pypi: Circos | Projects | Ecosyste.ms: Papers

10.1007/s10142-017-0555-y

Transcriptome profile of the human placenta
Cited by: 27
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Kamil Myszczyński, Marek Gowkielewicz, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.103650

hsa_circRNA6448-14 promotes carcinogenesis in esophageal squamous cell carcinoma
Cited by: 5
Author(s): Yaowen Zhang, Xiang Yuan, Ning J. Yue, Lidong Wang, Junqi Liu, Ning Dai, Haijun Yang, Ruitai Fan, Fuyou Zhou
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.113.007229

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing
Cited by: 67
Author(s): Justin T. Page, Mark D. Huynh, Zach S. Liechty, Kara Grupp, David M. Stelly, Amanda M. Hulse, Hamid Ashrafi, Allen Van Deynze, Jonathan F. Wendel, Joshua A. Udall
Software Mentions: 2
Published: about 11 years ago

10.1534/g3.113.010090

Genome Sequence of Saccharomyces carlsbergensis, the World’s First Pure Culture Lager Yeast
Cited by: 120
Author(s): Andrea Walther, Ana Hesselbart, Jürgen Wendland
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2148-10-346

Origin and evolution of a placental-specific microRNA family in the human genome
Cited by: 53
Author(s): Zhixiang Yuan, Xiao Sun, Dong-Ke Jiang, Yan Ding, Zhiyuan Lǚ, Li Gong, Hongde Liu, Jingjing Xie
Software Mentions: 2
Published: about 14 years ago

10.1080/21505594.2019.1637699

Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum
Cited by: 14
Author(s): Marina Muñoz, Daniel Restrepo-Montoya, Nitin Kumar, Gregorio Iraola, Giovanny Herrera, Dora I. Ríos-Chaparro, Diana Díaz-Arévalo, Manuel A. Patarroyo, Trevor D. Lawley, Juan David Ramírez
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.114.015933

Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains
Cited by: 20
Author(s): Stephen L. Pearce, John G. Oakeshott, Gyanendra Pandey
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-019-5981-x

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits
Cited by: 14
Author(s): Jitao Li, Jianjian Lv, Ping Liu, Ping Chen, Jiajia Wang, Jian Li
Software Mentions: 2
Published: over 5 years ago

10.1186/1752-0509-8-S2-I1

Data integration in the era of omics: current and future challenges
Cited by: 295
Author(s): David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew E. Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam‐Rudloff, Ana Conesa, Jesper Tegnér
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-020-02345-z

Identification of NHXs in Gossypium species and the positive role of GhNHX1 in salt tolerance
Cited by: 27
Author(s): Lu Long, Jing-Ruo Zhao, Dandan Guo, Xiaonan Ma, Fuchun Xu, Wenwen Yang, Wei Gao
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0027354

Molecular Basis of Virulence in Staphylococcus aureus Mastitis
Cited by: 70
Author(s): Caroline Le Maréchal, Núbia Seyffert, Julien Jardin, David Hernández, Gwenaël Jan, Lucie Rault, Vasco Azevedo, Patrice François, Jacques Schrenzel, Maarten van de Guchte, Sergine Even, Nadejda Berkova, Richard Thiéry, J. Ross Fitzgerald, Eric Vautor, Yves Le Loir
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-15-914

The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV
Cited by: 34
Author(s): Seyed Yahya Anvar, J. Howard Frank, Arjan Pol, Arnoud Schmitz, Ken Kraaijeveld, Johan T. den Dunnen, Huub J. M. Op den Camp
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-13-477

In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing
Cited by: 35
Author(s): Dorothee Nickles, Lohith Madireddy, Shan Yang, Pouya Khankhanian, Steve Lincoln, Stephen L. Hauser, Jorge R. Oksenberg, Sergio E. Baranzini
Software Mentions: 2
Published: about 12 years ago

10.1534/g3.119.400262

Developing a High-Quality Linkage Map for the Atlantic KillifishFundulus heteroclitus
Cited by: 10
Author(s): Jeffrey T. Miller, Noah M. Reid, Diane Nacci, Andrew Whitehead
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-021-07390-y

Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline
Cited by: 5
Author(s): Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis, Tariq M. Butt
Software Mentions: 2
Published: almost 4 years ago

10.1051/parasite/2020034

Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi
Cited by: 5
Author(s): Vivek Bhakta Mathema, Supatchara Nakeesathit, Nicholas J. White, Arjen M. Dondorp, Mallika Imwong
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13071-014-0622-3

Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery
Cited by: 11
Author(s): Nicholas J. Wheeler, Prince N Agbedanu, Michael J. Kimber, Paula Ribeiro, Tim A. Day, Mostafa Zamanian
Software Mentions: 2
Published: almost 10 years ago

10.1534/g3.120.401460

Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus
Cited by: 16
Author(s): Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yu‐Tao Xiang, Chaobo Tong, Jinxing Tu, Junyan Huang, Liu S
Software Mentions: 2
Published: about 4 years ago

10.1534/g3.120.401361

Completed Genomic Sequence ofBacillus thuringiensisHER1410 Reveals aCry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage
Cited by: 15
Author(s): Ana Lechuga, Cédric Lood, Margarita Salas, Vera van Noort, Rob Lavigne, Modesto Redrejo-Rodríguez
Software Mentions: 2
Published: about 4 years ago

10.1186/s13071-021-05015-7

Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing
Cited by: 4
Author(s): Yang Gao, Zeyang Suding, Xun Hu, Dandan Liu, Shijie Su, Jing Xu, Junjie Hu, Jianping Tao
Software Mentions: 2
Published: about 3 years ago

10.1186/s13568-017-0490-2

Metagenomic analysis reveals potential interactions in an artificial coculture
Cited by: 8
Author(s): Mei Ren, Guiying Zhang, Zi Ye, Zhixian Qiao, Meili Xie, Yan Lin, Tao Li, Jindong Zhao
Software Mentions: 2
Published: about 7 years ago

10.3390/pathogens9020100

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae
Cited by: 14
Author(s): Evgeny S. Gerasimov, Ksenia A Zamyatnina, Nadezda S Matveeva, Yulia A. Rudenskaya, Natalya Kraeva, Alexander Kolesnikov, Vyacheslav Yurchenko
Software Mentions: 2
Published: almost 5 years ago

10.1093/g3journal/jkaa007

Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains
Cited by: 6
Author(s): Guillermo Vidal-Diez de Ulzurrun, Yi-Yun Lee, Jason E. Stajich, Erich M. Schwarz, Yu-Ting Hsueh
Software Mentions: 2
Published: almost 4 years ago

10.1093/g3journal/jkab209

Transcriptomic and photosynthetic responses to grafting of the Nod1 gene in nodulated and non-nodulated soybeans
Cited by: 2
Author(s): Qingyuan He, Shihua Xiang, Wubin Wang, Yingjie Shu, Zhengpeng Li, Songhua Wang, Lei Chen, Xiao-Yan Yang, Tuanjie Zhao
Software Mentions: 2
Published: over 3 years ago

10.3390/pathogens10060759

Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt
Cited by: 14
Author(s): Aman Ullah Khan, Falk Melzer, Ashraf E. Sayour, Waleed S. Shell, Jörg Linde, Mostafa Y. Abdel-Glil, Sherif Abdel Ghafar Elsayed El-Soally, Mandy C. Elschner, Hossam E. M. Sayour, Eman S. Ramadan, Shereen Aziz Mohamed, Ashraf Hendam, Rania I. Ismail, Lubna F. Farahat, Uwe Roesler, Heinrich Neubauer, Hosny El-Adawy
Software Mentions: 2
Published: over 3 years ago

10.2196/10297

Exploring Genetic Data Across Individuals: Design and Evaluation of a Novel Comparative Report Tool
Cited by: 6
Author(s): Lauren Westendorf, Orit Shaer, Christina Pollalis, Clarissa Verish, Oded Nov, Mad Price Ball
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2164-11-543

