10.1371/journal.pgen.1001061

Telomere Disruption Results in Non-Random Formation of De Novo Dicentric Chromosomes Involving Acrocentric Human Chromosomes
Cited by: 61
Author(s): Kaitlin M. Stimpson, Ihn Young Song, Anna Jauch, Heidi Holtgreve-Grez, Karen Hayden, Joanna M. Bridger, Beth A. Sullivan
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1008116

Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis
Cited by: 24
Author(s): Danyu Shen, Zhaoyang Tang, Wei Cong, Jing Wang, Yue Dong, Yang Chen, Yun Wei, Biao Cheng, Meiqian Zhang, Laura J. Grenville‐Briggs, Brett M. Tyler, Daolong Dou, Ai Xia
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006025

Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome
Cited by: 37
Author(s): Hafez El Sayyed, Ludovic Le Chat, Elise Lebailly, Elise Vickridge, C. Pagès, François Cornet, Marco Cosentino Lagomarsino, Olivier Espéli
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1000714

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
Cited by: 152
Author(s): Paul J. McMurdie, Sebastian Behrens, Jochen A. Müller, Jonathan Göke, Kirsti M. Ritalahti, Ryan D. Wagner, Eugene Goltsman, Alla Lapidus, Susan Holmes, Frank E. Löffler, Alfred M. Spormann
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1005644

Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting
Cited by: 78
Author(s): Marta Sánchez-Delgado, Alejandro Martin-Trujillo, Chiharu Tayama, Enrique Vidal, Manel Esteller, Isabel Iglesias-Platas, Nandita Deo, Olivia Barney, Ken Maclean, Kenichiro Hata, Kazuhiko Nakabayashi, Rosemary A. Fisher, David Gabriel Monk
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1005072

The Role of China in the Global Spread of the Current Cholera Pandemic
Cited by: 71
Author(s): Xavier Didelot, Bo Pang, Zhemin Zhou, A. McCann, Peixiang Ni, Dongfang Li, Mark Achtman, Biao Kan
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1008365

Convergent evolution of linked mating-type loci in basidiomycete fungi
Cited by: 28
Author(s): Sheng Sun, Marco A. Coelho, Joseph Heitman, Minou Nowrousian
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1005721

Origins of De Novo Genes in Human and Chimpanzee
Cited by: 115
Author(s): Jorge Ruiz-Orera, Jessica Hernández-Rodríguez, Cristina Chiva, Eduard Sabidó, Ivanela Kondova, Ronald E. Bontrop, Tomàs Marquès-Bonet, M. Mar Albà
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1006630

Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants
Cited by: 107
Author(s): Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyżorek, Éric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004272

Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity
Cited by: 82
Author(s): Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1003191

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
Cited by: 94
Author(s): María Lluch‐Senar, Khai Luong, Verónica Lloréns‐Rico, Javier Delgado, Gang Fang, Kristi Spittle, Tyson A. Clark, Eric E. Schadt, Stephen W. Turner, Jonas Korlach, Luís Serrano
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1005391

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates
Cited by: 42
Author(s): Jiayu Chen, Qing Sunny Shen, Wei‐Zhen Zhou, Jiguang Peng, Bin He, Yumei Li, Chu‐Jun Liu, Xuke Luan, Wanqiu Ding, Shuxian Li, Chunyan Chen, Bertrand Chin‐Ming Tan, Yong E. Zhang, Aibin He, Chuan-Yun Li
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1005876

Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control
Cited by: 61
Author(s): Rafael Arango, Caucasella Díaz-Trujillo, Braham Dhillon, Andrea Aerts, Jean Carlier, Charles F. Crane, Tristan de Jong, Ineke de Vries, Robert A. Dietrich, Andrew Farmer, Claudia Fortes Fereira, Suzana Garcia, M. Guzmán, Richard Hamelin, Erika Lindquist, Rahim Mehrabi, O. Quirós, Jeremy Schmutz, Harris Shapiro, Elizabeth K. Reynolds, Gabriel Scalliet, M.T. Souza, Ioannis Stergiopoulos, Theo A. J. van der Lee, P.J.G.M. de Wit, M.F. Zapater, L.H. Zwiers, Igor V. Grigoriev, Stephen B. Goodwin, G.H.J. Kema
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pmed.1002750

Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization
Cited by: 35
Author(s): Simon Eng, Florence Aeschlimann, Mira van Veenendaal, Roberta Berard, Alan Rosenberg, Quaid Morris, Rae S. M. Yeung
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0006839

Virulotyping of Salmonella enterica serovar Typhi isolates from Pakistan: Absence of complete SPI-10 in Vi negative isolates
Cited by: 12
Author(s): Sadia Liaquat, Yasra Sarwar, Aamir Ali, Abdul Haque, Muhammad Farooq, Ilargi Martínez-Ballesteros, Lorena Laorden, Javier Garaizar, Joseba Bikandi
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0002039

National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries
Cited by: 45
Author(s): Zhenyang Guo, Xiaoyan Tao, Chenghong Yin, Ning Han, Jinning Yu, Hao Li, Haizhou Liu, Fang Wei, J. Hume Adams, Jun Wang, Guodong Liang, Qing Tang, Simon Rayner
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0020090

Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting
Cited by: 60
Author(s): John Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Ke Hao, Eugene Chudin, Hunter B. Fraser, Joshua Millstein, Mark D. Ferguson, Christine Suver, Irena L. Ivanovska, Martin Scott, Ulrike Philippar, Dimple Bansal, Zhan Zhang, Julja Burchard, Ryan M. Smith, Danielle M. Greenawalt, Michele A. Cleary, Jonathan M.J. Derry, Andrey Loboda, James Watters, Ronnie T. P. Poon, Sheung Tat Fan, Chun Yeung, Nikki P.Y. Lee, Justin Guinney, Cliona Molony, Valur Emilsson, Carolyn Buser-Doepner, Jun Zhu, Stephen H. Friend, Mao Mao, Peter M. Shaw, Hongyue Dai, John M. Luk, Eric E. Schadt
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0011748

The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications
Cited by: 161
Author(s): Hélène Falentin, Stéphanie-Marie Deutsch, Gwenaël Jan, Valentin Loux, Anne Thierry, Sandrine Parayre, Marie-Bernadette Maillard, Julien Dherbécourt, Fabien Cousin, Julien Jardin, Patricia Siguier, Arnaud Couloux, Valérie Barbe, Benoît Vacherie, Patrick Wincker, Jean‐François Gibrat, Claude Gaillardin, Sylvie Lortal
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0171201

OxyR-activated expression of Dps is important for Vibrio cholerae oxidative stress resistance and pathogenesis
Cited by: 28
Author(s): Xiaoyun Xia, Jessie Larios-Valencia, Zhi Liu, Fu Xiang, Biao Kan, Hui Wang, Jun Zhu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0136101

Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle
Cited by: 19
Author(s): Pedro Manuel Martínez-García, Pablo Rodrı́guez-Palenzuela, Eva Arrebola, Víctor J. Carrión, José A. Gutiérrez‐Barranquero, Alejandro Pérez-Garcı́a, Cayo Ramos, Francisco M. Cazorla, Antonio de Vicente
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0211635

Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development
Cited by: 8
Author(s): Yunpeng Cao, Dong Meng, Tianzhe Chen, Yu Chen, Wei Zeng, Lei Zhang, Qi Wang, W Enchao C Hen, Qing Jin, Yi Lin, Yongping Cai
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0087045

De novo Genome Assembly of the Fungal Plant Pathogen Pyrenophora semeniperda
Cited by: 20
Author(s): Marcus M. Soliai, Susan E. Meyer, Joshua A. Udall, David E. Elzinga, Russell A. Hermansen, Paul Bodily, Aaron A. Hart, Craig E. Coleman
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0067742

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species
Cited by: 116
Author(s): Kajal Kumari, Mehanathan Muthamilarasan, Gopal Misra, Sarika Gupta, A. Subramanian, Swarup K. Parida, Debasis Chattopadhyay
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0086852

Genome-Wide Investigation and Expression Analyses of WD40 Protein Family in the Model Plant Foxtail Millet (Setaria italica L.)
Cited by: 101
Author(s): Awdhesh Kumar Mishra, Mehanathan Muthamilarasan, Yusuf Khan, Swarup K. Parida
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0161369

Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors
Cited by: 5
Author(s): C Brunner, Bettina Brunner-Herglotz, Andrea Ziegler, Christian Frech, Gabriele Amann, Ruth Ladenstein, Inge M. Ambros, Peter F. Ambros
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0026742

Genome Analysis of a Highly Virulent Serotype 1 Strain of Streptococcus pneumoniae from West Africa
Cited by: 19
Author(s): Todd A. Williams, Nicholas J. Loman, Chinelo Ebruke, Daniel M. Musher, Richard A. Adegbola, Mark J. Pallen, George M. Weinstock, Martín Antonio
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0090087

New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs
Cited by: 79
Author(s): Isabel N. Sierra-García, Javier Correa Álvarez, Suzan Pantaroto de Vasconcellos, Anete Pereira de Souza, Eugênio Vaz dos Santos Neto, Valéria Maia de Oliveira
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0084713

Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors
Cited by: 33
Author(s): Georgi K. Marinov, Yun E. Wang, David C. Chan, B Wold
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0157901

Deciphering the Draft Genome of Toxoplasma gondii RH Strain
Cited by: 27
Author(s): Yee Ling Lau, Wenn-Chyau Lee, Ranganath Gudimella, Gui Ping Zhang, Xiao Teng Ching, Rozaimi Mohamad Razali, Farhanah Abdul Aziz, Arif Anwar, Mun Yik Fong
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0179073

Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens
Cited by: 28
Author(s): Yuzhe Wang, Xianglin Cao, Yaofeng Zhao, Fei Jing, Xiaoxiang Hu, Ning Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0080149

miRNA Signatures in Sera of Patients with Active Pulmonary Tuberculosis
Cited by: 65
Author(s): Paolo Miotto, Grace Mwangoka, Ilaria C. Valente, Luca Norbis, Giovanni Sotgiu, Roberta Bosu, Alessandro Ambrosi, Luigi Codecasa, Delia Goletti, Alberto Matteelli, Elias N. Ntinginya, Francesco Aloi, Norbert Heinrich, Klaus Reither, Daniela María Cirillo
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0164469

Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance
Cited by: 18
Author(s): Qiang Xu, Yang Shi, Ting Yu, Xuewen Xu, Yali Yan, Xiaohua Qi, Xuehao Chen
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0098986

Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)
Cited by: 48
Author(s): Cody E. Hinchliff, Stephen A. Smith
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0240908

Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain
Cited by: 5
Author(s): Jingxin Zhang, Mohammad Arif, Huolin Shen, John Hu, Dan Sun, Xiaoming Pu, Qiyun Yang, Birun Lin
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0080835

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats
Cited by: 83
Author(s): Е. В. Лебедева, Roland Hatzenpichler, Éric Pelletier, Nathalie Schuster, Sandra Hauzmayer, А. Г. Булаев, N. V. Grigor’eva, Alexander Galushko, Markus Schmid, Márton Palatinszky, Denis Le Paslier, Holger Daims, Michael Wagner
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0154975

Complete Nucleotide Sequence of IncP-1β Plasmid pDTC28 Reveals a Non-Functional Variant of the blaGES-Type Gene
Cited by: 8
Author(s): Bingjun Dang, Daqing Mao, Yi Luo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0155590

Characterization and Comparison of the CPK Gene Family in the Apple (Malus × domestica) and Other Rosaceae Species and Its Response to Alternaria alternata Infection
Cited by: 7
Author(s): Menghan Wei, Sanhong Wang, Hui Dong, Baiyan Cai, Jianmin Tao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0189673

Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages
Cited by: 4
Author(s): Joshua Marc Cambridge, Alexandra Blinkova, Erick I. Salvador Rocha, Addys Bode Hernández, Maday Moreno, Edwin A. Gines-Candelaria, Benjamin M. Goetz, Scott Patrick Hunicke-Smith, Ed Satterwhite, Haley O. Tucker, James R. Walker
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0156281

Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors
Cited by: 19
Author(s): Kai Tang, C.Y. Dong, Jinyuan Liu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0099848

Genetic Architecture of Winter Hardiness and Frost Tolerance in Triticale
Cited by: 19
Author(s): Wenxin Liu, Hans Peter Maurer, Guoliang Li, Matthew R. Tucker, Manje Gowda, Elmar A. Weissmann, Volker Hahn, Tobias Würschum
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0092639

Mapping the Structure and Dynamics of Genomics-Related MeSH Terms Complex Networks
Cited by: 11
Author(s): J. Mario Siqueiros-García, Enrique Hernández‐Lemus, Rodrigo García-Herrera, Andrea Robina-Galatas
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0194356

Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome
Cited by: 8
Author(s): Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill Sup Nou
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0227716

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane
Cited by: 12
Author(s): Mingxing Cai, Jishan Lin, Zeyun Li, Zhicong Lin, Yaying Ma, Yibin Wang, Ray Ming
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0163635

The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing
Cited by: 17
Author(s): K. B. Rebijith, R. Asokan, H. Ranjitha Hande, N. K. Krishna Kumar
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0166341

Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton
Cited by: 18
Author(s): Muhammad Imran, Kai Tang, Jinyuan Liu
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0036939

Genomic Sequencing and Comparative Analysis of Epstein-Barr Virus Genome Isolated from Primary Nasopharyngeal Carcinoma Biopsy
Cited by: 78
Author(s): Hin‐Fai Kwok, Amy Tong, Chi-Ho Lin, Si Lok, Patrick J. Farrell, Dora Lai Wan Kwong, Alan Kwok Shing Chiang
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0217846

Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease
Cited by: 15
Author(s): Svetlana Frenkel, Çharles N. Bernstein, Michael Sargent, Qin Kuang, Wenxin Jiang, John Wei, Bhooma Thiruvahindrapuram, Elizabeth L. Spriggs, Stephen W. Scherer, Pingzhao Hu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0245600

Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice
Cited by: 5
Author(s): Zezhen Du, Suren Deng, Zhenqiang Wu, Chuang Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0191015

Genome-wide identification and role of MKK and MPK gene families in clubroot resistance of Brassica rapa
Cited by: 10
Author(s): Yinglan Piao, Kaining Jin, Ying He, Jiaxiu Liu, Shuang Liu, Xiaonan Li, Zhongyun Piao
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0080508

Insights from the Complete Chloroplast Genome into the Evolution of Sesamum indicum L
Cited by: 51
Author(s): Haiyang Zhang, Chun-Chun Li, Hongmei Miao, Songjin Xiong
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0141329

Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective
Cited by: 52
Author(s): Gurusamy Raman, Seon-Joo Park
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0123081

Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions
Cited by: 18
Author(s): Yu Wang, Wei Li, Yingying Xia, Chongzhi Wang, Y. Tom Tang, Wenying Guo, Jinliang Li, Xing‐Ming Zhao, Yueru Sun, Juan Hu, Hefu Zhen, Xiandong Zhang, Chao Chen, Yujian Shi, Li Lin, Hongzhi Cao, Hongli Du, Jian Li
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0055127

Impact of Whole-Genome and Tandem Duplications in the Expansion and Functional Diversification of the F-Box Family in Legumes (Fabaceae)
Cited by: 28
Author(s): Daniel Bellieny-Rabelo, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0141952

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics
Cited by: 14
Author(s): Thomas Arn Hansen, Helena Fridholm, Tobias Guldberg Frøslev, Kristín Rós Kjartansdóttir, Eske Willerslev, Lars Peter Nielsen, Anders J. Hansen
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0142529

Depletion of CG-Specific Methylation in Mycoplasma hyorhinis Genomic DNA after Host Cell Invasion
Cited by: 9
Author(s): Andrei V. Chernov, Leticia Reyes, Scott N. Peterson, Alex Y. Strongin
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0072082

A Comparative Genome Analysis of PME and PMEI Families Reveals the Evolution of Pectin Metabolism in Plant Cell Walls
Cited by: 87
Author(s): Maojun Wang, Daojun Yuan, Wenhui Gao, Li Yang, Jiafu Tan, Xianlong Zhang
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0037164

