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

10.1371/journal.ppat.1009886
A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road
Cited by: 7
Author(s): Xutong Wu, Chao Ning, Felix M. Key, Aida Andrades Valtueña, Aditya Kumar Lankapalli, Shizhu Gao, Yang Xuan, Fan Zhang, Linlin Liu, Zhongzhi Nie, Jian Ma, Johannes Krause, Alexander Herbig, Yinqiu Cui
Software Mentions: 2
Published: about 3 years ago
10.3389/fpls.2016.01874
Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri)
Cited by: 57
Author(s): Yunpeng Cao, Yuepeng Han, Dong Meng, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
Software Mentions: 2
Published: almost 8 years ago
10.1186/1742-4690-11-17
Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB
Cited by: 35
Author(s): Matthew S. Dahabieh, Marcel Ooms, Chanson J. Brumme, Jeremy M. G. Taylor, P. Richard Harrigan, Viviana Simon, Ivan Sadowski
Software Mentions: 2
Published: almost 11 years ago
10.1186/1742-4690-10-126
Functional conservation of HIV-1 Gag: implications for rational drug design
Cited by: 56
Author(s): Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 2
Published: about 11 years ago
10.1186/s12284-019-0270-5
Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection
Cited by: 8
Author(s): Zhenhui Zhong, Lian‐Yu Lin, Meilian Chen, Lili Lin, Xiaofeng Chen, Yunzhi Lin, Xi Chen, Zonghua Wang, Justice Norvienyeku, Huakun Zheng
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0059620
Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms
Cited by: 51
Author(s): Chao Shi, Yuan Liu, Hui Huang, Enhua Xia, Haibin Zhang, Li‐Zhi Gao
Software Mentions: 2
Published: over 11 years ago
10.1126/sciadv.abh3032
Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies
Cited by: 26
Author(s): Namshik Han, Woochang Hwang, Konstantinos Tzelepis, Patrick Schmerer, Eliza Yankova, Méabh MacMahon, Winnie Lei, Nicholas M Katritsis, Anika Liu, Ulrike Felgenhauer, Alison Schuldt, Robert G. Harris, Kathryn Chapman, Frank McCaughan, Friedemann Weber, Tony Kouzarides
Software Mentions: 2
Published: over 3 years ago
10.1038/sdata.2015.72
Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus
Cited by: 50
Author(s): Thomas Schmutzer, Birgit Samans, Emmanuelle Dyrszka, Chris Ulpinnis, Stéphan Weise, Doreen Stengel, Christian Colmsee, Denis Lespinasse, Zeljko Micic, Stefan Abel, Peter Duchscherer, Frank Breuer, Amine Abbadi, Gunhild Leckband, Rod J. Snowdon, Uwe Scholz
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpls.2018.00976
FNBtools: A Software to Identify Homozygous Lesions in Deletion Mutant Populations
Cited by: 8
Author(s): Liang Sun, Yinbing Ge, Andrew Charles Bancroft, Xiaofei Cheng, Jiangqi Wen
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0074132
Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates
Cited by: 25
Author(s): Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0170181
Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue
Cited by: 12
Author(s): Alejandro Quiroz-Zárate, Benjamin J. Harshfield, Rong Hu, Nicholas W. Knoblauch, Andrew H. Beck, Susan E. Hankinson, Vincent J. Carey, Rulla M. Tamimi, David J. Hunter, John Quackenbush, Aditi Hazra
Software Mentions: 2
Published: almost 8 years ago
10.3389/fpubh.2021.633792
Evolutionary Analysis of Pre-S/S Mutations in HBeAg-Negative Chronic Hepatitis B With HBsAg < 100 IU/ml
Cited by: 3
Author(s): Yongdong Wu, Zhiqiang Zhu, Jiang Wu, Wenzi Bi, Wei Xu, Xiaoping Xia, Dongsheng Han
Software Mentions: 2
Published: over 3 years ago
10.1038/srep14941
Profiling RNA editing in human tissues: towards the inosinome Atlas
Cited by: 187
Author(s): Ernesto Picardi, Caterina Manzari, Francesca Mastropasqua, Italia Aiello, Anna Maria D’Erchia, Graziano Pesole
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0090391
Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression
Cited by: 14
Author(s): Avinash M. Veerappa, Megha Murthy N, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Raviraj V. Suresh, Somanna Ajjamada Nachappa, Nelchi Prashali, Sangeetha Nuggehalli Yadav, Manjula Arsikere Srikanta, Dinesh S. Manjegowda, Keshava B. Seshachalam, Nallur B. Ramachandra
Software Mentions: 2
Published: over 10 years ago
10.1038/srep15443
Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: about 9 years ago
