10.1093/gbe/evu201

Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation
Cited by: 27
Author(s): Yudong Li, Weiping Zhang, Dao-Qiong Zheng, Zhan Zhou, Wenwen Yu, Lei Zhang, Lei Feng, Xinmiao Liang, Wenjun Guan, Jingwen Zhou, Jian Chen, Zhenguo Lin
Software Mentions: 1
Published: about 11 years ago

10.1093/gbe/evab177

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution
Cited by: 10
Author(s): Tim Regan, Lewis Stevens, Carolina Peñaloza, Ross D. Houston, Diego Robledo, Tim P. Bean
Software Mentions: 1
Published: over 4 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 6 years ago

10.1093/gbe/evu175

Genomic Signatures of Distributive Conjugal Transfer among Mycobacteria
Cited by: 38
Author(s): Tatum D Mortimer, Caitlin S. Pepperell
Software Mentions: 1
Published: about 11 years ago

10.1186/s13073-015-0164-0

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Cited by: 299
Author(s): Francesc Español i Coll, Ruth McNerney, Mark D. Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant A. Hill-Cawthorne, Kim Mallard, Mridul Nair, Armandina Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R. Glynn, Nigel Martin, Arnab Pain, Taane G. Clark
Software Mentions: 1
Published: over 10 years ago

10.1186/s13073-017-0399-z

Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells
Cited by: 21
Author(s): Sjors Middelkamp, Sebastiaan van Heesch, Arie Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J. van Roosmalen, Martijn J. E. Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E. Verbeek, Elly F. Ippel, Youri Adolfs, R. Jeroen Pasterkamp, Wigard P. Kloosterman, Ewart Kuijk, Edwin Cuppen
Software Mentions: 1
Published: almost 9 years ago

10.1093/gbe/evu037

Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence
Cited by: 60
Author(s): Simon Renny‐Byfield, Joseph P. Gallagher, Corrinne E. Grover, Emmanuel Szadkowski, Justin T. Page, Joshua A. Udall, Xiyin Wang, Andrew H. Paterson, Jonathan F. Wendel
Software Mentions: 1
Published: over 11 years ago

10.1186/s13059-018-1458-5

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice
Cited by: 200
Author(s): Xu Tang, Guanqing Liu, Jianping Zhou, Qiao Ren, Qi You, Li Tian, Xuhui Xin, Zhiyong Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn, Zhiyun Gong, Yiping Qi, Tao Zhang, Yong Zhang
Software Mentions: 1
Published: over 7 years ago

10.1186/gb-2013-14-11-r126

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors
Cited by: 81
Author(s): Miriam Ragle Aure, Suvi‐Katri Leivonen, Thomas Fleischer, Qi Zhu, Jens Overgaard, Jan Alsner, Trine Tramm, Riku Louhimo, Grethe I.G. Alnæs, Merja Perälä, Florence Busato, Nizar Touleimat, Jörg Tost, Anne‐Lise Børresen‐Dale, Sampsa Hautaniemi, Olga G. Troyanskaya, Ole Christian Lingjærde, Kristine Kleivi Sahlberg, Vessela N. Kristensen
Software Mentions: 1
Published: almost 13 years ago

10.1186/gb-2012-13-9-r48

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
Cited by: 235
Author(s): Kevin Y. Yip, Chao Cheng, Nitin Bhardwaj, James Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter J. Bickel, M Snyder, Mark Gerstein
Software Mentions: 1
Published: almost 14 years ago

10.1016/j.gpb.2020.05.002

MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals
Cited by: 8
Author(s): Xiaoxu Yang, Chengliang Yang, Xianing Zheng, Luoxing Xiong, Yu‐Tian Tao, Meng Wang, Adam Yongxin Ye, Qixi Wu, Yanmei Dou, Junyu Luo, Liping Wei, August Yue Huang
Software Mentions: 1
Published: over 5 years ago

10.1186/2047-217X-3-19

iReport: a generalised Galaxy solution for integrated experimental reporting
Cited by: 4
Author(s): Saskia Hiltemann, Youri Hoogstrate, Peter van der Spek, Guido Jenster, Andrew Stubbs
Software Mentions: 1
Published: about 11 years ago