A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome
Cited by: 105
Author(s): Yuxiao Fang, Hao Wu, Tongwu Zhang, Meng Yang, Yuxin Yin, Li-Long Pan, Xiongbin Yu, Xiaowei Zhang, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0028135

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean
Cited by: 57
Author(s): Carlos H. Galeano, Andrea C. Fernandez, Natalia Franco-Herrera, Karen A. Cichy, Phillip E. McClean, Jos Vanderleyden, Matthew W. Blair
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0181573

Genome-wide identification of the potato WRKY transcription factor family
Cited by: 57
Author(s): Chao Zhang, Dongdong Wang, Chan Yang, Nana Kong, Zheng Zheng Shi, Peng Zhao, Yunyou Nan, Nie Tengkun, Ruoqiu Wang, Hongwei Ma, Qin Chen
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0159268

Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.)
Cited by: 28
Author(s): Morad M. Mokhtar, Sami S. Adawy, Salah El-Din Sayed El-Assal, E. Hussein
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0117843

Expression Profiling of Preadipocyte MicroRNAs by Deep Sequencing on Chicken Lines Divergently Selected for Abdominal Fatness
Cited by: 23
Author(s): Weishi Wang, Zhiqiang Du, Baoping Cheng, Yuxiang Wang, Jing Yao, Yumao Li, Cao Zhi, Ping Luan, Ning Wang, Hui Li
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0048262

Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in Osteosarcoma
Cited by: 86
Author(s): Stine H. Kresse, Halfdan Rydbeck, Magne Skårn, Heidi M. Namløs, Ana H. Barragan-Polania, Anne Marie Cleton-Jansen, Massimo Serra, Knut Liestøl, Pancras C.W. Hogendoorn, Eivind Hovig, Ola Myklebost, Leonardo A. Meza‐Zepeda
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0089018

Genome-Wide High-Throughput Screening to Investigate Essential Genes Involved in Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Survival
Cited by: 24
Author(s): Mads Brøkner Christiansen, Rolf Sommer Kaas, Roy R. Chaudhuri, Mark A. Holmes, Henrik Hasman, Frank Møller Aarestrup
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0123225

Genome-Wide Identification, Classification, and Expression Analysis of 14-3-3 Gene Family in Populus
Cited by: 46
Author(s): Fei Tian, Tan Wang, Yuning Xie, Jin Zhang, Jianjun Hu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0123897

Genome-Wide SNP Identification and Characterization in Two Soybean Cultivars with Contrasting Mungbean Yellow Mosaic India Virus Disease Resistance Traits
Cited by: 32
Author(s): Chandra Bhan Yadav, Priyanka Bhareti, Mehanathan Muthamilarasan, Minakshi Mukherjee, Yusuf Khan, Pushpendra Rathi, Manoj Prasad
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0142034

Single Base-Resolution Methylome of the Dizygotic Sheep
Cited by: 5
Author(s): Yangzi Wang, Jianghong Wu, Xiao Ma, Bin Liu, Rui Su, Yu Jiang, Wen Wang, Yang Dong
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0028495

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers
Cited by: 66
Author(s): Paweł Milczarski, Hanna Bolibok-Brągoszewska, Beata Myśków, Stefan Stojałowski, Katarzyna Heller-Uszyńska, Magdalena Góralska, Piotr Brągoszewski, Grzegorz Uszyński, Andrzej Kilian, Monika Rakoczy-Trojanowska
Software Mentions: 1
Published: almost 15 years ago

10.1111/cpr.12862

High‐efficient generation of VCAM‐1⁺ mesenchymal stem cells with multidimensional superiorities in signatures and efficacy on aplastic anaemia mice
Cited by: 35
Author(s): Yimeng Wei, Leisheng Zhang, Ying Cheng, Xiang Ren, Yuchen Gao, Baoquan Song, Chengwen Li, Zhibo Han, Zhongchao Han
Software Mentions: 1
Published: over 6 years ago