10.3389/fvets.2021.625609
Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3
Cited by: 1
Author(s): Jiao Hu, Xuehong Shuai, Yichen Luo, Zhixiong Zhou, Yu Zhao, Bowen Li, Guojing Gu, Wenjie Li, Mengjuan Li, Hui Zeng, Xi Guo, Yinlong Xiao, Zhenhui Song, Ling Gan, Qingzhou Huang
Software Mentions: 2
Published: over 3 years ago
10.1038/srep18227
MycoCAP - Mycobacterium Comparative Analysis Platform
Cited by: 4
Author(s): Siew Woh Choo, Mia Yang Ang, Avirup Dutta, Shi Tan, Cheuk Chuen Siow, Hamed Heydari, Naresh V.R. Mutha, Wei Yee Wee, George T.F. Wong
Software Mentions: 2
Published: almost 9 years ago
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
10.1371/journal.pone.0099069
Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry
Cited by: 33
Author(s): Osama Alsmadi, Sumi Elsa John, Gaurav Thareja, Prashantha Hebbar, Dinu Antony, Kazem Behbehani, Thangavel Alphonse Thanaraj
Software Mentions: 2
Published: over 10 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 <i>Saccharomyces carlsbergensis</i>, 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
10.1038/srep20650
Feature co-localization landscape of the human genome
Cited by: 11
Author(s): Siu-Kin Ng, Taobo Hu, Xi Long, Colin Chan, Suk Ying Tsang, Hong Xue
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0192898
Identification of fungi in shotgun metagenomics datasets
Cited by: 66
Author(s): Paul D. Donovan, Gabriel González, Desmond G. Higgins, Geraldine Butler, Kimihito Ito
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0194071
Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA
Cited by: 20
Author(s): Xiaofen Zhang, Guoyun Wang, Bin Chen, Heshan Du, Fenglan Zhang, Haiying Zhang, Qian Wang, Sansheng Geng
Software Mentions: 2
Published: over 6 years ago
10.1038/srep24501
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts
Cited by: 84
Author(s): Chao Bian, Yinchang Hu, Vydianathan Ravi, Irina M. Kuznetsova, Xueyan Shen, Xuemei Mu, Yu Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey Komissarov, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Jingjing Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Donghong Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojie Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gaosi Xu, Pao Xu, Junmin Xu, Stephen J. O’Brien, László Orbán, Byrappa Venkatesh, Qiong Shi
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0037919
Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
Cited by: 315
Author(s): Bo Liu, Lina L. Faller, Niels Klitgord, Varun Mazumdar, Mohammad Ghodsi, Daniel Sommer, Theodore Gibbons, Todd J. Treangen, Ya-Pei Chang, Shan Li, O. Colin Stine, Hatice Hastürk, Simon Kasif, Daniel Segrè, Mihai Pop, Salomon Amar
Software Mentions: 2
Published: over 12 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
10.1371/journal.pone.0121052
Genomic Characterization of Burkholderia pseudomallei Isolates Selected for Medical Countermeasures Testing: Comparative Genomics Associated with Differential Virulence
Cited by: 23
Author(s): Jason W. Sahl, Christopher John Allender, Rebecca E. Colman, Katy J. Califf, James M. Schupp, Bart J. Currie, Kristopher E. Van Zandt, H. Carl Gelhaus, Paul Keim, Apichai Tuanyok
Software Mentions: 2
Published: over 9 years ago
10.1038/srep29017
Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry
Cited by: 64
Author(s): Charles Hawkins, Julie Caruana, Erin Schiksnis, Zhongchi Liu
Software Mentions: 2
Published: over 8 years ago
10.1038/srep30158
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features
Cited by: 28
Author(s): Songtao Gui, Zhihua Wu, Hongyuan Zhang, Yinzhen Zheng, Zhixuan Zhu, Dequan Liang, Yi Ding
Software Mentions: 2
Published: over 8 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
10.1038/srep30135
Full transcription of the chloroplast genome in photosynthetic eukaryotes
Cited by: 46
Author(s): Chao Shi, Shuo Wang, Enhua Xia, Jianjun Jiang, Fan-Chun Zeng, Li‐Zhi Gao
Software Mentions: 2
Published: over 8 years ago
10.1038/srep31209
Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: over 8 years ago
10.1038/srep32013
Evolutionary and Expression Analysis Provides Evidence for the Plant Glutamate-like Receptors Family is Involved in Woody Growth-related Function
Cited by: 13