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate
Cited by: 126
Author(s): Jon Jerlström-Hultqvist, Oscar Franzén, Johan Ankarklev, Feifei Xu, Eva Nohýnková, Jan O. Andersson, Staffan G. Svärd, Björn Andersson
Software Mentions: 2
Published: about 14 years ago

10.3390/genes9020035

Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress
Cited by: 31
Author(s): Jianxia Liu, Runmei Wang, Wenying Liu, Hongli Zhang, Yi Guo, Rong Wen
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes9020070

Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)
Cited by: 38
Author(s): Hong Yue, Duntao Shu, Meng Wang, Guangwei Xing, Haoshuang Zhan, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes9040185

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
Cited by: 17
Author(s): Sergei Kliver, Mikhail Rayko, Alexey Komissarov, Evgeny Bakin, Daria V. Zhernakova, Kasavajhala V. S. K. Prasad, Catherine A. Rushworth, Ramamurthy Baskar, Dmitry Smetanin, Jeremy Schmutz, Daniel S. Rokhsar, Thomas Mitchell‐Olds, Ueli Grossniklaus, Vladimir Brukhin
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11647

Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum
Cited by: 10
Author(s): Nida Mushtaq, Faiza Munir, Alvina Gul, Rabia Amir, Rehan Zafar Paracha
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.9936

Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L.
Cited by: 7
Author(s): Jingjing Wang, Zhaohai Du, Xuehan Huo, Juan Zhou, Chunmei Yu, Jingxia Zhang, Ao Pan, Xiaoyang Wang, Furong Wang, Jun Zhang
Software Mentions: 2
Published: about 4 years ago

10.3390/genes9110547

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes
Cited by: 32
Author(s): Shuaibin Wang, Qingwei Song, Shanshan Li, Zhigang Hu, Dong Gao, Chi Song, Hongwen Huang, Yifei Liu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-016-2492-x

A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration
Cited by: 16
Author(s): Lakshmi Kuttippurathu, Egle Juskeviciute, Rachael P. Dippold, Jan B. Hoek, Rajanikanth Vadigepalli
Software Mentions: 2
Published: over 8 years ago

10.3390/genes10010071

Genome-Wide Identification and Expression Profiling of Sugar Transporter Protein (STP) Family Genes in Cabbage (Brassica oleracea var. capitata L.) Reveals their Involvement in Clubroot Disease Responses
Cited by: 29
Author(s): Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Li Yu, Hong Wang, Jianbin Li
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes10020081

Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1
Cited by: 7
Author(s): Shagufta Jabeen, Huan Yong Yap, Faez Firdaus Jesse Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung-Chie Tan, Yap S Joo, Dilan Amila Satharasinghe, Abdul Rahman Omar
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes10020131

Evolution and Identification of the WRKY Gene Family in Quinoa (Chenopodium quinoa)
Cited by: 20
Author(s): Hong Yue, Xi Chang, Yongqiang Zhi, Lan Wang, Guangwei Xing, Weining Song, Xiaojun Nie
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes10020119

Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis
Cited by: 27
Author(s): Xianyan Zou, Àiyīng Liú, Zhen Zhang, Qún Gě, Senmiao Fan, Wànkuí Gǒng, Jùnwén Lǐ, Jǔwǔ Gōng, Yùzhēn Shí, Bin Tian, Yanling Wang, Ruixian Liu, Kang Lei, Qi Zhang, Xiao Jiang, Yulong Feng, Shuya Zhang, Tingting Jia, Lipeng Zhang, Yǒulù Yuán, Hǎihóng Shāng
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.10616

Transcriptome analysis reveals the mechanism of improving erect-plant-type peanut yield by single-seeding precision sowing
Cited by: 1
Author(s): Sha Yang, Jialei Zhang, Yi Geng, Zhongwei Tang, Wang Jian-guo, Feng Guo, Jingjing Meng, Quan Wang, Shubo Wan, Xinguo Li
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.6698

