10.3389/fpls.2016.01186

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: about 10 years ago

10.3389/fpls.2016.01083

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: almost 9 years ago

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2019.00586

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis
Cited by: 27
Author(s): Marco Kreuzer, Caroline Howard, Bhim Adhikari, Colin A. Pendry, Julie A. Hawkins
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-14-S1-S5

Genomic differences between cultivated soybean, G. max and its wild relative G. soja
Cited by: 31
Author(s): Trupti Joshi, Babu Valliyodan, J. G. Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen
Software Mentions: 3
Published: over 13 years ago

10.3389/fpls.2018.01332

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family
Cited by: 28
Author(s): Yueying Li, Liangliang He, Jing Li, Jianghua Chen, Changning Liu
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.3134

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Cited by: 44
Author(s): Sean P. Jungbluth, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.3406

MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
Cited by: 25
Author(s): Koji Ishiya, Shintaroh Ueda
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2019.00918

A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus
Cited by: 10
Author(s): Diego Zappacosta, Jimena Gallardo, José Luís Carballo, M Meier, Juan Manuel Rodrigo, Cristian Gallo, Juan Pablo Selva, Juliana Stein, Juan Pablo Amelio Ortiz, Emidio Albertini, Viviana Echenique
Software Mentions: 3
Published: about 7 years ago

10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants
Cited by: 23
Author(s): Gangyi Yang, Wenlong Luo, Jian Zhang, Xian-cheng Yan, Yuguo Du, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2018.00771

Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection
Cited by: 28
Author(s): Paulo A. Zaini, Rafael Nascimento, Hossein Gouran, Dario Cantu, Sandeep Chakraborty, My L. Phu, Luíz Ricardo Goulart, Abhaya M. Dandekar
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 11 years ago

10.7717/peerj.740

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Cited by: 97
Author(s): Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2021.668623

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns
Cited by: 16
Author(s): Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Cláudio Benício Cardoso-Silva, Melina Cristina Mancini, Danilo Augusto Sforça, Lucas Borges dos Santos, James Shiniti Nagai, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Monalisa Sampaio Carneiro, Thiago Willian Almeida Balsalobre, Marcos G. Quiles, Welison Andrade Pereira, Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2021.684619

Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)
Cited by: 4
Author(s): Tingting Li, Wenqiu Pan, Yiyuan Yuan, Ying Liu, Yihan Li, Xiaoyu Wu, Fei Wang, Licao Cui
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1008337

Comprehensive analysis of iron utilization by Mycobacterium tuberculosis
Cited by: 52
Author(s): Lei Zhang, R. Curtis Hendrickson, Virginia Meikle, Elliot J. Lefkowitz, Thomas R. Ioerger, Michael Niederweis
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2014.00789

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
Cited by: 38
Author(s): Vikash Singh, Mukesh Jain, Rohini Garg
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: over 12 years ago

10.3389/fpls.2020.545042

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense
Cited by: 3
Author(s): Kai Fan, Zhijun Mao, Jiaxin Zheng, Yunrui Chen, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jinwen Huang, Wenxiong Lin
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2021.721253

Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat (Triticum aestivum L.)
Cited by: 12
Author(s): Zhenyu Wang, Ruoyu Zhang, Yue Cheng, Pengzheng Lei, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-017-3499-7

Visualization of consensus genome structure without using a reference genome
Cited by: 3
Author(s): Isao Tada, Yasuhiro Tanizawa, Masanori Arita
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-017-3852-x

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida
Cited by: 97
Author(s): Anna Faddeeva-Vakhrusheva, Ken Kraaijeveld, Martijn F.L. Derks, Seyed Yahya Anvar, Valeria Agamennone, Wouter Suring, Andries A. Kampfraath, Jacintha Ellers, Giang Le Ngoc, Cornelis A.M. van Gestel, Janine Mariën, Sandra Smit, Nico M. van Straalen, Dick Roelofs
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2015.01238

The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots
Cited by: 45
Author(s): Nanette Christie, Peri A Tobias, Sanushka Naidoo, Carsten Külheim
Software Mentions: 3
Published: over 10 years ago

10.3892/mmr.2015.3318

PUFA diets alter the microRNA expression profiles in an inflammation rat model
Cited by: 34
Author(s): Zheng Zhang, Yubin Ge, Jinyu Zhang, Meilan Xue, Quan Li, Dongliang Lin, Wenhui Ma
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: almost 8 years ago

