10.1186/s12864-015-1233-x

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: over 11 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-016-0788-2

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
Cited by: 33
Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: over 10 years ago

10.1186/s12915-020-00802-7

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Cited by: 25
Author(s): Timothy Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren E. Hagen, Christine G. Elsik, Kevin R. Macaluso, Abdu F. Azad
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-018-5157-0

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)
Cited by: 39
Author(s): Rui Hu, Jie Xiao, Tao Gu, Xiao‐Lan Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-016-3070-y

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Cited by: 27
Author(s): Pablo Ivan Pereira Ramos, Márlon Grégori Flores Custódio, Guadalupe del Rosario Quispe Saji, Thiago Bérgamo Cardoso, Gisele Lucchetti da Silva, Graziela Braun, Willames M. B. S. Martins, Raquel Girardello, Ana Tereza Ribeiro de Vasconcelos, Elmer Fernández, Ana Cristina Gales, Marisa Fabiana Nicolás
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-15-198

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2164-13-202

Comparing thousands of circular genomes using the CGView Comparison Tool
Cited by: 234
Author(s): Jason R. Grant, Adriano S. Arantes, Paul Stothard
Software Mentions: 4
Published: over 14 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 13 years ago

10.7717/peerj.3162

The genomic sequence of<i>Exiguobacterium chiriqhucha</i>str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 9 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: about 5 years ago

10.1155/2014/264519

A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Cited by: 6
Author(s): Preston Leung, Rowena A. Bull, Andrew R. Lloyd, Fabio Luciani
Software Mentions: 4
Published: over 12 years ago

10.1186/s12859-015-0818-3

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Cited by: 11
Author(s): Xiao Zhu, Ho-fung Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.116.037556

Construction of a High-Density American Cranberry (<i>Vaccinium macrocarpon</i>Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
Cited by: 27
Author(s): Brandon Schlautman, Giovanny Covarrubias‐Pazaran, Luis Diaz‐Garcia, Massimo Iorizzo, James J. Polashock, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: almost 11 years ago

10.3390/cancers12123738

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients
Cited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0255822

Evaluation of the severity of nonalcoholic fatty liver disease through analysis of serum exosomal miRNA expression
Cited by: 5
Author(s): Jeong‐An Gim, Soo Min Bang, Young‐Sun Lee, Sun Young Yim, Young Kul Jung, Hayeon Kim, Baek-hui Kim, Ji Hoon Kim, Yeon Seok Seo, Hyung Joon Yim, Jong Eun Yeon, Soon Ho Um, Kwan Soo Byun
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic <i>Escherichia coli</i> Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: about 9 years ago

10.1186/s13072-021-00395-7

Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina
Cited by: 13
Author(s): Florian Carlier, M. Li, Laetitia Maroc, Robert Debuchy, Charbel Souaid, Daan Noordermeer, Pierre Grognet, Fabienne Malagnac
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-57546-1

Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001
Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: almost 6 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: about 13 years ago

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: about 10 years ago

10.1128/mBio.01650-17

<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown Rust
Cited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: over 8 years ago

10.1093/infdis/jiz318

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach
Cited by: 13
Author(s): Sarah Mollerup, Maria E. Asplund, Jens Friis-Nielsen, Kristín Rós Kjartansdóttir, Helena Fridholm, Thomas Arn Hansen, José Alejandro Romero Herrera, Christopher J. Barnes, Randi Holm Jensen, Stine Raith Richter, Ida Broman Nielsen, Carlotta Pietroni, David E. Alquezar‐Planas, Alba Rey‐Iglesia, Pernille V. S. Olsen, Ewa Rajpert De Meyts, Line Groth‐Pedersen, Christian von Buchwald, David Hebbelstrup Jensen, Robert Gniadecki, Estrid Høgdall, Jill Levin Langhoff, Imre Pete, Ildikó Vereczkey, Zsolt Baranyai, Karen Dybkær, Hans Erik Johnsen, Torben Steiniche, Peter Hokland, Jacob Rosenberg, Ulrik Baandrup, Thomas Sicheritz-Pontén, Eske Willerslev, Søren Brunak, Ole Lund, Tobias Mourier, Lasse Vinner, Jose M. G. Izarzugaza, Lars Peter Nielsen, Anders J. Hansen
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: almost 11 years ago

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2016.01416

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing
Cited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: over 7 years ago

10.1186/s40246-018-0170-6

Forward and reverse mutations in stages of cancer development
Cited by: 11
Author(s): Taobo Hu, Yogesh Kumar, Shazia Iram, Si Duan, Yang Li, Lei Chen, Jinfei Chen, Rong Yin, Ava Kwong, Gilberto Ka Kit Leung, Wai Kin Mat, Zhenggang Wu, Xi Long, Colin Chan, Si Chen, Peggy Lee, Siu Kin Ng, Timothy Y. C. Ho, Jianfeng Yang, Xueliang Ding, Suk Ying Tsang, Xinrui Zhou, Danhua Zhang, Enbo Zhou, Lin Xu, Wai-sang Poon, Hongyang Wang, Hong Xue
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2020.00736

