Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: Circos

https://packages.ecosyste.ms/registries/pypi.org/packages/Circos

Circos plots in Python!
10 versions
Latest release: about 1 year ago
55 downloads last month

Papers Mentioning Circos 2,252

10.1007/s00122-016-2762-7
High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat
Cited by: 51
Author(s): Huihuang Yan, Wubishet A. Bekele, Charlene P. Wight, Yuanying Peng, Tim Langdon, Robert G. Latta, Yong‐Bi Fu, Axel Diederichsen, Catherine Howarth, Eric N. Jellen, Brian Boyle, Yuming Wei, Nicholas A. Tinker
Software Mentions: 3
Published: over 8 years ago
10.1007/s00122-019-03517-8
Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
Cited by: 22
Author(s): Beatrice Corsi, Lawrence Percival‐Alwyn, Rowena Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram
Software Mentions: 3
Published: almost 5 years ago
10.7150/thno.53737
Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-021-88029-6
Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-021-89146-y
Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-015-1959-5
Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 9 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 3 years ago
10.1038/s41598-020-69389-x
A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Cited by: 22
Author(s): Honghao Lv, Yong Wang, Fengqing Han, Jialei Ji, Zhiyuan Fang, Mu Zhuang, Zhansheng Li, Yangyong Zhang, Limei Yang
Software Mentions: 3
Published: over 4 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 4 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 8 years ago
10.1038/s41598-019-54720-y
Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity
Cited by: 7
Author(s): C. K. Sruthi, Meher K. Prakash
Software Mentions: 3
Published: almost 5 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 5 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 5 years ago
10.1038/s41598-019-52139-z
8-OxoG in GC-rich Sp1 binding sites enhances gene transcription in adipose tissue of juvenile mice
Cited by: 6
Author(s): Jong Woo Park, Young In Han, Sung Woo Kim, Tae Min Kim, Su Cheong Yeom, Jaeku Kang, Joonghoon Park
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-019-53469-8
Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)
Cited by: 6
Author(s): Xinhua Wang, Haiyang Liu, Maolin Pang, Bishi Fu, Xin Yu, Shunping He, Jingou Tong
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-019-50624-z
Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants
Cited by: 66
Author(s): Hailemariam Abrha Assress, Ramganesh Selvarajan, Hlengilizwe Nyoni, Khayalethu Ntushelo, Bhekie B. Mamba, Titus A.M. Msagati
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-018-36059-y
Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-018-37792-0
Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: almost 6 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 3 years ago
10.1371/journal.pbio.2003769
Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Cited by: 88
Author(s): Eleni Gentekaki, Bruce A. Curtis, Courtney W. Stairs, Vladimír Klimeš, Marek Eliáš, Dayana E. Salas‐Leiva, Emily K. Herman, Laura Eme, María Cecilia Arias, Bernard Henrissat, Frédérique Hilliou, Mary J. Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolísko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger
Software Mentions: 3
Published: about 7 years ago
10.1038/s41598-019-39286-z
Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)
Cited by: 41
Author(s): Dahe Qiao, Chun Yang, Juan Chen, Yan Guo, Yán Li, Suzhen Niu, Kemei Cao, Zhengwu Chen
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-019-5485-8
The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
Cited by: 51
Author(s): Rick E. Masonbrink, Tom Maier, Usha Muppirala, Arun S. Seetharam, Étienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nia Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves‐van den Akker, Matthew E. Hudson, Andrew J. Severin, Thomas J. Baum
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-018-33744-w
Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube
Cited by: 42
Author(s): Zhijun Zhong, Xingang Li
Software Mentions: 3
Published: about 6 years ago
10.1186/s12864-018-5041-y
Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)
Cited by: 30
Author(s): Chongjing Xia, Meinan Wang, Chuntao Yin, Omar E. Cornejo, Scot H. Hulbert, X. M. Chen
Software Mentions: 3
Published: about 6 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: almost 11 years ago
10.1038/s41598-018-23334-1
Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 6 years ago
10.1111/tpj.14115
High intraspecific diversity of <i>Restorer‐of‐fertility‐like</i> genes in barley
Cited by: 21
Author(s): Joanna Melonek, Ruonan Zhou, Philipp E. Bayer, David Edwards, Nils Stein, Ian Small
Software Mentions: 3
Published: about 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: about 5 years ago
10.1038/s41598-018-28299-9
Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 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 6 years ago
10.1038/s41598-018-22237-5
Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Cited by: 13
Author(s): Álvaro Chiner‐Oms, Fernando Gónzález-Candelas, Iñaki Comas
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: over 4 years ago
10.1111/tpj.12600
The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression
Cited by: 31
Author(s): Katie Baker, Micha Bayer, Nicola Cook, Steven Dreißig, Taniya Dhillon, Joanne Russell, Pete E. Hedley, Jenny Morris, Luke Ramsay, Isabelle Colas, Robbie Waugh, Brian J. Steffenson, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell
Software Mentions: 3
Published: over 10 years ago
10.1038/s41598-018-30583-7