10.1038/s41422-018-0008-8

KRAB-type zinc-finger proteins PITA and PISA specifically regulate p53-dependent glycolysis and mitochondrial respiration
Cited by: 27
Author(s): Shan Wang, Zhiqiang Peng, Siying Wang, Lihua Yang, Yuhan Chen, Xue Kong, Shanshan Song, Pei Pei, Chunyan Tian, Hui Yan, Peipei Ding, Weiguo Hu, Cui Hua Liu, Xin Zhang, Fuchu He, Lingqiang Zhang
Software Mentions: 1
Published: over 8 years ago

10.3390/cells7090120

Identification and Characterization of LRR-RLK Family Genes in Potato Reveal Their Involvement in Peptide Signaling of Cell Fate Decisions and Biotic/Abiotic Stress Responses
Cited by: 28
Author(s): Xiaoxu Li, Saboor Ahmad, Chunfang Guo, Jing Yu, Songxiao Cao, Xiao‐Ming Gao, Wei Li, Hong Li, Yongfeng Guo
Software Mentions: 1
Published: about 8 years ago

10.3390/cells7070077

Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in Two Pyrus Species
Cited by: 13
Author(s): Yunpeng Cao, Dong Meng, Yu Chen, Muhammad Abdullah, Qing Jin, Yi Lin, Yongping Cai
Software Mentions: 1
Published: about 8 years ago

10.3390/cells8060520

In Silico Genome-Wide Analysis of Respiratory Burst Oxidase Homolog (RBOH) Family Genes in Five Fruit-Producing Trees, and Potential Functional Analysis on Lignification of Stone Cells in Chinese White Pear
Cited by: 29
Author(s): Xi Cheng, Guohui Li, Muhammad Aamir Manzoor, Han Wang, Muhammad Abdullah, Xueqiang Su, Jingyun Zhang, Tao‐Shan Jiang, Qing Jin, Yongping Cai, Yi Lin
Software Mentions: 1
Published: over 7 years ago

10.3390/cells8050490

Integrative Analysis of the Wheat PHT1 Gene Family Reveals A Novel Member Involved in Arbuscular Mycorrhizal Phosphate Transport and Immunity
Cited by: 17
Author(s): Yi Zhang, Lizong Hu, De‐Quan Yu, Kedong Xu, Ju Zhang, Xiaoli Li, Pengfei Wang, Guo Chen, Zhihui Liu, Chunfeng Peng, Chengwei Li, Tao Guo
Software Mentions: 1
Published: over 7 years ago

10.1186/s40169-015-0060-7

Human Chromosome Y and Haplogroups; introducing YDHS Database
Cited by: 5
Author(s): Timo Tiirikka, Jukka S. Moilanen
Software Mentions: 1
Published: over 11 years ago

10.1101/mcs.a001032

Homozygous inactivation of <i>CHEK2</i> is linked to a familial case of multiple primary lung cancer with accompanying cancers in other organs
Cited by: 15
Author(s): Yoji Kukita, Jiro Okami, Noriko Yoneda-Kato, Ikuko Nakamae, Takeshi Kawabata, Masahiko Higashiyama, Jun‐ya Kato, Ken Kodama, Kikuya Kato
Software Mentions: 1
Published: about 10 years ago

10.1038/s42003-019-0553-9

Compression-induced expression of glycolysis genes in CAFs correlates with EMT and angiogenesis gene expression in breast cancer
Cited by: 35
Author(s): Baek Gil Kim, Jin Sol Sung, Yeonsue Jang, Yoon Jin, Suki Kang, Hyunho Han, Juhyun Lee, Nam Hoon Cho
Software Mentions: 1
Published: about 7 years ago

10.1038/s42003-021-01689-y

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt
Cited by: 22
Author(s): Simone Rampelli, Silvia Turroni, Carolina Mallol, Constantino Criado Hernández, Bertila Galván, Ainara Sistiaga, Elena Biagi, Annalisa Astolfi, Patrizia Brigidi, Stefano Benazzi, Cecil M. Lewis, Christina Warinner, Courtney A. Hofman, Stephanie L. Schnorr, Marco Candela
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-021-01747-5

RSPO4-CRISPR alleviates liver injury and restores gut microbiota in a rat model of liver fibrosis
Cited by: 13
Author(s): Linghua Yu, Linlin Wang, Xiaojun Wu, Huixing Yi
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-020-1105-z

