Ecosyste.ms: Papers

10.1186/1471-2105-13-58

Methods for visual mining of genomic and proteomic data atlases
Cited by: 8
Author(s): John P. Boyle, Richard Kreisberg, Ryan Bressler, Sarah Killcoyne
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-13-S15-S7

IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
Cited by: 43
Author(s): Fan Zhang, Renee Drabier
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-14-22

Kerfuffle: a web tool for multi-species gene colocalization analysis
Cited by: 7
Author(s): Robert Aboukhalil, Bernard J. Fendler, Gurinder S. Atwal
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-15-139

Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
Cited by: 21
Author(s): Susanne Bornelöv, Simon Marillet, Jan Komorowski
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-017-1939-7

Synima: a Synteny imaging tool for annotated genome assemblies
Cited by: 36
Author(s): Rhys A. Farrer
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-14-S1-S7

Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress
Cited by: 31
Author(s): Éderson Akio Kido, José Ribamar Costa Ferreira Neto, Roberta L. O. Silva, Luis Carlos Belarmino, João Pacífico Bezerra Neto, Nina da Mota Soares-Cavalcanti, Valesca Pandolfi, Manassés D. Silva, Alexandre Lima Nepomuceno, Ana Maria Benko‐Iseppon
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12859-019-2902-6

Pairwise visual comparison of small RNA secondary structures with base pair probabilities
Cited by: 3
Author(s): Serge Léger, Maria Beatriz Walter Costa, Dan Tulpan
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-12-S10-S8

Analysis of cancer metabolism with high-throughput technologies
Cited by: 13
Author(s): Aleksandra Markovets, Damir Herman
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-14-246

ArkMAP: integrating genomic maps across species and data sources
Cited by: 9
Author(s): Trevor Paterson, Andy Law
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-13-190

A web-based multi-genome synteny viewer for customized data
Cited by: 19
Author(s): Kashi Vishwanath Revanna, Daniel Munro, Alvin Gao, Chi-Chen Chiu, Anil D. Pathak, Qunfeng Dong
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-14-277

SynTView — an interactive multi-view genome browser for next-generation comparative microorganism genomics
Cited by: 24
Author(s): Pierre Lechat, Erika Souche, Ivan Moszer
Software Mentions: 1
Published: about 11 years ago

10.1186/s12859-019-3242-2

MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
Cited by: 3
Author(s): Xikang Feng, Zishuai Wang, Hechen Li, Shuai Cheng Li
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12915-018-0550-3

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk
Cited by: 47
Author(s): Elvire Berthenet, Koji Yahara, Kaisa Thorell, Ben Pascoe, Guillaume Méric, Jane Mikhail, Lars Engstrand, Helena Enroth, A Burette, Françis Mégraud, Christine Varon, John C. Atherton, Sinead Smith, Thomas S. Wilkinson, Matthew D. Hitchings, Daniel Falush, Samuel K. Sheppard
Software Mentions: 1
Published: over 6 years ago

10.1186/s12915-015-0130-8

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks
Cited by: 118
Author(s): Baocheng Guo, Jacquelin DeFaveri, Graciela Sotelo, Abhilash Nair, Juha Merilä
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-020-00789-1

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution
Cited by: 16
Author(s): Dick Roelofs, Arthur Zwaenepoel, Tom Sistermans, Joey Nap, Andries A. Kampfraath, Yves Van de Peer, Jacintha Ellers, Ken Kraaijeveld
Software Mentions: 1
Published: over 4 years ago

10.1186/s12915-020-00830-3

Genome-wide pQTL analysis of protein expression regulatory networks in the human liver
Cited by: 42
Author(s): Bing He, Jian Shi, Xinwen Wang, Hui Jiang, Hao Zhu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12896-015-0153-9

Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood
Cited by: 7
Author(s): Fan Gao, Kai Wang
Software Mentions: 1
Published: over 9 years ago

10.1186/s12862-017-1056-2

Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era
Cited by: 49
Author(s): Martin Kollmar, Stefanie Mühlhausen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12862-020-1582-1

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome
Cited by: 38
Author(s): Shenglong Kan, Tingting Shen, Ping Gong, Jin-Hua Ran, Xiaoquan Wang
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2148-9-209