The synergistic effect of concatenation in phylogenomics: the case in Pantoea
Cited by: 11
Author(s): Marike Palmer, Stephanus N. Venter, Alistair R. McTaggart, Martin Petrus Albertus Coetzee, Stephanie van Wyk, Juanita R. Avontuur, Chrizelle W. Beukes, Gerda Fourie, Quentin C. Santana, Magriet A. van der Nest, Jochen Blom, Emma Theodora Steenkamp
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10070537

Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development
Cited by: 15
Author(s): Qingyun Li, Huayang Li, Chongyang Yin, Xiaotong Wang, Qing Jiang, Rui Zhang, Fangfang Ge, Yudong Chen, Long Yang
Software Mentions: 2
Published: over 5 years ago

10.3390/genes10100730

Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis
Cited by: 14
Author(s): Ruibin Sun, Shaohui Wang, Dan Ma, Yilin Li, Chuanliang Liu
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.8190

Characterization and expression profiling of the ICE-CBF-COR genes in wheat
Cited by: 36
Author(s): Jie Guo, Yongkang Ren, Zhongwei Tang, Weiping Shi, Meixue Zhou
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-017-3693-7

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa
Cited by: 7
Author(s): Christian Karlsen, Erik Hjerde, Terje Klemetsen, Nils Peder Willassen
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-5342-1

Genome-wide identification of SERK genes in apple and analyses of their role in stress responses and growth
Cited by: 13
Author(s): Liwei Zheng, Junsheng Ma, Jiangping Mao, Shiliang Fan, Dong Zhang, Caiping Zhao, Na An, Mingyu Han
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes11040353

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans
Cited by: 18
Author(s): Haiyan Li, Yuanzheng Yue, Wenjie Ding, Gongwei Chen, Ling Li, Yuli Li, Tingting Shi, Xia Yang
Software Mentions: 2
Published: over 4 years ago

10.3390/genes11050510

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)
Cited by: 17
Author(s): S.-H. Rong, Zhiyang Wu, Zizhang Cheng, Shan Zhang, Huan Liu, Qianming Huang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0101419

Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus
Cited by: 49
Author(s): Grant A. Hill-Cawthorne, Lyndsey O. Hudson, Moataz Abd El Ghany, Olaf Piepenburg, Mridul Nair, Andrew Dodgson, Matthew S. Forrest, Taane G. Clark, Arnab Pain
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-2230-9

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Cited by: 25
Author(s): Kuei Han Lin, Ben-Yang Liao, Hung-Sheng Chang, Shu‐Mei Huang, Ting Yan Chang, Cheng Yu Yang, Yu Bin Wang, Yu Teh Kirk Lin, Yu Wei Wu, Sen Lin Tang, Hongjun Yu
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.9551

Genome-wide identification and expression profiles of ERF subfamily transcription factors inZea mays
Cited by: 16
Author(s): Lidong Hao, Suhua Shi, Haibin Guo, Ming Li, Pan Hu, Yadong Wei, Yuehua Feng
Software Mentions: 2
Published: over 4 years ago

10.3390/genes11091026

Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence
Cited by: 17
Author(s): K N S Usha Kiranmayee, C. Tom Hash, Sivasubramani Selvanayagam, Punna Ramu, BhanuPrakash Amindala, Abhishek Rathore, P. B. Kavi Kishor, Rajeev Gupta, Santosh Deshpande
Software Mentions: 2
Published: about 4 years ago

10.3390/genes11101134

Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance
Cited by: 16
Author(s): Shichao Liu, Ruibin Sun, Xiaojian Zhang, Zili Feng, Feng Wei, Lihong Zhao, Yalin Zhang, Longfu Zhu, Hongjie Feng, Heqin Zhu
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-017-3895-z

Interpreting whole genome and exome sequencing data of individual gastric cancer samples
Cited by: 10
Author(s): Daniela Esser, Niklas Holze, Jill D. Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel, Christoph Röcken
Software Mentions: 2
Published: over 7 years ago

10.1186/s13104-020-05169-0

Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast
Cited by: 12
Author(s): William T. Molin, Allison Yaguchi, Mark Blenner, Christopher A. Saski
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.9328

Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia
Cited by: 15
Author(s): Chunxiao Liu, Xiaoyang Xu, Jialiang Kan, Zong-Ming Cheng, Chang YouHong, Jing Lin, Hui Li
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-019-0611-3

An improved neuroanatomical model of the default-mode network reconciles previous neuroimaging and neuropathological findings
Cited by: 197
Author(s): Pedro Nascimento Alves, Chris Foulon, Vyacheslav Karolis, Danilo Bzdok, Daniel S. Margulies, Emmanuelle Volle
Software Mentions: 2
Published: about 5 years ago

10.3390/genes12030401

A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni
Cited by: 4
Author(s): Isa Schön, Fernando Rodríguez, Matthew Dunn, Koenraad Martens, Michael Shribak, Irina R. Arkhipova
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12040535

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere
Cited by: 6
Author(s): Matthew Chekwube Enebe, Olubukola Oluranti Babalola
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12040608

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles
Cited by: 2
Author(s): Sofia M. Kolchanova, Aleksey Komissarov, Sergei Kliver, Anyi Mazo‐Vargas, Yashira Afanador, Jafet Vélez-Valentín, Ricardo Valentín de la Rosa, Stephanie O Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter Wolfsberger, Taylor Hains, André Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus Peter Koepfli, Tarás K. Oleksyk
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.2516

Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
Cited by: 27
Author(s): Saliha Hammoumi, Tatiana Vallaeys, Ayi Santika, Philippe Leleux, Ewa Borzym, Christophe Klopp, Jean‐Christophe Avarre
Software Mentions: 2
Published: about 8 years ago

10.1186/s12863-015-0249-1

Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci
Cited by: 43
Author(s): Shalabh Dixit, Alexandre Grondin, Cheng‐Ruei Lee, Amelia Henry, Thomas Mitchell-Olds, Arvind Kumar
Software Mentions: 2
Published: over 9 years ago

10.3390/genes12071022

The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics
Cited by: 12
Author(s): Matthew Chekwube Enebe, Olubukola Oluranti Babalola
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.7995

Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt
Cited by: 11
Author(s): Zhanji Liu, Mingchuan Fu, Hao Li, Yizhen Chen, Liguo Wang, Renzhong Liu
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.10617

Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)
Cited by: 3
Author(s): Jie Li, Xinhao Liu, Qingmei Wang, Jianfang Sun, Dexian He
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-021-04056-0

Alvis: a tool for contig and read ALignment VISualisation and chimera detection
Cited by: 9
Author(s): S. J. Martin, Richard M. Leggett
Software Mentions: 2
Published: over 3 years ago

10.1590/1678-4685-GMB-2018-0235

Genome-wide identification and characterization of R2R3-MYB genes in Medicago truncatula
Cited by: 15
Author(s): Wei Li, Ying Liu, Jianfeng Zhao, Xin Zhen, Changhong Guo, Yongjun Shu
Software Mentions: 2
Published: about 5 years ago

10.1590/1678-4685-GMB-2020-0155

Genomic sequencing of two isolates of Ralstonia solanacearum causing Sergipe facies and comparative analysis with Bugtok disease isolates
Cited by: 3
Author(s): Jéssica Rodrigues da Silva, Ana Karolina Leite Pais, Greecy Mirian Rodrigues Albuquerque, Adriano Márcio Freire Silva, Wilson José Silva, Valdir de Queiroz Balbino, M. E. N. Fonseca, Marco Aurélio Siqueira da Gama, Elineide Barbosa de Souza, Rosa de Lima Ramos Mariano
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12711-021-00657-8

Long-range linkage disequilibrium in French beef cattle breeds
Cited by: 7
Author(s): Abdelmajid El Hou, Dominique Rocha, Eric Venot, Véronique Blanquet, Romain Philippe
Software Mentions: 2
Published: over 3 years ago

10.1534/genetics.117.300546

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population
Cited by: 36
Author(s): Boby Mathew, Jens Léon, Wiebke Sannemann, Mikko J. Sillanpää
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.10878

Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation
Cited by: 2
Author(s): Mengyao Li, Qi He, Ying Huang, Yunbo Luo, Yong Zhang, Yan Wang, Yuanxiu Lin, Yunting Zhang, Zejing Liu, Xiaorong Wang, Haoru Tang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-1148-9

IGDD: a database of intronless genes in dicots
Cited by: 21
Author(s): Hanwei Yan, Xiaogang Dai, Kai Feng, Qiuyue Ma, Tongming Yin
Software Mentions: 2
Published: over 8 years ago

10.1128/genomeA.00802-14

Whole-Genome Sequences of Three Symbiotic Endozoicomonas Strains
Cited by: 52
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-14-297

Genome-wide analysis of the GH3 family in apple (Malus × domestica)
Cited by: 65
Author(s): Hao Yuan, Kai Zhao, Hengjiu Lei, Xinjie Shen, Yun Liu, Xiudong Liao, Tianhong Li
Software Mentions: 2
Published: over 11 years ago

10.7717/peerj.7950

Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)
Cited by: 22
Author(s): Yongbin Wang, Lei Ling, Zhenfeng Jiang, Weiwei Tan, Zhaojun Liu, Liang Wu, Youbing Zhao, Shanyong Xia, Jun Ma, Guangjin Wang, Wenbin Li
Software Mentions: 2
Published: almost 5 years ago

10.7717/peerj.10014

Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
Cited by: 10
Author(s): Youmei Huang, Qing Liu, Man Zhang, Mengnan Chai, Qing-Yu He, Bello Hassan Jakada, Fangqian Chen, Huihuang Chen, Xingyue Jin, Hanyang Cai, Yuan Qin
Software Mentions: 2
Published: about 4 years ago

10.1186/gb-2009-10-9-r94

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Cited by: 141
Author(s): Scott DiGuistini, Nancy Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K. Chan, T. Roderick Docking, İnanç Birol, Robert A. Holt, Martin Hirst, Elaine R. Mardis, Marco A. Marra, Richard Hamelin, Jörg Bohlmann, Colette Breuil, Steven J.M. Jones
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12864-015-2138-4

Integrated genomics approach to identify biologically relevant alterations in fewer samples
Cited by: 8
Author(s): Pratik Chandrani, Pawan Upadhyay, Prajish Iyer, Mayur Tanna, Madhur Shetty, Gorantala Venkata Raghuram, Ninad Oak, Ankita Singh, Rohan Chaubal, Manoj P. Ramteke, Sudeep Gupta, Amit Dutt
Software Mentions: 2
Published: about 9 years ago

10.1186/gb-2010-11-10-r104

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Cited by: 141
Author(s): Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stéphane Terry, David Z. Chen, Joel Rozowsky, Ashutosh Tewari, Naoki Kitabayashi, Benjamin Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark Gerstein
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-13-505

Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma
Cited by: 31
Author(s): Jared J. Gartner, Sean Davis, Xiaomu Wei, Jimmy C. Lin, Niraj Trivedi, Jamie K. Teer, Paul S. Meltzer, Steven A. Rosenberg, Yardena Samuels
Software Mentions: 2
Published: about 12 years ago

10.1186/gb-2011-12-10-r103

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Cited by: 176
Author(s): Wigard P. Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S.P. Vermaat, Markus J. van Roosmalen, Stef van Lieshout, Isaäc J Nijman, Wijnand M. Roessingh, Ruben van ‘t Slot, José van de Belt, Victor Guryev, Marco J. Koudijs, Emile E. Voest, Edwin Cuppen
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-019-6146-7

DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
Cited by: 15
Author(s): Haoling Huang, Ping Wu, Shaolun Zhang, Qi Shang, Haotong Yin, Qirui Hou, Jinbo Zhong, Xijie Guo
Software Mentions: 2
Published: about 5 years ago

10.1186/gb-2013-14-11-r129

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2014-15-2-r40

Genome-wide discovery and characterization of maize long non-coding RNAs
Cited by: 385
Author(s): Liang-In Lin, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng‐Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Evans Mulenga, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C.P. Timmermans, Nathan M. Springer, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 11 years ago