The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: over 6 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 5 years ago
10.1186/s12864-016-3336-4
The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance
Cited by: 53
Author(s): William T. Molin, Alice A. Wright, Amy Lawton‐Rauh, Christopher Saski
Software Mentions: 3
Published: almost 8 years ago
10.1111/pbi.12940
Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor <i>Triticum dicoccoides</i>
Cited by: 27
Author(s): Bala Anı Akpınar, Sezgi Biyiklioglu, Burcu Alptekin, M. Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernández, Hikmet Budak
Software Mentions: 3
Published: over 6 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 4 years ago
10.1038/s41438-020-0269-5
A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Cited by: 9
Author(s): Ting Xue, Xinqing Zheng, Duo Chen, Limin Liang, Nan Chen, Zhen Huang, Wenfang Fan, Jiannan Chen, Chengsong Wan, Shuai Chen, Jinmao Zhu, Binghua Chen, Xingtan Zhang, Youqiang Chen
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-017-17484-x
Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals
Cited by: 109
Author(s): Christian Cr Voolstra, Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean‐François Flot, Sylvie Tambutté, Denis Allemand, Manuel Aranda
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-017-17203-6
Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 7 years ago
10.1093/gigascience/giab020
A chromosome-level genome assembly for the Pacific oyster <i>Crassostrea gigas</i>
Cited by: 70
Author(s): Carolina Peñaloza, Alejandro P. Gutiérrez, Lél Eöry, Shan Wang, Ximing Guo, Alan Archibald, Tim P. Bean, Ross D. Houston
Software Mentions: 3
Published: over 3 years ago
10.1186/s12920-017-0245-6
Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer
Cited by: 17
Author(s): Shirley Pepke, Greg Ver Steeg
Software Mentions: 3
Published: over 7 years ago
10.1186/s13099-016-0084-6
Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient
Cited by: 2
Author(s): Min Jung Kwak, Myoung Soo Kim, Soon Kyeong Kwon, Seung Hak Cho, Jihyun F. Kim
Software Mentions: 3
Published: over 8 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 9 years ago
10.1186/s12864-016-2736-9
Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family
Cited by: 42
Author(s): Fengya Zheng, Haiyang Wu, Rongzhi Zhang, Shiming Li, Weiming He, Fuk‐Ling Wong, Genying Li, Shancen Zhao, Hon‐Ming Lam
Software Mentions: 3
Published: over 8 years ago
10.1038/s41598-018-20862-8
Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-018-31770-2
Characterisation and functional predictions of canine long non-coding RNAs
Cited by: 24
Author(s): Céline Le Béguec, Valentin Wucher, Laëtitia Lagoutte, Édouard Cadieu, Nadine Botherel, Benoît. Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte
Software Mentions: 3
Published: about 6 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 6 years ago
10.7717/peerj.8359
A novel computational approach to the silencing of <i>Sugarcane Bacilliform Guadeloupe A Virus</i> determines potential host-derived MicroRNAs in sugarcane (<i>Saccharum officinarum</i> L.)
Cited by: 10
Author(s): Fakiha Ashraf, Muhammad Aleem Ashraf, Xiaowen Hu, Shuzhen Zhang
Software Mentions: 3
Published: almost 5 years ago
10.1016/j.gpb.2018.06.002
5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer
Cited by: 51
Author(s): Ji Zhang, Xiao Han, Chun-Chun Gao, Yurong Xing, Qi Zheng, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Ying Yang, Xiangnan Li, Bao‐Fa Sun, Xin Tian
Software Mentions: 3
Published: over 6 years ago
10.1093/gbe/evaa063
An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)
Cited by: 23
Author(s): W. Brian Simison, James F. Parham, Theodore J. Papenfuss, Athena Lam, James Henderson
Software Mentions: 3
Published: over 4 years ago
10.1186/s13073-015-0127-5
Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations
Cited by: 6
Author(s): Ankit Malhotra, Yong Wang, Jill Waters, Ken Chen, Funda Meric‐Bernstam, Ira M. Hall, Nicholas E. Navin
Software Mentions: 3
Published: almost 10 years ago
10.1016/j.gpb.2018.10.004
C: Consensus Cancer Driver Gene Caller
Cited by: 2
Author(s): Chenyu Zhu, Chi Zhou, Yun-Qin Chen, Albert Yuh-Jer Shen, Zong-Ming Guo, Zhaoyi Yang, Xiangyun Ye, Shen Qu, Jia Wei, Qi Liu
Software Mentions: 3
Published: over 5 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: almost 10 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 7 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 7 years ago
10.1186/s12864-019-6416-4
Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line
Cited by: 10
Author(s): Shumin Zhou, Jinpeng Zhang, Hongyu Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li, Lihui Li
Software Mentions: 3
Published: almost 5 years ago
10.1093/gbe/evt189
The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution
Cited by: 27
Author(s): Bram Verhelst, Yves Van de Peer, Pierre Rouzé
Software Mentions: 3
Published: about 11 years ago
10.1093/gbe/evz048
A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes
Cited by: 40
Author(s): Yann Dussert, Isabelle D. Mazet, Carole Couture, Jérôme Gouzy, Marie-Christine Piron, Claire Kuchly, Olivier Bouchez, Claude Rispe, Pere Mestre, François Delmotte
Software Mentions: 3
Published: over 5 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 5 years ago
10.1186/s13059-018-1552-8
Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Cited by: 56
Author(s): Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David J. Miller
Software Mentions: 3
Published: about 6 years ago
10.1186/s13059-019-1631-5
Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication
Cited by: 37