10.1186/2047-217X-1-14

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education
Cited by: 41
Author(s): Tarás K. Oleksyk, Jean‐François Pombert, Daniel Siu, Anyi Mazo‐Vargas, Brian P. Ramos, Wilfried Guiblet, Yashira Afanador, Christina Ruiz-Rodriguez, Michael L. Nickerson, David M. Logue, Michael Dean, L. Figueroa, Ricardo Valentin, Juan-Carlos Martinez-Cruzado
Software Mentions: 1
Published: about 13 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 7 years ago

10.1186/gb-2011-12-9-r94

Comparison of solution-based exome capture methods for next generation sequencing
Cited by: 246
Author(s): Anna-Maija Sulonen, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen, Henna Tyynismaa, Perttu Salo, Caroline A. Heckman, Heikki Joensuu, Taneli Raivio, Anu Suomalainen, Janna Saarela
Software Mentions: 1
Published: almost 15 years ago

10.3389/fgene.2014.00183

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps
Cited by: 0
Author(s): Keith Batesole, Kokulapalan Wimalanathan, Lin Liu, Fan Zhang, Craig S. Echt, Chun Liang
Software Mentions: 1
Published: over 11 years ago

10.3389/fgene.2020.609184

Genome-Wide Characterization of the HSP20 Gene Family Identifies Potential Members Involved in Temperature Stress Response in Apple
Cited by: 22
Author(s): Feng Yao, Chunhui Song, Hongtao Wang, Shangwei Song, Jian Jiao, Miaomiao Wang, Xianbo Zheng, Tuanhui Bai
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2019.00980

Identification and Analysis of the GASR Gene Family in Common Wheat (Triticum aestivum L.) and Characterization of TaGASR34, a Gene Associated With Seed Dormancy and Germination
Cited by: 26
Author(s): Xinran Cheng, Shengxing Wang, Dongmei Xu, Liyan Xue, Xinyu Li, Weiwei Xiao, Junhui Cao, Hao Jiang, Xiaoyu Min, Jianfeng Wang, Haiping Zhang, Cheng Chang, Jie Lu, Chunyan Ma
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms19102914

Gummy Stem Blight Resistance in Melon: Inheritance Pattern and Development of Molecular Markers
Cited by: 17
Author(s): Zahid Hassan, Abdur Rahim, Sathishkumar Natarajan, Arif Hasan Khan Robin, Hoy‐Taek Kim, Jong-In Park, Ill–Sup Nou
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2021.658148

Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses
Cited by: 5
Author(s): Wenying Xu, Tong Liu, Huiying Zhang, Hong Zhu
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2021.660428

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population
Cited by: 9
Author(s): Gihan Daw Elbait, Andreas Henschel, Guan K. Tay, Habiba S. Al Safar
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2020.00086

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)
Cited by: 14
Author(s): D.S. Kishor, Jeonghwan Seo, Joong Hyoun Chin, Hee‐Jong Koh
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.00822

Genomics and Virulence of Fonsecaea pugnacius, Agent of Disseminated Chromoblastomycosis
Cited by: 5
Author(s): Amanda Bombassaro, Gabriela Xavier Schneider, Flávia F. Costa, Aniele Carolina Ribas Leão, Bruna da Silva Soley, Fernanda Medeiros, Nickolas M da Silva, Bruna Jacomel Favoreto de Souza Lima, Raffael Júnio Araújo de Castro, Anamélia Lorenzetti Bocca, Valter A. Baura, Eduardo Balsanelli, Vânia C. S. Pankievicz, Nyvia Milicio Coblinski Hrysay, Rosana Hermínia Scola, Leandro Ferreira Moreno, Conceição M. P. S. de Azevedo, Emanuel Maltempi de Souza, Renata Rodrigues Gomes, Sybren de Hoog, Vânia Aparecida Vicente
Software Mentions: 1
Published: about 5 years ago

10.1093/gigascience/giz038

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing
Cited by: 23
Author(s): Ruby Dhar, Ashikh Seethy, Karthikeyan Pethusamy, Sunil Kumar Singh, Vishwajeet Rohil, Kakali Purkayastha, Indrani Mukherjee, Sandeep Goswami, Rakesh Singh, Ankita Raj, Tryambak Srivastava, Sovon Acharya, Balaji Rajashekhar, Subhradip Karmakar
Software Mentions: 1
Published: over 6 years ago