10.3389/fonc.2018.00183

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Cited by: 8
Author(s): Anne Steininger, Grit Ebert, B Becker, Chalid Assaf, Markus Möbs, Christian A. Schmidt, Piotr Grabarczyk, Lars Riff Jensen, Grzegorz K. Przybylski, Matthias Port, Andreas W. Kuß, Reinhard Ullmann
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2015.01247

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula
Cited by: 84
Author(s): Yongjun Shu, Ying Liu, Jun Zhang, Lili Song, Changhong Guo
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2016.01857

Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula
Cited by: 10
Author(s): David J. Burks, Rajeev K. Azad
Software Mentions: 3
Published: almost 10 years ago

10.3389/fonc.2021.669270

A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer
Cited by: 11
Author(s): Peide Huang, Fengyu Li, Zongchao Mo, Chunyu Geng, Wen Fang, Chunyan Zhang, Jia Guo, Song Wu, Lin Li, Nils Brünner, Jan Stenvang
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2017.00358

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study
Cited by: 7
Author(s): Edgar Guevara, Wyston C. Pierre, Camille Tessier, Luis Akakpo, Irène Londono, Frédéric Lesage, Gregory A. Lodygensky
Software Mentions: 3
Published: about 9 years ago

10.3389/fneur.2020.00184

Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke
Cited by: 13
Author(s): Yanfei Zhang, Ling‐Bing Meng, Meng-lei Hao, Jiao Yang, Tong Zou
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.591893

Screening and Identification of Key Biomarkers of Gastric Cancer: Three Genes Jointly Predict Gastric Cancer
Cited by: 3
Author(s): Mengjie Shan, Ling‐Bing Meng, Peng Guo, Yuanmeng Zhang, Dexian Kong, Ya-Bin Liu
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 11 years ago

10.1093/molbev/msaa109

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Cited by: 12
Author(s): Bryan D. Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez‐Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Minjun Shi, Christine Hein Vu, Shu Dan Yeh, Laura Fanti, Xiao Qin Xia, Julio Rozas, José M. Ranz
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.01009

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 9 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: about 8 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: over 6 years ago

10.1111/tpj.14538

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
Cited by: 82
Author(s): Tyler Alioto, Konstantinos G. Alexiou, Amélie Bardil, Fabio Barteri, Raúl Castanera, Fernando Cruz, Amit Dhingra, Henri Duval, Angel V. Fernández i Martí, Leonor Frías, Beatriz Galán, José Luis Garcı́a, Werner Howad, Jèssica Gómez‐Garrido, Marta Gut, Irene Julca, Jordi Morata, Pere Puigdomènech, Paolo Ribeca, María José Rubio Cabetas, Anna Vlasova, M. Wirthensohn, Jordi García-Más, Toni Gabaldón, Josep M. Casacuberta, Pere Arús
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-14-617

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
Cited by: 99
Author(s): Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: about 13 years ago

10.3389/fgene.2019.00116

Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium
Cited by: 14
Author(s): Yupeng Cui, Jianjiang Ma, Guoyuan Liu, Nuohan Wang, Wenfeng Pei, Man Wu, Xingli Li, Jinfa Zhang, Jie-Ae Yu
Software Mentions: 3
Published: over 7 years ago

10.3390/microorganisms8070981

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
Cited by: 15
Author(s): Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen, Yuxin Yang
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.671650

A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)
Cited by: 7
Author(s): Weidong Ding, Xinhui Zhang, Xiaomeng Zhao, Jing Wu, Zhen Cao, Jia Li, Yu Huang, Xinxin You, Min Wang, Qiong Shi, Xuwen Bing
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-95

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
Cited by: 34
Author(s): Jinkui Cheng, Zhiai Xu, Guomin Ren, Zhihua Liu
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2020.598183

Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L.
Cited by: 19
Author(s): Jin Wang, Yi Liu, Bi‐Yu Tang, Xiang Dai, Lingling Xie, Liping Feng, Xuexiao Zou
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00731

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection
Cited by: 36
Author(s): Yunji Xiu, Guangpeng Jiang, Shun Zhou, Jing Diao, Hongjun Liu, Baofeng Su, Chao Li
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2021.730821

