The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis
Cited by: 30
Author(s): Xiaoyang Xu, Yuan Huang, Xiaqing Yu, Shihua Huang, Yuming Sun, Ting Zhang, Qingquan Liu, Haiying Tong, Yongxia Zhang, Yinjie Wang, Chunxiao Liu, Lei Wu, Menglan Hou, Yongheng Yang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-021-00559-2

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis
Cited by: 22
Author(s): Da-Xia Chen, Yuan Pan, Yu Wang, Yanze Cui, Yingjun Zhang, Rangyu Mo, Xiaoli Wu, Jun Tan, Jian Zhang, Lianan Guo, Zhao Xiao, Wenkai Jiang, Tsieh Sun, Xiaodi Hu, Longyun Li
Software Mentions: 2
Published: over 5 years ago

10.1038/hortres.2016.52

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array
Cited by: 38
Author(s): M. Vukosavljev, Paul Arens, Roeland E. Voorrips, Wendy Pc van ‘t Westende, G. Esselink, Peter M. Bourke, Peter Cox, Eric van de Weg, R.G.F. Visser, Chris Maliepaard, M.J.M. Smulders
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41438-020-00435-5

Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis
Cited by: 19
Author(s): Pei Li, Baishi Wang, Jian Ye, Xiaodi Hu, Lihong Fu, Kui Li, Zhiyu Ni, Zhenlong Wang, Yujie Wei, Luye Shi, Ying Zhang, Xue Bai, Mengwan Jiang, Shuhui Wang, Chunling Ma, Shujin Li, Kaihui Liu, Wanshui Li, Bin Cong
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-020-00399-6

The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis)
Cited by: 20
Author(s): Yue Gao, Shengnan Huang, Gaoyang Qu, Wei Fu, Meidi Zhang, Zhiyong Liu, Hui Feng
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-020-00409-7

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset
Cited by: 8
Author(s): Kiflu Tesfamicael, Endale Gebre, Timothy J. March, Beata Sznajder, D. E. Mather, Carlos M. Rodríguez López
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-019-0202-y

A high-quality Actinidia chinensis (kiwifruit) genome
Cited by: 89
Author(s): Haolin Wu, Tao Ma, Minghui Kang, Fandi Ai, Junlin Zhang, Guanyong Dong, Jianquan Liu
Software Mentions: 2
Published: about 7 years ago

10.1038/hortres.2017.79

Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics
Cited by: 20
Author(s): Peng Wu, Wenli Wang, Ying Liu, Xilin Hou
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41438-020-00373-2

Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits
Cited by: 2
Author(s): Yufang Guo, Ryan M. Warner
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-019-0191-x

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
Cited by: 37
Author(s): Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Hazem Hassan, Bihong Feng, Nathan K Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
Software Mentions: 2
Published: about 7 years ago

10.1038/s41438-020-0261-0

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
Cited by: 31
Author(s): Xiaoming Song, Fulei Nie, Wei Chen, Xiao Ma, Ke Gong, Qing Yang, Jinpeng Wang, Nan Li, Pengchuan Sun, Qiaoying Pei, Tong Yu, Jingjing Hu, Xinyu Li, Tong Wu, Shuyan Feng, Xiuqing Li, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0253-0

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization
Cited by: 37
Author(s): Xiaoming Song, Jinpeng Wang, Pengchuan Sun, Xiao Ma, Qing Yang, Jingjing Hu, Shiqun Sun, Yuxian Li, Jigao Yu, Shuyan Feng, Qiaoying Pei, Tong Yu, Ning Yang, Yinzhe Liu, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0333-1

High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.)
Cited by: 25
Author(s): Xueqin Song, Yuhui Xu, Guolian Kang, Guangxun Fan, Fan Zhang, Chengyan Deng, Silan Dai, Hua He, Huaigen Xin, Yingying Li
Software Mentions: 2
Published: over 6 years ago

10.1016/j.meegid.2016.07.010

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus
Cited by: 16
Author(s): David J. King, Graham Freimanis, Richard Orton, Ryan Waters, Daniel T. Haydon, Donald P. King
Software Mentions: 2
Published: about 10 years ago

10.1128/IAI.00041-18

Adipocyte Model of Mycobacterium tuberculosis Infection Reveals Differential Availability of Iron to Bacilli in the Lipid-Rich Caseous Environment
Cited by: 10
Author(s): Aditya Nandy, Anupam Mondal, Rajesh Pandey, Prakash Arumugam, Stanzin Dawa, Neetika Jaisinghani, Vittal Rao, Debasis Dash, Sheetal Gandotra
Software Mentions: 2
Published: over 8 years ago