10.1093/gigascience/giz063

A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Cited by: 44
Author(s): Jay Ghurye, Sergey Koren, Scott T. Small, Seth Redmond, Paul Howell, Adam M. Phillippy, Nora J. Besansky
Software Mentions: 1
Published: over 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 10 years ago

10.1093/gigascience/giaa020

Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly
Cited by: 3
Author(s): Fanming Meng, Zhuoying Liu, Han Han, Dmitrijs Finkelbergs, Yangshuai Jiang, Mingfei Zhu, Yang Wang, Zongyi Sun, Chao Chen, Yadong Guo, Jifeng Cai
Software Mentions: 1
Published: over 5 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 5 years ago

10.3390/ijerph17051597

Global Mapping of Interventions to Improve Quality of Life of People with Diabetes in 1990–2018
Cited by: 11
Author(s): Bach Xuan Tran, Long Hoang Nguyen, Ngoc Minh Pham, Huyen Thi Thanh Vu, Hung Trong Nguyen, Duong Huong Phan, Giang Hai Ha, Hai Quang Pham, Thao Phuong Nguyen, Carl A. Latkin, Cyrus S.H. Ho, Roger Ho
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/giaa092

Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)
Cited by: 5
Author(s): Feng Shao, Arne Ludwig, Yang Mao, Geoffrey Liu, Zuogang Peng
Software Mentions: 1
Published: over 5 years ago

10.1093/gigascience/giaa099

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods
Cited by: 10
Author(s): Damien Courtine, Jan Provazník, Jérôme Reboul, Guillaume Blanc, Vladimír Beneš, Jonathan J. Ewbank
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2021.538733

Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)
Cited by: 10
Author(s): Hong Nan, Richard A. Ludlow, Min Lü, Hongyu An
Software Mentions: 1
Published: over 4 years ago

10.3389/fgene.2012.00299

Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis
Cited by: 6
Author(s): Zhengyu Jiang, Yan Zhou, Karthik Devarajan, Carolyn Slater, Mary B. Daly, Xiaowei Chen
Software Mentions: 1
Published: almost 14 years ago

10.1186/s13099-014-0040-2

Genome sequencing and genomic characterization of a tigecycline-resistant Klebsiella pneumoniae strain isolated from the bile samples of a cholangiocarcinoma patient
Cited by: 14
Author(s): Beiwen Zheng, Ang Li, Xin Jiang, Xinjun Hu, Jian Yao, Lina Zhao, Jinru Ji, Min Ye, Yonghong Xiao
Software Mentions: 1
Published: about 11 years ago

10.1186/s13099-015-0059-z

Draft genomes of four enterotoxigenic Escherichia coli (ETEC) clinical isolates from China and Bangladesh
Cited by: 5
Author(s): Fei Liu, Xi Yang, Zhiyun Wang, Matilda Nicklasson, Firdausi Qadri, Yi Yao, Yezi Zhu, Na Lv, Jing Li, Ruifen Zhang, Huijuan Guo, Baoli Zhu, Åsa Sjöling, Yongfei Hu
Software Mentions: 1
Published: over 10 years ago

10.3389/fgene.2018.00690

Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton
Cited by: 19
Author(s): Yun Song, Linxuan Li, Zhaoen Yang, Ge Zhao, Xueyan Zhang, Lingling Wang, Lei Zheng, Fei Zhuo, Huan Yin, Xiaoyang Ge, Chaojun Zhang, Zuoren Yang, Maozhi Ren
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13099-017-0156-2

Comparative genomic analysis of Shiga toxin-producing and non-Shiga toxin-producing Escherichia coli O157 isolated from outbreaks in Korea
Cited by: 3
Author(s): Taesoo Kwon, Won Kim, Seung-Hak Cho
Software Mentions: 1
Published: over 8 years ago

10.1186/s13099-017-0216-7

Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China
Cited by: 2
Author(s): Junhang Pan, Yi Sun, Wenwu Yao, Haiyan Mao, Yanjun Zhang, Maoyan Zhu
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13099-019-0284-y

The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039
Cited by: 4
Author(s): Binit Lamichhane, Eng Guan Chua, Michael J. Wise, Connor Laming, Barry J. Marshall, Chin Yen Tay
Software Mentions: 1
Published: over 6 years ago

10.1186/s13099-019-0298-5

Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes
Cited by: 7
Author(s): Xuelin Zhang, Saisong Xiao, Xuege Jiang, Yun Li, Fan Zhang, Yi Yu, Peng Wang, Diangeng Li, Xian Zhao, Changting Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s13099-021-00399-4