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm
Cited by: 13
Author(s): Di Yuan, Jian-Feng Xing, Meiwei Luan, Kai-Kai Ji, Jun Guo, Shuang Xie, Yuanming Zhang
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-11327-5

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea
Cited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.3390/ijerph16203966

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China
Cited by: 16
Author(s): Lei Zhang, Yu Cheng, Guang Gao, Jiahu Jiang
Software Mentions: 4
Published: almost 7 years ago

10.3390/genes7040013

Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2017.01279

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: over 10 years ago

10.3389/fonc.2020.01778

Seven-Gene Signature Based on Glycolysis Is Closely Related to the Prognosis and Tumor Immune Infiltration of Patients With Gastric Cancer
Cited by: 36
Author(s): Shanshan Yu, Chuan Hu, Luya Cai, Xuedan Du, Fan Lin, Qiongjie Yu, Lixiao Liu, Cheng Zhang, Xuan Li, Wenfeng Li, Yu Zhan
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: over 6 years ago

10.1186/s12977-015-0148-6

An integrated map of HIV genome-wide variation from a population perspective
Cited by: 83
Author(s): Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 12 years ago

10.3389/fnut.2020.00150

High-Resolution Mass Spectrometer–Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle
Cited by: 17
Author(s): Alka Chopra, Syed Azmal Ali, Shveta Bathla, Preeti Rawat, Vikas Vohra, Sudarshan Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22010347

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
Cited by: 8
Author(s): Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1008334

Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)-driven pulmonary immunopathogenesis
Cited by: 32
Author(s): Junsong Zhang, Jun Li, Yuhong Yuan, Feng Huang, Rong Ma, Baohong Luo, Zhihui Xi, Ting Pan, Bingfeng Liu, Yiwen Zhang, Xu Zhang, Yong Luo, Jin Wang, Meng Zhao, Gen Liu, Kai Deng, Hui Zhang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: almost 11 years ago

10.1093/gigascience/giz012

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Cited by: 138
Author(s): Marivi Colle, Courtney P. Leisner, Ching Man Wai, Shujun Ou, Kevin A. Bird, Jie Wang, Jennifer H. Wisecaver, Alan E. Yocca, Elizabeth I. Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo Qing Song, Kevin L. Childs, Anthony L. Schilmiller, Nicholi Vorsa, C. Robin Buell, Robert VanBuren, Ning Jiang, Patrick P. Edger
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0146916

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
Cited by: 15
Author(s): Sophie Weiss, Thomas J. Mansell, Pooneh Mortazavi, Rob Knight, Ryan T. Gill
Software Mentions: 4
Published: over 10 years ago

10.1093/gigascience/gix015

Enhancing knowledge discovery from cancer genomics data with Galaxy
Cited by: 7
Author(s): Marco A. Albuquerque, Bruno M. Grande, Elie Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal, Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 8 years ago

10.1186/s13073-021-00889-9

Single-cell sequencing of the small and AT-skewed genome of malaria parasites
Cited by: 4
Author(s): Shiwei Liu, Adam C Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell, Jennifer L. Guler
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.01400

Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 9 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 8 years ago

10.1111/jpy.13079

Foliose <i>Ulva</i> Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
Cited by: 20
Author(s): Antoine Fort, Marcus McHale, Kévin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2021.736411

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Cited by: 2
Author(s): Dong Han, Qiaojuan Yan, Jun Li, Zhengqiang Jiang, Shanchao Yang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12951-021-00916-2

Silicon dioxide nanoparticles induced neurobehavioral impairments by disrupting microbiota–gut–brain axis
Cited by: 23
Author(s): Jun Diao, Yinyin Xia, Xuejun Jiang, Jingfu Qiu, Shuqun Cheng, Junhao Su, Xinhao Duan, Min Gao, Xia Qin, Jun Zhang, Jie Fan, Zhen Zou, Chengzhi Chen
Software Mentions: 4
Published: over 5 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
Cited by: 14
Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-020-02138-5

Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
Cited by: 40
Author(s): Scott A. Lujan, Matthew J. Longley, Margaret H. Humble, Christopher A. Lavender, Adam Burkholder, Emma L. Blakely, Charlotte L. Alston, Gráinne Gorman, D.M. Turnbull, Robert McFarland, Robert W. Taylor, Thomas A. Kunkel, William C. Copeland
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22041811