Transcriptome-wide association study for restless legs syndrome identifies new susceptibility genes
Cited by: 9
Author(s): Fulya Akçimen, Faezeh Sarayloo, Calwing Liao, Jay P. Ross, Rachel De Barros Oliveira, Patrick A. Dion, Guy A. Rouleau
Software Mentions: 1
Published: about 6 years ago

10.1038/s42003-020-01643-4

Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution
Cited by: 36
Author(s): Feng Wu, Kangkang Niu, Yong Cui, Cencen Li, Mo Lyu, Yandong Ren, Yanfei Chen, Huimin Deng, Lihua Huang, Sichun Zheng, Lin Liu, Jian Wang, Qisheng Song, Hui Xiang, Qili Feng
Software Mentions: 1
Published: over 5 years ago

10.1016/j.cub.2016.10.061

17th Century Variola Virus Reveals the Recent History of Smallpox
Cited by: 184
Author(s): Ana T. Duggan, Maria F. Perdomo, Dario Piombino–Mascali, Stephanie Marciniak, Debi Poinar, Matthew V. Emery, Jan P. Buchmann, Sebastián Duchêne, Rimantas Jankauskas, Margaret Humphreys, G. Brian Golding, John Southon, Alison Devault, Jean Marie Rouillard, Jason W. Sahl, Olivier Dutour, Klaus Hedman, Antti Sajantila, Geoffrey L. Smith, Edward C. Holmes, Hendrik N. Poinar
Software Mentions: 1
Published: almost 10 years ago

10.1007/s40471-017-0100-5

Analytic Complexity and Challenges in Identifying Mixtures of Exposures Associated with Phenotypes in the Exposome Era
Cited by: 44
Author(s): Chirag Patel
Software Mentions: 1
Published: over 9 years ago

10.1007/s00294-018-0815-y

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses
Cited by: 10
Author(s): Osamu Miura, Toshihiro Ogake, Takashi Ohyama
Software Mentions: 1
Published: over 8 years ago

10.1007/s00294-018-0907-8

A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats
Cited by: 5
Author(s): Osamu Miura, Toshihiro Ogake, Hiroki Yoneyama, Yo Kikuchi, Takashi Ohyama
Software Mentions: 1
Published: almost 8 years ago

10.1093/dnares/dsu020

A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome
Cited by: 28
Author(s): Julio C. M. Iehisa, Ryoko Ohno, Tatsuro Kimura, Hiroyuki Enoki, Satoru Nishimura, Yuki Okamoto, Shuhei Nasuda, Shigeo Takumi
Software Mentions: 1
Published: over 12 years ago

10.1093/dnares/dsu016

Evolutionary History of Trihelix Family and Their Functional Diversification
Cited by: 45
Author(s): Yao Qin, Xin Ma, Guanghui Yu, Qi Wang, Liang Wang, Lingrang Kong, Wook Kim, Hong W ei Wang
Software Mentions: 1
Published: over 12 years ago

10.1093/dnares/dst039

Development of 5123 Intron-Length Polymorphic Markers for Large-Scale Genotyping Applications in Foxtail Millet
Cited by: 98
Author(s): Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Garima Pandey, Kajal Kumari, Swarup K. Parida
Software Mentions: 1
Published: about 13 years ago

10.1016/j.dib.2019.104203

Genome-wide copy number variant data for inflammatory bowel disease in a caucasian population
Cited by: 0
Author(s): Svetlana Frenkel, Çharles N. Bernstein, Yong Won Jin, Michael Sargent, Qin Kuang, Wenxin Jiang, John Wei, Bhooma Thiruvahindrapuram, Stephen W. Scherer, Pingzhao Hu
Software Mentions: 1
Published: about 7 years ago

10.1016/j.dib.2020.106341

Genome sequencing data for wild and cultivated bananas, plantains and abacá
Cited by: 4
Author(s): Christine Sambles, Lakshmipriya Venkatesan, Olanrewaju M. Shittu, James W. Harrison, Karen Moore, Leena Tripathi, Murray Grant, Rachel Warmington, David J. Studholme
Software Mentions: 1
Published: almost 6 years ago