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice
Cited by: 74
Author(s): Thomas Thiel, Andreas Graner, Robbie Waugh, Ivo Große, Timothy J. Close, Nils Stein
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2148-11-9

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family
Cited by: 92
Author(s): Eudald Illa, Daniel J. Sargent, Elena López‐Girona, Jill M. Bushakra, Alessandro Cestaro, Ross N. Crowhurst, Massimo Pindo, Antonio G. Cabrera, Esther van der Knaap, Amy Iezzoni, Susan E. Gardiner, Riccardo Velasco, Pere Arús, David Chagné, Michela Troggio
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12863-015-0184-1

Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder
Cited by: 17
Author(s): Rachel L. Kember, Benjamin Georgi, Joan E. Bailey-Wilson, Dwight Stambolian, Steven M. Paul, Maja Bućan
Software Mentions: 1
Published: over 9 years ago

10.1186/s12863-020-00885-9

Characterization, identification and expression profiling of genome-wide R-genes in melon and their putative roles in bacterial fruit blotch resistance
Cited by: 5
Author(s): Md. Rafiqul Islam, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Hee-Jeong Jung, Hoy‐Taek Kim, Jong-In Park, Ill–Sup Nou
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2156-15-59

Mapping dynamic QTL for plant height in triticale
Cited by: 61
Author(s): Tobias Würschum, Wenxin Liu, Lucas Busemeyer, Matthew R. Tucker, Jochen C. Reif, Elmar A. Weissmann, Volker Hahn, Arno Ruckelshausen, Hans Peter Maurer
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12863-017-0596-1

Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton
Cited by: 169
Author(s): Richard Odongo Magwanga, Lei Pu, Joy Nyangasi Kirungu, Hejun Lu, Xingxing Wang, Xiaoyan Cai, Zhenmei Zhang, Haron Salih, Kunbo Wang, Fang Liu
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2156-12-60

A genetic linkage map and comparative mapping of the prairie vole (Microtus ochrogaster) genome
Cited by: 15
Author(s): Lisa A. McGraw, Jamie K. Davis, Larry J. Young, James W. Thomas
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-016-2846-4

Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401
Cited by: 66
Author(s): Nathan Chrismas, Gary Barker, Alexandre M. Anesio, Patricia Sánchez‐Baracaldo
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-020-6765-z

Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica
Cited by: 14
Author(s): Ruimin Gao, Sohail Naushad, Sylvain Moineau, Roger C. Levesque, Lawrence Goodridge, Dele Ogunremi
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-021-07844-3

The DUB family in Populus: identification, characterization, evolution and expression patterns
Cited by: 2
Author(s): Wenqing Zheng, Liqing Du
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-13-324

Composition and organization of active centromere sequences in complex genomes
Cited by: 20
Author(s): Karen Hayden, Huntington F. Willard
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-019-5575-7

Genome of lethal Lepiota venenata and insights into the evolution of toxin-biosynthetic genes
Cited by: 12
Author(s): Yunjiao Lüli, Qing Cai, Zuo H. Chen, Hong Sun, Xue-Tai Zhu, Xuan Li, Zhu L. Yang, Hong Luo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5070-6

Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV)
Cited by: 10
Author(s): Anderson F. Brito, Fernando Lucas Melo, Daniel Mendes Pereira Ardisson-Araújo, W. Sihler, Marlinda Lobo de Souza, Bergmann Morais Ribeiro
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-016-3343-5

Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium
Cited by: 62
Author(s): Shiyou Liu, Dawn M. Roellig, Yaqiong Guo, Na Li, Michael Frace, Kevin Tang, Longxian Zhang, Yaoyu Feng, Lihua Xiao
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-14-117

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
Cited by: 219
Author(s): Rafik Neme, Diethard Tautz
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-021-07625-y

Whole-genome resequencing using next-generation and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741
Cited by: 3
Author(s): Xinghao Chen, Yan Dong, Yali Huang, Jinjiang Fan, Minsheng Yang, Jun Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-017-3517-9

Expansion and stress responses of the AP2/EREBP superfamily in cotton
Cited by: 73
Author(s): Chunxiao Liu, Tianzhen Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-3629-2