Genome-Wide Investigation of SBT Family Genes in Pineapple and Functional Analysis of AcoSBT1.12 in Floral Transition
Cited by: 5
Author(s): Xingyue Jin, Qing Liu, Zongliu Hou, Yunfei Zhang, Yunying Fang, Youmei Huang, Hanyang Cai, Yuan Qin, Yan Cheng
Software Mentions: 3
Published: about 5 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.3389/fcimb.2018.00313

Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains
Cited by: 9
Author(s): Emilia Bonar, Michał Bukowski, Marcin Hydzik, Urszula Jankowska, Sylwia Kędracka‐Krok, Magdalena Groborz, Grzegorz Dubin, Viktoria Akkerboom, Jacek Międzobrodzki, Artur J. Sabat, Alexander Friedrich, Benedykt Władyka
Software Mentions: 3
Published: about 8 years ago

10.1186/s40168-019-0638-1

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
Cited by: 52
Author(s): Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian Firek, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2020.603815

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala
Cited by: 14
Author(s): Yulong Chen, Shiming Wan, Qing Li, Xiaoru Dong, Jinghan Diao, Qing Liao, Guiying Wang, Zexia Gao
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00561

Genome-Wide Identification and Homoeologous Expression Analysis of PP2C Genes in Wheat (Triticum aestivum L.)
Cited by: 44
Author(s): Xiao‐Lan Yu, Jiapeng Han, Efan Wang, Jie Xiao, Rui Hu, Guangxiao Yang, Guoqing He
Software Mentions: 3
Published: over 7 years ago

10.1099/mgen.0.000265

Insertion sequences drive the emergence of a highly adapted human pathogen
Cited by: 18
Author(s): Erwin Sentausa, Pauline Basso, Alice Berry, Annie Adrait, Gwendoline Bellement, Yohann Couté, Stephen Lory, Sylvie Elsen, Ina Attrée
Software Mentions: 3
Published: about 6 years ago

10.3390/v11030267

Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus
Cited by: 3
Author(s): Motohiro Akashi, Masaharu Takemura
Software Mentions: 3
Published: over 7 years ago

10.1155/2017/1278932

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis
Cited by: 39
Author(s): Georgios A. Pavlopoulos, David Páez-Espino, Nikos C. Kyrpides, Ioannis Iliopoulos
Software Mentions: 3
Published: about 9 years ago

10.3389/fbioe.2014.00088

Discovery of Protein–lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
Cited by: 55
Author(s): Junhao Li, Shun Liu, Ling‐Ling Zheng, Jie Wu, Wenju Sun, Zelin Wang, Hui Zhou, Liang‐Hu Qu, Jianhua Yang
Software Mentions: 3
Published: over 11 years ago

10.3389/fgene.2020.00652

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes
Cited by: 25
Author(s): Bin Zeng, Ting Chen, Junyi Luo, Mei-Ying Xie, Limin Wei, Qianyun Xi, Jiajie Sun, Yongliang Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-255

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
Cited by: 19
Author(s): Ismael A. Vergara, Maja Tarailo‐Graovac, Christian Frech, Jun Wang, Zhaozhao Qin, Ting Zhang, Rong She, Jeffrey Shih-Chieh Chu, Ke Wang, Nansheng Chen
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-021-07378-8

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Cited by: 19
Author(s): Dou Liu, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Hǎihóng Shāng, Hongbin Li, Gao Xiao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-6319-4

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Cited by: 14
Author(s): Jing Li, Xiaotong Gao, Shiye Sang, Changning Liu
Software Mentions: 3
Published: almost 7 years ago

10.1111/1751-7915.13655

Geographic pattern of antibiotic resistance genes in the metagenomes of the giant panda
Cited by: 20
Author(s): Ting Hu, Qinlong Dai, Hua Chen, Zheng Zhang, Qiang Dai, Xun Gu, Xiangdong Yang, Yang Zhang, Lifeng Zhu
Software Mentions: 3
Published: about 6 years ago

10.1186/s12866-020-02024-x

High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis
Cited by: 15
Author(s): Yunfeng Luo, Zhongke Wang, Ya-Ling He, Guifang Li, Xinhua Lv, Zhuang Li
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 8 years ago

10.1099/mgen.0.000154

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: over 8 years ago

10.1099/mgen.0.000188

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
Cited by: 32
Author(s): Arnold Bainomugisa, Tânia Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben J. Marais, Lachlan Coin
Software Mentions: 3
Published: over 8 years ago