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes
Cited by: 15
Author(s): Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Software Mentions: 4
Published: over 5 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: about 8 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.11351

Multivariate analysis of electrophysiological diversity of Xenopus visual neurons during development and plasticity
Cited by: 21
Author(s): Christopher M. Ciarleglio, Arseny S. Khakhalin, Angelia F Wang, Alexander C Constantino, Sarah P Yip, Carlos D. Aizenman
Software Mentions: 4
Published: almost 11 years ago

10.7554/eLife.29391

Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites
Cited by: 25
Author(s): Fabien Sindikubwabo, Shibin Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y. Botté, Artur Scherf, Mohamed-Ali Hakimi
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.61562

Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans
Cited by: 40
Author(s): Alice V. Easton, Shenghan Gao, Scott P Lawton, Sasisekhar Bennuru, Asis Khan, Eric Dahlstrom, Rita G. Oliveira, Stella Kepha, Stephen F. Porcella, Joanne P. Webster, Roy M. Anderson, Michael E. Grigg, Richard E. Davis, Jianbin Wang, Thomas B. Nutman
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.120.401550

Solyntus, the New Highly Contiguous Reference Genome for Potato (<i>Solanum tuberosum</i>)
Cited by: 34
Author(s): Natascha van Lieshout, Ate van der Burgt, Michiel E. de Vries, Menno ter Maat, David Eickholt, Danny Esselink, Martijn van Kaauwen, Linda Kodde, Richard G. F. Visser, P. Lindhout, Richard Finkers
Software Mentions: 4
Published: about 6 years ago

10.3390/genes9080379

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Cited by: 22
Author(s): George C. diCenzo, Klaudia Dębiec, Jan Krzysztoforski, Witold Uhrynowski, Alessio Mengoni, Camilla Fagorzi, Adrian Górecki, Łukasz Dziewit, Tomasz Bajda, Grzegorz Rzepa, Łukasz Drewniak
Software Mentions: 4
Published: about 8 years ago

10.1038/srep18616

Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer
Cited by: 15
Author(s): Ning An, Xue Yang, Shujun Cheng, Guiqi Wang, Kaitai Zhang
Software Mentions: 4
Published: almost 11 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: about 11 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-018-1392-6

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions
Cited by: 99
Author(s): Paul Bailey, Christian Schudoma, William J. Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew J. Moscou, Ksenia V. Krasileva
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00692-19

The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation
Cited by: 39
Author(s): Shouke Zhang, Jinping Shu, Huai‐Jun Xue, Wei Zhang, Yabo Zhang, Yaning Liu, Linxin Fang, Yangdong Wang, Haojie Wang
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.116.037150

The Long Noncoding RNA Transcriptome of<i>Dictyostelium discoideum</i>Development
Cited by: 8
Author(s): Rafael D. Rosengarten, Balaji Santhanam, Janez Kokošar, Gad Shaulsky
Software Mentions: 3
Published: over 9 years ago

10.3390/ijerph15040708

Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China
Cited by: 29
Author(s): Xiaojuan Wang, Jie Gu, Hua Gao, Xiaoqing Qian, Haichao Li
Software Mentions: 3
Published: over 8 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

10.3389/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: about 5 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: almost 10 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

10.1371/journal.pone.0125964

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species
Cited by: 34
Author(s): S. P. Singh, Suresh Chand, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 3
Published: over 11 years ago

10.3390/jof6010007

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1
Cited by: 5
Author(s): Ling Peng, Liangwei Li, Xiaochuan Liu, Jianwei Chen, Chengcheng Shi, Wenjie Guo, Qiwu Xu, Guangyi Fan, Xin Liu, Dehai Li
Software Mentions: 3
Published: over 6 years ago

10.1155/2021/6289174

Comparative Analysis of the Glutathione S-Transferase Gene Family of Four Triticeae Species and Transcriptome Analysis of GST Genes in Common Wheat Responding to Salt Stress
Cited by: 24
Author(s): Yongchao Hao, Shoushen Xu, Zhongfan Lyu, Hong Wei Wang, Lingrang Kong, Silong Sun
Software Mentions: 3
Published: over 5 years ago

10.3390/ijerph17031009

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China
Cited by: 15
Author(s): Shengnan Chen, Hao He, Rongrong Zong, Kaiwen Liu, Miaomiao Yan, Lei Xu, Yutian Miao
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.633310

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum
Cited by: 27
Author(s): Luis Díaz-Garcia, Luis Fernando García-Ortega, María González-Rodriguez, Luis Delaye, Massimo Iorizzo, Juan Zalapa
Software Mentions: 3
Published: over 5 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

10.1371/journal.pone.0184119

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome
Cited by: 25
Author(s): Sarah M. Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W. Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 3
Published: about 9 years ago