The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air
Cited by: 6
Author(s): Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Akira Uchida, Rikky W. Purbojati, Kavita K. Kushwaha, Alexander Putra, Puramadathil Sasi Santhi, Benjamin W. Y. Khoo, Anthony Wong, Vineeth Kodengil Vettath, Daniela I. Drautz–Moses, Ana Carolina M. Junqueira, Stephan C. Schuster
Software Mentions: 1
Published: almost 5 years ago

10.1097/HS9.0000000000000031

Molecular Profiling Defines Distinct Prognostic Subgroups in Childhood AML: A Report From the French ELAM02 Study Group
Cited by: 36
Author(s): Alice Marceau-Renaut, Nicolas Duployez, Benoît Ducourneau, Myriam Labopin, Arnaud Petit, Alexandra Rousseau, Sandrine Geffroy, Maria Pia Bucci, Wendy Cuccuini, Odile Fenneteau, Philippe Ruminy, Brigitte Nelken, Stéphane Ducassou, Virginie Gandemer, Thierry Leblanc, Michel Gautier, Yves Bertrand, André Baruchel, Guy Leverger, Claude Preudhomme, Hélène Lapillonne
Software Mentions: 1
Published: almost 8 years ago

10.1002/hon.2864

Targeted locus amplification to detect molecular markers in mantle cell and follicular lymphoma
Cited by: 5
Author(s): Elisa Genuardi, Petra Klous, Barbara Mantoan, Daniela Drandi, Martina Ferrante, Federica Cavallo, Beatrice Alessandria, Irene Dogliotti, Daniele Grimaldi, S Ragaini, Michele Clerico, Mariella Lo Schirico, Elona Saraci, Mehmet Yılmaz, Gian Maria Zaccaria, Sergio Cortelazzo, Umberto Vitolo, Stefano Luminari, Massimo Federico, Mario Boccadoro, Max van Min, Erik Splinter, Marco Ladetto, Simone Ferrero
Software Mentions: 1
Published: over 4 years ago

10.1186/s13053-016-0049-2

PALB2: research reaching to clinical outcomes for women with breast cancer
Cited by: 26
Author(s): Melissa C. Southey, Ingrid Winship, Tú Nguyen-Dumont
Software Mentions: 1
Published: over 9 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: over 6 years ago

10.1038/s41437-021-00459-0

Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population
Cited by: 4
Author(s): Sanjeev Kumar Sharma, Karen McLean, Richard Colgan, D. Rees, Stephen Young, Mads Sønderkær, Leon A. Terry, Colin Turnbull, Mark A. Taylor, Glenn J. Bryan
Software Mentions: 1
Published: over 4 years ago

10.1038/oncsis.2015.34

Multiple region whole-exome sequencing reveals dramatically evolving intratumor genomic heterogeneity in esophageal squamous cell carcinoma
Cited by: 49
Author(s): Wei Cao, Wei Wu, Ming Yan, Fei Tian, Chi Ma, Q Zhang, X Li, Peng Han, Z Liu, Jianying Gu, Fred G. Biddle
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms19030769

Evolution and Stress Responses of Gossypium hirsutum SWEET Genes
Cited by: 30
Author(s): Wei Li, Zhongying Ren, Zhenyu Wang, Kuan Sun, Xinwu Pei, Yangai Liu, Kunlun He, Fei Zhang, Chengxiang Song, Xin Zhou, Wensheng Zhang, Xiongfeng Ma, Daigang Yang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41438-019-0223-6

Defect in Brnym1, a magnesium-dechelatase protein, causes a stay-green phenotype in an EMS-mutagenized Chinese cabbage (Brassica campestris L. ssp. pekinensis) line
Cited by: 21
Author(s): Nan Wang, Yun Zhang, Shengnan Huang, Yong Li, Chengyu Li, Hui Feng
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41438-020-00422-w

A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance
Cited by: 6
Author(s): Li Huang, Ying Ma, Jiebei Jiang, Ting Li, Wenjie Yang, Lei Zhang, Lei Wu, Landi Feng, Zhenxiang Xi, Xiaoting Xu, Jianquan Liu, Quanjun Hu
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.18990

Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
Cited by: 39
Author(s): Donato Giovannelli, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani
Software Mentions: 1
Published: over 8 years ago