Author(s): Xutong Wang, Liyang Chen, Jianxin Ma
Software Mentions: 3
Published: almost 6 years ago
10.1186/s13059-015-0837-4
Genomic legacy of the African cheetah, Acinonyx jubatus
Cited by: 159
Author(s): Pavel Dobrynin, Shi Ping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergei Kliver, Anne Schmidt‐Küntzel, Klaus‐Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel García-Pérez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alex Makunin, Vladimir Brukhin, Wei‐Lin Qiu, Long Zhang, Fang Li, Jine Yi, Carlos A. Driscoll, Agostinho Antunes, Tarás K. Oleksyk, Eduardo Eizirik, Polina L. Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomàs Marquès‐Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O’Brien
Software Mentions: 3
Published: almost 9 years ago
10.1186/gb-2014-15-2-r39
Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Cited by: 226
Author(s): Linhai Wang, Shanlin Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Liu S, Rajeev K. Varshney, Jun Wang, Xiurong Zhang
Software Mentions: 3
Published: almost 11 years ago
10.1186/s12859-017-1653-5
ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 7 years ago
10.3390/genes12030417
Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)
Cited by: 9
Author(s): Fulei Mo, Nian Zhang, Yefeng Qiu, Lingjun Meng, Mozhen Cheng, Jiayin Liu, Lanning Yao, Rui Lv, Yuxin Liu, Yao Zhang, Xiuling Chen, Aoxue Wang
Software Mentions: 3
Published: over 3 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: almost 10 years ago
10.3390/genes12050784
Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 3 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 4 years ago
10.1093/g3journal/jkab002
<i>De novo</i>whole-genome assembly and resequencing resources for the roan (<i>Hippotragus equinus</i>), an iconic African antelope
Cited by: 4
Author(s): Margarida Gonçalves, Hans R. Siegismund, Bettine Jansen van Vuuren, Klaus‐Peter Koepfli, Nathalie Ferrand, Raquel Godinho
Software Mentions: 3
Published: almost 4 years ago
10.1186/gb-2012-13-8-r74
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 13 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 7 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: almost 5 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 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: over 3 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: almost 4 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: over 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: almost 6 years ago
10.1186/s12864-016-2967-9
Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection
Cited by: 44
Author(s): Stanford Kwenda, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: over 8 years ago
10.1186/s12864-019-6404-8
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis
Cited by: 0
Author(s): Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao‐Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung‐Yen Lin
Software Mentions: 3
Published: over 4 years ago
10.3389/fmicb.2021.674952
Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals
Cited by: 19
Author(s): Syed Mashab Ali Shah, Moein Khojasteh, Qi Wang, S. Mohsen Taghavi, Zhi-Hong Xu, Pejman Khodaygan, Lifang Zou, Sedighe Mohammadikhah, Gongyou Chen, Ebrahim Osdaghi
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2016.00941
Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 8 years ago
10.1534/g3.115.026666
The <i>HIST1</i> Locus Escapes Reprogramming in Cloned Bovine Embryos
Cited by: 5
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Kyuheum Jeon, Yong‐Kook Kang
Software Mentions: 3
Published: over 8 years ago
10.3389/fmicb.2018.02668
Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
Cited by: 41
Author(s): Philippe Colson, Anthony Levasseur, Bernard La Scola, Vikas Sharma, Arshan Nasir, Pierre Pontarotti, Gustavo Caetano‐Anollés, Didier Raoult
Software Mentions: 3
Published: almost 6 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 4 years ago
10.3389/fmicb.2021.682356
Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH
Cited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2017.01448
PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Cited by: 33
Author(s): Jade L. L. Teng, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Samson S. Y. Wong, Pak C. Sham, Susanna K. P. Lau, Patrick C. Y. Woo
Software Mentions: 3
Published: over 7 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: about 7 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: almost 7 years ago
10.3389/fmicb.2020.01930
New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: over 4 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: almost 12 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: over 4 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 6 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 4 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: almost 10 years ago
10.3389/fmicb.2020.01142
Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover
Cited by: 10
Author(s): Hongmiao Wu, Jinshen Xia, Xianjin Qin, Huiming Wu, Shengkai Zhang, Yanlin Zhao, Christopher Rensing, Wenxiong Lin
Software Mentions: 3
Published: over 4 years ago
10.1186/s12864-015-2233-6
Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress
Cited by: 66
Author(s): Xiaosan Huang, Kongqing Li, Xiaogang Xu, Zhenghong Yao, Can Jin, Shaoling Zhang
Software Mentions: 3
Published: almost 9 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 6 years ago
10.3389/fmicb.2019.01325
Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Cited by: 29
Author(s): Aniela B. Mundinger, Christopher E. Lawson, Mike S. M. Jetten, Hanna Koch, Sebastian Lücker
Software Mentions: 3
Published: over 5 years ago