10.1186/gb-2013-14-6-r64

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Cited by: 45
Author(s): Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Frédéric Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M. Martis, Klaus Mayer, Abraham B. Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-014-0415-1

Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops
Cited by: 81
Author(s): Ke Cao, Zhijun Zheng, Lirong Wang, Xin Liu, Guoqiang Zhu, Weichao Fang, Shifeng Cheng, Peng Zeng, Chang Wen Chen, Xinwei Wang, Min Xie, Xiao Bo Zhong, Xiaoli Wang, Pei Zhao, Chao Bian, Yuxia Zhu, Jiahui Zhang, MA Guo-sheng, Chengxuan Chen, Yanjun Li, Fengge Hao, Yong Li, Guodong Huang, Yuxiang Li, Haiyan Li, Jian Guo, Xun Xu, Jun Wang
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-014-0408-0

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
Cited by: 159
Author(s): Shaoke Lou, Heung‐Man Lee, Hao Qin, Jing‐Woei Li, Zhibo Gao, Xin Liu, Landon L. Chan, Vincent K. Lam, Wing‐Yee So, Ying Wang, Si Lok, Jun Wang, Ronald Cw, Stephen Kwok‐Wing Tsui, Juliana C.N. Chan, Ting-Fung Chan, Kevin Y. Yip
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-015-0648-7

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
Cited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-015-0849-0

Circlator: automated circularization of genome assemblies using long sequencing reads
Cited by: 715
Author(s): Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-016-0948-6

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
Cited by: 55
Author(s): Alice M. Walsh, John W. Whitaker, Chaohua Huang, Yauheniya Cherkas, S. Lamberth, Carrie Brodmerkel, Mark Curran, Radu Dobrin
Software Mentions: 2
Published: over 8 years ago

10.1186/s12870-014-0281-8

Non-specific lipid transfer proteins in maize
Cited by: 68
Author(s): Kaifa Wei, Xiaojun Zhong
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-016-1080-3

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes
Cited by: 35
Author(s): Anthony J. Studer, James C. Schnable, S. Weissmann, Allison R. Kolbe, Michael R. McKain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-018-4974-5

Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period
Cited by: 37
Author(s): Bing Yang, Beilei Jiao, Wei Ge, Xiaolan Zhang, Shanhe Wang, Hang Zhao, Xin Wang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0223441

Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content
Cited by: 14
Author(s): Saminathan Subburaj, Kayoun Lee, Yongsam Jeon, Luhua Tu, Gilwoo Son, SuBok Choi, Yong-Pyo Lim, Cecilia McGregor, Geung–Joo Lee
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.7528

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
Cited by: 8
Author(s): Jianzhou Qu, Shutu Xu, Xiaokang Tian, Ting Li, Licheng Wang, Yuyue Zhong, Jiquan Xue, Dongwei Guo
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-019-1724-1

Genomics and data science: an application within an umbrella
Cited by: 42
Author(s): Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Software Mentions: 2
Published: over 5 years ago

10.1186/s40169-017-0174-1

Post‐zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia
Cited by: 11
Author(s): Christina A Castellani, M.G. Melka, Jane L. Gui, Anthony J. Gallo, Richard O’Reilly, Shiva M. Singh
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13601-020-00345-8

Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma
Cited by: 29
Author(s): Chengjie Huang, Yaling Yu, Wei Du, Yahui Liu, Ranran Dai, Wei Tang, Ping Wang, Chenhong Zhang, Guochao Shi
Software Mentions: 2
Published: about 4 years ago

10.1186/s12870-019-1944-2

Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition
Cited by: 21
Author(s): Ying Wang, Zeyang Xiong, Qian Li, Yueyang Sun, Jing Jin, Hao Chen, Yu Zeng, Xingguo Huang, Yi Ding
Software Mentions: 2
Published: over 5 years ago

Projects: pypi: Circos

Papers Mentioning Circos 2,252