10.4161/epi.26017

DNA methylation analysis of murine hematopoietic side population cells during aging
Cited by: 42
Author(s): Oluwatosin Taiwo, Gareth A. Wilson, Warren Emmett, Tiffany Morris, Dominique Bonnet, Eugene F. Schuster, Tomas Adejumo, Stephan Beck, Daniel J. Pearce
Software Mentions: 3
Published: about 13 years ago

10.1186/s12866-020-01737-3

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Cited by: 7
Author(s): Jiaokun Li, Tianyuan Gu, Liangzhi Li, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, Guanzhou Qiu, Weimin Zeng
Software Mentions: 3
Published: over 6 years ago

10.12688/f1000research.7302.1

Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence
Cited by: 21
Author(s): Neeraja M. Krishnan, Saurabh Gupta, Vinayak Palve, Linu Varghese, Swetansu Pattnaik, Promil Jain, Costerwell Khyriem, Arun K Hariharan, Kunal Dhas, Jayalakshmi Nair, Manisha Pareek, Venkatesh K Prasad, Gangotri Siddappa, Amritha Suresh, Vikram D. Kekatpure, Moni Abraham Kuriakose, Binay Panda
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-13-545

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
Cited by: 98
Author(s): Jihye Park, Ying Zhang, Anne M. Buboltz, Xuqing Zhang, Stephan C. Schuster, Umesh Ahuja, Minghsun Liu, Jeff F. Miller, Mohammed Sebaihia, Stephen D. Bentley, Julian Parkhill, Eric T. Harvill
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12870-019-2122-2

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties
Cited by: 29
Author(s): Heshan Du, Jingjing Yang, Bin Chen, Xiaofen Zhang, Jian Zhang, Kun Yang, Sansheng Geng, Changlong Wen
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41375-018-0103-3

Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms
Cited by: 62
Author(s): Phuc H. Hoang, Sara E. Dobbins, Alex J. Cornish, Daniel Chubb, Philip Law, Martin Kaiser, Richard S. Houlston
Software Mentions: 3
Published: over 8 years ago

10.15252/embj.201489282

Aberrant methylation of t<scp>RNA</scp>s links cellular stress to neuro‐developmental disorders
Cited by: 426
Author(s): Sandra Blanco, Sabine Dietmann, Joana V. Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M. Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valérie Gailus‐Durner, Martin Hrabé de Angelis, Ragnhildur Thóra Káradóttir, Mark Helm, Jernej Ule, Joseph G. Gleeson, Duncan T. Odom, Michaela Frye
Software Mentions: 3
Published: about 12 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.1038/s41375-020-0762-8

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing
Cited by: 38
Author(s): Wibowo Arindrarto, Daniel Borràs, Ruben A.L. De Groen, Redmar R van den Berg, Irene J. Locher, Saskia A.M.E. van Diessen, Rosalie van der Holst, Edith D. van der Meijden, M. Willy Honders, Rick H. de Leeuw, Wina Verlaat, Inge Jedema, Wilma G. M. Kroes, Jeroen Knijnenburg, Tom van Wezel, Joost S.P. Vermaat, Peter J.M. Valk, Bart Janssen, Peter de Knijff, Cornelis A.M. van Bergen, Erik B. van den Akker, Peter A C ‘t Hoen, Szymon M. Kiełbasa, Jeroen F. J. Laros, Marieke Griffioen, Hendrik Veelken
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-020-06877-4

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max
Cited by: 4
Author(s): Kai Fan, Yunrui Chen, Zhijun Mao, Fang Yao, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang
Software Mentions: 3
Published: about 6 years ago

10.1002/ece3.5991

New genome assembly of the barn owl (<i>Tyto alba alba</i>)
Cited by: 8
Author(s): Anne‐Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid‐Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M. San‐Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xénarios, Alexandre Roulin, Jérôme Goudet
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-53802-1

Oral microbiome diversity in chimpanzees from Gombe National Park
Cited by: 14
Author(s): Andrew T. Ozga, Ian C. Gilby, Rebecca Nockerts, Michael L. Wilson, Anne E. Pusey, Anne C. Stone
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1008646

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Cited by: 26
Author(s): Yufeng Fang, Marco A. Coelho, Haidong Shu, Klaas Schotanus, Bhagya C. Thimmappa, Vikas Yadav, H Chen, Ewa Malc, Jeremy Wang, Piotr A. Mieczkowski, Brent Kronmiller, Brett M. Tyler, Kaustuv Sanyal, Suomeng Dong, Minou Nowrousian, Joseph Heitman
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-54446-x