QTL mapping for fruit quality in Citrus using DArTseq markers
Cited by: 42
Author(s): Maiara Curtolo, Mariângela Cristofani–Yaly, Rodrigo Gazaffi, Marco Aurélio Takita, Antônio Figueira, Marcos Antônio Machado
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-6205-0

Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum)
Cited by: 20
Author(s): Moyang Liu, Qin Huang, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li, Hui Chen
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-015-1252-7

Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5
Cited by: 62
Author(s): Erika van Eijk, Seyed Yahya Anvar, Hilary P. Browne, Wai Yi Leung, J. Howard Frank, Arnoud Schmitz, Adam P. Roberts, Wiep Klaas Smits
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-019-6406-6

Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)
Cited by: 20
Author(s): Lingxia Zhao, Youjun Lü, Wei Chen, Jinbo Yao, Yan Li, Qiulin Li, Jingwen Pan, Shengtao Fang, Jie Sun, Yongshan Zhang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-015-2106-z

Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China
Cited by: 51
Author(s): Weisheng Cheng, Fang Liu, Man Li, Xiaodong Hu, He Chen, Faustina Pappoe, Qingli Luo, Hao Wen, Xing Tian, Yuanhong Xu, Jilong Shen
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-017-4259-4

Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.)
Cited by: 29
Author(s): Zhiguo Liu, Liman Zhang, Chaoling Xue, Fang Hu, Jin Zhao, Mengjun Liu
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-017-3822-3

Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping
Cited by: 22
Author(s): Kamlesh Kumar Sahu, Debasis Chattopadhyay
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-3462-z

Construction of high-resolution recombination maps in Asian seabass
Cited by: 27
Author(s): Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye, Gen Hua Yue
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-15-187

Paleo-evolutionary plasticity of plant disease resistance genes
Cited by: 47
Author(s): Rongzhi Zhang, Florent Murat, Caroline Pont, Thierry Langin, Jérôme Salse
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1397-4

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes
Cited by: 51
Author(s): Johana Carolina Soto, Jorge Ortíz, Laura Perlaza-Jiménez, Andrea Vásquez, Luis Augusto Becerra López-Lavalle, Boby Mathew, Jens Léon, Adriana Bernal, Agim Ballvora, Camilo López
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5677-2

New insights into the genome of Rhodococcus ruber strain Chol-4
Cited by: 18
Author(s): Govinda Guevara, María Castillo López, Sergio Alonso, Julián Perera, Juana María Navarro Lloréns
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-13-711

An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2
Cited by: 27
Author(s): Jaemin Kim, Taeheon Lee, Tae-Hun Kim, Kyung-Tai Lee, Heebal Kim
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-020-6548-6

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)
Cited by: 10
Author(s): Zhiguo Liu, Lixin Wang, Chaoling Xue, Yuetong Chu, Wei Gao, Yitong Zhao, Jin Zhao, Mengjun Liu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-6573-5

Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis
Cited by: 7
Author(s): Vimla Kany G. Ami, Rami Balasubramanian, Shubhada R. Hegde
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-015-1249-2

Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum)
Cited by: 83
Author(s): Jinyan Wang, Zhongze Hu, Tongmin Zhao, Youxin Yang, Tianzi Chen, Mali Yang, Wenbao Yu, Baolong Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-016-2759-2

Transcriptome profiling of Diachasmimorpha longicaudata towards useful molecular tools for population management
Cited by: 3
Author(s): M. Constanza Mannino, Máximo Rivarola, Alejandra Carla Scannapieco, Sergio González, Marisa Diana Farber, Jorge Luis Cladera, Silvia Beatriz Lanzavecchia
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-019-5789-8

Genome-wide analysis of the WRKY gene family and their positive responses to phytoplasma invasion in Chinese jujube
Cited by: 23
Author(s): Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Fang Hu, Mengjun Liu, Jin Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-020-6501-8

Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress
Cited by: 21
Author(s): Man Zhang, Qing Liu, Qing-Yu He, Mengnan Chai, Youmei Huang, Fangqian Chen, Xiaomei Wang, Yeqiang Liu, Hanyang Cai, Yuan Qin
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-07201-w