10.1093/database/bav124

CCSI: a database providing chromatin–chromatin spatial interaction information
Cited by: 13
Author(s): Xiaowei Xie, Wenbin Ma, Zhou Songyang, Zhenhua Luo, Junfeng Huang, Zhiming Dai, Yuanyan Xiong
Software Mentions: 1
Published: almost 11 years ago

10.1002/ece3.3762

Genome-wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips,<i>Thrips tabaci</i>Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)
Cited by: 8
Author(s): K. B. Rebijith, R. Asokan, Ranjitha H. Hande, S. J. Gawande, N. K. Krishna Kumar
Software Mentions: 1
Published: over 8 years ago

10.1002/ece3.5620

Analysis of new retrogenes provides insight into dog adaptive evolution
Cited by: 6
Author(s): Xiang Gao, Yan Li, Adeyinka Abiola Adetula, Yu Wei Wu, Hong Chen
Software Mentions: 1
Published: about 7 years ago

10.1080/22221751.2020.1852058

Prolonged shedding of severe acute respiratory syndrome coronavirus 2 in patients with COVID-19
Cited by: 63
Author(s): Qian Li, Xiao Zheng, Xu Shen, Rui Hao, Xi Wang, Qi Wang, Bei Li, Wei Zhang, Yan Zhu, Ruijiao Jiang, Kai Zhao, Hui Wang, Zheng Li Shi, Hui Lan Zhang, Rong Du, Peng Zhou
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13072-016-0068-2

The chicken erythrocyte epigenome
Cited by: 23
Author(s): Sanzida Jahan, Wayne Xu, Shihua He, Carolina González, Geneviève P. Delcuve, James R. Davie
Software Mentions: 1
Published: over 10 years ago

10.1038/ejhg.2017.128

The Y chromosome: a blueprint for men’s health?
Cited by: 85
Author(s): Akhlaq Ahmed Maan, James Eales, Artur Akbarov, Joshua Rowland, Xiaoguang Xu, Mark A. Jobling, Fadi J. Charchar, Maciej Tomaszewski
Software Mentions: 1
Published: about 9 years ago

10.1038/s41431-019-0343-3

Using dried blood spot samples from a trio for linked-read whole-exome sequencing
Cited by: 6
Author(s): Ólavur Mortensen, Leivur N. Lydersen, Katrin Didriksen Apol, Guðrið Andorsdóttir, Bjarni á Steig, Noomi Gregersen
Software Mentions: 1
Published: over 7 years ago

10.1111/eva.13062

Application of simultaneous selective pressures slows adaptation
Cited by: 0
Author(s): Lauren M.F. Merlo, Kathleen Sprouffske, Taylor C. Howard, Kristin L. Gardiner, Aleah F. Caulin, Steven M. Blum, Perry Evans, Antonio Bedalov, Paul D. Sniegowski, Carlo C. Maley
Software Mentions: 1
Published: about 6 years ago

10.12688/f1000research.2-258.v1

C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison
Cited by: 28
Author(s): Ilya Minkin, Hoa Pham, Ekaterina V. Starostina, Nikolay Vyahhi, Son Pham
Software Mentions: 1
Published: almost 13 years ago

10.12688/f1000research.14383.1

Case Report: Exome sequencing reveals recurrent RETSAT mutations and a loss-of-function POLDIP2 mutation in a rare undifferentiated tongue sarcoma
Cited by: 9
Author(s): Jason Ying Kuen Chan, P.W.F. Poon, Yong Zhang, Cherrie W K Ng, Wen Piao, Meng Ma, Kevin Y. Yip, Amy B.W. Chan, Vivian Wai Yan Lui
Software Mentions: 1
Published: over 8 years ago

10.3390/foods10081701

Codesign of Food System and Circular Economy Approaches for the Development of Livestock Feeds from Insect Larvae
Cited by: 20
Author(s): Sandeep Jagtap, Guillermo García-García, Linh Duong, Mark Swainson, Wayne Martindale
Software Mentions: 1
Published: about 5 years ago