High throughput barcoding method for genome-scale phasing
Cited by: 13
Author(s): David Redin, Tobias Frick, Hooman Aghelpasand, Max Käller, Erik Borgström, Remi‐André Olsen, Afshin Ahmadian
Software Mentions: 3
Published: almost 7 years ago

10.1038/s42003-020-1096-9

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Cited by: 27
Author(s): Austin B. Mudd, Jessen V. Bredeson, Rachel Baum, Dirk Hockemeyer, Daniel S. Rokhsar
Software Mentions: 3
Published: about 6 years ago

10.1038/s42003-020-1060-8

The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface
Cited by: 36
Author(s): Khaled M. Hazzouri, Naganeeswaran Sudalaimuthuasari, Biduth Kundu, David R. Nelson, Mohammad Ali Al-Deeb, Alain Le Mansour, J. Spencer Johnston, Claude Desplan, Khaled M. A. Amiri
Software Mentions: 3
Published: over 6 years ago

10.3389/fnagi.2017.00249

DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment
Cited by: 48
Author(s): Lara Ianov, Alberto Riva, Ashok Kumar, Thomas C. Foster
Software Mentions: 3
Published: about 9 years ago

10.3390/cells8101253

Genome-Wide Mapping Defines a Role for C/EBPβ and c-Jun in Non-Canonical Cyclic AMP Signalling
Cited by: 5
Author(s): Jolanta Wiejak, Boy van Basten, Graham Hamilton, Stephen J. Yarwood
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: over 12 years ago

10.1038/s42003-021-02559-3

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: over 11 years ago

10.1038/cr.2017.124

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
Cited by: 152
Author(s): Changsong Zou, A Chen, Li Xiao, H.-A. Müller, Peter Ache, Georg Haberer, M Zhang, Jia Wei, Ping Deng, Ru Huang, Daniel Lang, Li Feng, Dong Zhan, Xiaoyong Wu, H Zhang, Jennifer Böhm, Ruirui Liu, Lana Shabala, Rainer Hedrich, J-K Zhu
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.celrep.2019.05.014

Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas
Cited by: 13
Author(s): Joy J. Bianchi, Valentine Murigneux, Marie Bedora-Faure, Chloé Lescale, Ludovic Deriano
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0240916

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors
Cited by: 5
Author(s): Luisa M. Arias-Giraldo, Marina Muñoz, Carolina Hernández, Giovanny Herrera, Natalia Velásquez-Ortiz, Omar Cantillo-Barraza, Plutarco Urbano, Juan David Ramírez
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13068-017-0885-y

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
Cited by: 23
Author(s): Man Zhou, Peng Guo, Tao Wang, Limin Gao, Hang Yin, Cheng Cai, Jie Gu, Xin Lü
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0129396

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome
Cited by: 26
Author(s): Ching-Ping Lin, Chih‐Yuan Ko, Ching-I Kuo, Mao-Sen Liu, Roland Schafleitner, Long-Fang Oliver Chen
Software Mentions: 3
Published: over 11 years ago

10.1186/s13068-020-1651-0

Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742
Cited by: 6
Author(s): Youzhi Miao, Xing Chen, Tuo Li, Han Zhu, Tang Si-yu, Dongyang Liu, Qirong Shen
Software Mentions: 3
Published: over 6 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-020-01172-0

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression
Cited by: 23
Author(s): Ryoichi Yano, Tohru Ariizumi, Satoko Nonaka, Yoichi Kawazu, Silin Zhong, Lukas A. Mueller, James Giovannoni, Jocelyn K. C. Rose, Hiroshi Ezura
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms20184593

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)
Cited by: 16
Author(s): Hong Chen, Huihui Li, Xiaoyan Lu, Longzheng Chen, Jing Liu, Hongmiao Wu
Software Mentions: 3
Published: about 7 years ago

10.1042/BSR20191139

Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues
Cited by: 4
Author(s): Zhenxu Zhou, Xiaoming Chen, Yuqi Zhang, Peng Liu, Xiangyang Xue, Guoxin Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-020-02809-2

Tight association of genome rearrangements with gene expression in conifer plastomes
Cited by: 5
Author(s): Ching‐Yi Wu, Edi Sudianto, Shu‐Miaw Chaw
Software Mentions: 3
Published: over 5 years ago