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress
Cited by: 9
Author(s): Guodong Chen, Jizhong Wang, Xin Qiao, Can Jin, Weike Duan, Xiaochuan Sun, Juyou Wu
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-016-2656-8

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato
Cited by: 15
Author(s): Francisco Javier Herraiz, José Blanca, Peio Ziarsolo, Pietro Gramazio, Jaime Prohens, Gregory J. Anderson, Jaime Prohens, Santiago Vilanova
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-13-311

Comparative genomics of Shiga toxin encoding bacteriophages
Cited by: 79
Author(s): Darren Smith, David J. Rooks, Paul C. M. Fogg, Alistair C. Darby, Nicholas R. Thomson, Alan J. McCarthy, Heather E. Allison
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-017-4213-5

Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction
Cited by: 50
Author(s): Shiliang Fan, Dong Zhang, Lizhi Zhang, Giampiero Cai, Mingzhi Xin, Muhammad Mobeen Tahir, Youmei Li, Junsheng Ma, Mingyu Han
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-020-07115-7

A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli
Cited by: 7
Author(s): Guosong Zhang, Jie Li, Jiajia Zhang, Xuefang Liang, Tao Wang, Shaowu Yin
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-016-2870-4

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis
Cited by: 70
Author(s): Huayu Zhu, Pengyao Song, Dal‐Hoe Koo, Luqin Guo, Yanman Li, Shouru Sun, Yiqun Weng, Luming Yang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-018-5051-9

Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory
Cited by: 14
Author(s): Zhenyi Wang, Kanglu Zhao, Yuxin Pan, Jinpeng Wang, Xiaoming Song, Weina Ge, Min Yuan, Tianyu Lei, Li Wang, Lan Zhang, Yuxian Li, Tao Liu, Wei Chen, Wenjing Meng, Changkai Sun, Xiaobo Cui, Yun Bai, Xiyin Wang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-018-4513-4

Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes
Cited by: 40
Author(s): Aida Z. Kebede, Anne Johnston, Danielle Schneiderman, Whynn Bosnich, Linda J. Harris
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-12-564

AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome
Cited by: 15
Author(s): Lingling Mei, Xueliang Ding, Suk Ying Tsang, Frank W. Pun, Siu Kin Ng, Jianfeng Yang, Cunyou Zhao, Dezhi Li, Weiqing Wan, Chi Hung Yu, Tze-Ching Tan, Wai Sang Poon, Gilberto Ka Kit Leung, Ho Keung Ng, Liwei Zhang, Hong Xue
Software Mentions: 1
Published: about 13 years ago

10.1186/s12864-020-6572-6

Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus
Cited by: 13
Author(s): Liming Miao, Yingying Gao, Kun Zhao, Linggang Kong, Shubo Yu, Rongrong Li, Kaiwen Liu, Xiaolin Yu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-6678-x

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus
Cited by: 17
Author(s): Tong Wang, Jingjing Hu, Xiao Ma, Chunjin Li, Qing Yang, Shuyan Feng, Miaomiao Li, Nan Li, Xiaoming Song
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-06828-z

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)
Cited by: 14
Author(s): Huilin Xiao, Chaoping Wang, Nadeem Khan, Mengxia Chen, Weihong Fu, Le Guan, Xiangpeng Leng
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-4880-x

Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress
Cited by: 207
Author(s): Tongxin Xie, Chengjie Chen, Chuhao Li, Jiarou Liu, Chaoyang Liu, Yehua He
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5684-3

Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization
Cited by: 31
Author(s): Mengdi Li, Ruihua Wang, Zhengyi Liu, Xiaoming Wu, Jianbo Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4082-y

Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato
Cited by: 33
Author(s): Khadiza Khatun, Ujjal Kumar Nath, Arif Hasan Khan Robin, Jong-In Park, Do-Jin Lee, Min-Bae Kim, Chang Kil Kim, Ki-Byung Lim, Ill Sup Nou, Mi-Young Chung
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-017-3768-5

Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum
Cited by: 75
Author(s): Wei Wang, Xiaopei Zhang, Fenni Deng, Rui Yuan, Fafu Shen
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-15-322

Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288
Cited by: 55
Author(s): Shuangping Heng, Chao Wei, Bing Jing, Zhengjie Wan, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Tingdong Fu
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-15-581

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)
Cited by: 132
Author(s): Gina Cannarozzi, Sonia Plaza-Wüthrich, Korinna Esfeld, Stéphanie Larti, Yi Song Wilson, Dejene Girma, Edouard de Castro, Solomon Chanyalew, Regula Blösch, Laurent Farinelli, Eric Lyons, Michel Schneider, Laurent Falquet, Cris Kuhlemeier, Kebebew Assefa, Zerihun Tadele
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-14-887

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors
Cited by: 43
Author(s): Chenxi Chen, Bi Lian, Jinnan Hu, Huan-Chen Zhai, Xingxing Wang, R. C. Venu, Erming Liu, Zhilong Wang, Meilian Chen, Baohua Wang, Guoliang Wang, Zonghua Wang, Thomas K. Mitchell
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-020-07258-7

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25
Cited by: 8
Author(s): Bianca Büttner, Vera Draba, Klaus Pillen, Günther Schweizer, Andreas Maurer
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-13-420

Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss)
Cited by: 39
Author(s): Joseph D. Norman, M. E. Robinson, B. Glebe, Moira M. Ferguson, Roy G. Danzmann
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-021-07479-4

Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)
Cited by: 16
Author(s): Xiuming Zhang, Li Zhang, Miaomiao Ji, Yifei Wu, Songlin Zhang, Yanxun Zhu, Jin Yao, Zhi Li, Hua Gao, Xiping Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-020-6658-1

ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)
Cited by: 15
Author(s): Wei Yang, Yaorong Wang, Dongneng Jiang, Changxu Tian, Chunhua Zhu, Guangli Li, Huapu Chen
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-019-6374-x

Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)
Cited by: 37
Author(s): Ruibin Wang, Jingfei Ma, Qian Zhang, Chunlai Wu, Hongyan Zhao, Yanan Wu, Guangxiao Yang, Guangyuan He
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-13-542

The Caulobacter crescentus phage phiCbK: genomics of a canonical phage
Cited by: 81
Author(s): Jason J. Gill, Joel D. Berry, William K. Russell, Lauren Lessor, Diego A Escobar-Garcia, Daniel Antonio Hernández, Ashley Kane, Jennifer L. Keene, Matthew L. Maddox, Rebecca Martin, Sheba Mohan, Ashlyn M Thorn, David H. Russell, Ry Young
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-016-2589-2

The impact and origin of copy number variations in the Oryza species
Cited by: 29
Author(s): Zetao Bai, Jinfeng Chen, Yi Liao, Meijiao Wang, Liu Rong, Song Ge, Rod A. Wing, Mingsheng Chen
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-020-6496-1

Functional and population genetic features of copy number variations in two dairy cattle populations
Cited by: 17
Author(s): Young Lim Lee, Mirte Bosse, Erik Mullaart, M.A.M. Groenen, R.F. Veerkamp, A.C. Bouwman
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-017-3643-4

Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq
Cited by: 24
Author(s): Chao Shen, Xin Jin, De Zhu, Zhongxu Lin
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-020-07117-5

Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement
Cited by: 7
Author(s): Cecilie Bækkedal Sonnenberg, Tim Kahlke, Peik Haugen
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-13-468

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic
Cited by: 7
Author(s): Rachel Sealfon, Stephen K. Gire, Crystal N. Ellis, Stephen B. Calderwood, Firdausi Qadri, Lisa E. Hensley, M Kellis, Edward T. Ryan, Regina C. LaRocque, Jason B. Harris, Pardis C. Sabeti
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-019-5948-y

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum
Cited by: 15
Author(s): Hongguang Sun, Hengling Wei, Hantao Wang, Pengbo Hao, Lijiao Gu, Guoyuan Liu, Liang Ma, Zhengzheng Su, Shuang Yu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6207-y

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype
Cited by: 19
Author(s): Hugo Vianna Silva Rody, Renato Gustavo Hoffmann Bombardelli, Silvana Creste, L. E. A. Camargo, Marie‐Anne Van Sluys, Cláudia Barros Monteiro-Vitorello
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-6212-1

Evolutionary balance between LRR domain loss and young NBS–LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner
Cited by: 18
Author(s): Hui Song, Zhonglong Guo, Xiaohui Hu, Liying Qian, Fuhong Miao, Xiaojun Zhang, Jing Chen
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-12-639

Refinement of Bos taurus sequence assembly based on BAC-FISH experiments
Cited by: 13
Author(s): Giulia Partipilo, Pietro D’Addabbo, Giovanni Michele Lacalandra, George E. Liu, Mariano Rocchi
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-015-1361-3

A new platform for ultra-high density Staphylococcus aureus transposon libraries
Cited by: 80
Author(s): Marina Santiago, Leigh M. Matano, Samir H. Moussa, Michael S. Gilmore, Suzanne Walker, Timothy C. Meredith
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5788-9

Comparative analysis reveals conservation in genome organization among intestinal Cryptosporidium species and sequence divergence in potential secreted pathogenesis determinants among major human-infecting species
Cited by: 32
Author(s): Zhixiao Xu, Yaqiong Guo, Dawn M. Roellig, Yaoyu Feng, Lihua Xiao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-3123-2

Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum)
Cited by: 64
Author(s): Ying Huang, Mengyao Li, Peng Wu, Zhihong Xu, Qing Feng, Rui Wang, Ai‐Sheng Xiong
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-019-5936-2

Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube
Cited by: 29
Author(s): Hongtai Li, Wei Gao, Chaoling Xue, Yao Zhang, Zhiguo Liu, Yu Zhang, Meng Xu, Mengjun Liu, Jin Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-451

An integrated platform for bovine DNA methylome analysis suitable for small samples
Cited by: 34
Author(s): Habib A. Shojaei Saadi, Alan M. O’Doherty, Dominic Gagné, Éric Fournier, Jason R. Grant, Marc‐André Sirard, Claude Robert
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-016-2455-2

Dissecting genetics of cutaneous miRNA in a mouse model of an autoimmune blistering disease
Cited by: 9
Author(s): Yask Gupta, Steffen Möller, Mareike Witte, Meriem Belheouane, Tanya Sezin, Misa Hirose, Artem Vorobyev, Felix Niesar, Julia Bischof, Ralf J. Ludwig, Detlef Zillikens, Christian D. Sadik, Tobias Restle, Robert Häsler, John F. Baines, Saleh M. Ibrahim
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-07862-1

Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.
Cited by: 11
Author(s): Wei Su, Ali Raza, Zeng Liu, Ang Gao, Yan Lv, Xuezhi Ding, Yongqiang Cheng, Xiling Zou
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-15-458

Genetic dynamics underlying phenotypic development of biomass yield in triticale
Cited by: 18
Author(s): Wenxin Liu, Manje Gowda, Jochen C. Reif, Volker Hahn, Arno Ruckelshausen, Elmar A. Weissmann, Hans Peter Maurer, Tobias Würschum
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-020-6595-z

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species
Cited by: 17
Author(s): Michael J. Roach, Anthony R. Borneman
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-016-3212-2

Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions
Cited by: 46
Author(s): Zhaohua Liu, Zhibin Ji, Guizhi Wang, Tianle Chao, Lei Hou, Jianmin Wang
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-15-440

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics
Cited by: 35
Author(s): Shanming Wang, Bin Hao, Jiarui Li, Huijie Gu, Jie Peng, Fei Xie, Xinyin Zhao, Christian Frech, Nansheng Chen, Bin-Guang Ma, Youguo Li
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-15-309

High density SNP and SSR-based genetic maps of two independent oil palm hybrids
Cited by: 67
Author(s): Ngoot‐Chin Ting, J. Jansen, Sean Mayes, Festo Massawe, Ravigadevi Sambanthamurthi, Leslie Cheng‐Li Ooi, Cheuk Weng Chin, Xaviar Arulandoo, Seng TzerYing, Sharifah Shahrul Rabiah Syed Alwee, Maizura Ithnin, Rajinder Singh
Software Mentions: 1
Published: over 10 years ago