Author(s): Jianqing Chen, Yinghui Jing, Xinyue Zhang, Leiting Li, Peng Wang, Shaoling Zhang, Hongsheng Zhou, Juyou Wu
Software Mentions: 2
Published: over 8 years ago
10.1038/srep28594
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Cited by: 91
Author(s): Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu‐Chien, Minami Matsui
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0139328
Exome Capture with Heterologous Enrichment in Pig (Sus scrofa)
Cited by: 1
Author(s): Denis Guiatti, Elena Pomari, Slobodanka Radović, Alessandro Spadotto, Bruno Stefanon
Software Mentions: 2
Published: about 9 years ago
10.1038/srep32598
Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)
Cited by: 2
Author(s): Xu Zhang, Zhilin Qu, Bing Su
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0109920
Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)
Cited by: 91
Author(s): Mehanathan Muthamilarasan, Rohit Khandelwal, Chandra Bhan Yadav, Venkata Suresh Bonthala, Yusuf Khan, Manoj Prasad
Software Mentions: 2
Published: about 10 years ago
10.1038/srep40579
Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts
Cited by: 160
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0252390
Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer
Cited by: 3
Author(s): Tommaso Grassi, Frances Harris, James B. Smadbeck, Stephen J. Murphy, Matthew S. Block, Francesco Multinu, Janet L. Schaefer Klein, Piyan Zhang, Giannoula Karagouga, Minetta C. Liu, Alyssa Larish, Maureen A. Lemens, Marla Kay S. Sommerfield, Serena Cappuccio, John C. Cheville, George Vasmatzis, Andrea Mariani
Software Mentions: 2
Published: over 3 years ago
10.1038/srep41124
Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)
Cited by: 49
Author(s): Kazuki Mori, Kenta Shirasawa, Hitoshi Nogata, Chiharu Hirata, Kosuke Tashiro, Toshiyuki Habu, Sangwan Kim, Shuichi Himeno, Satoru Kuhara, Hiroyasu Ikegami
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0195974
Genome-wide analysis of basic helix-loop-helix superfamily members in peach
Cited by: 34
Author(s): Chunhua Zhang, Ruchao Feng, Ruijuan Ma, Zhijun Shen, Zeyu Cai, Zhizhong Song, Bin Peng, Mingliang Yu
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0188105
Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment
Cited by: 36
Author(s): Viju Vijayan Pillai, Darren Weber, Brett S. Phinney, Vimal Selvaraj
Software Mentions: 2
Published: about 7 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
10.1038/s41598-017-01446-4
Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment
Cited by: 38
Author(s): Hongwei Fang, Yishan Chen, Lei Huang, Guojian He
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.119.400262
Developing a High-Quality Linkage Map for the Atlantic Killifish<i>Fundulus heteroclitus</i>
Cited by: 10
Author(s): Jeffrey T. Miller, Noah M. Reid, Diane Nacci, Andrew Whitehead
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0075485
Genome Aberrations in Canine Mammary Carcinomas and Their Detection in Cell-Free Plasma DNA
Cited by: 45
Author(s): Julia Beck, Silvia Hennecke, Kirsten Bornemann-Kolatzki, Howard B. Urnovitz, Stephan Neumann, Philipp Ströbel, Franz‐Josef Kaup, Bertram Brenig, Ekkehard Schütz
Software Mentions: 2
Published: about 11 years ago
10.1038/s41598-017-03445-x
Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors
Cited by: 26
Author(s): Ramon M. Eichenberger, Chandra Ramakrishnan, Giancarlo Russo, Peter Deplazes, Adrian B. Hehl
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-03923-2
Nitric oxide mediated transcriptional modulation enhances plant adaptive responses to arsenic stress
Cited by: 82
Author(s): Pradyumna Kumar Singh, Yuvraj Indoliya, Abhisekh Singh Chauhan, Surendra Singh, Amit Singh, Sanjay Dwivedi, Rudra Deo Tripathi, Debasis Chakrabarty
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-05312-1
Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber
Cited by: 44
Author(s): Gang Yang, Mo Peng, Xiangli Tian, Shuanglin Dong
Software Mentions: 2
Published: over 7 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 <i>Brassica napus</i>
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
10.1038/s41598-017-07039-5
Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence
Cited by: 22
Author(s): Satoshi Sugimura, Norio Kobayashi, Hiroaki Okae, T. Yamanouchi, Hideo Matsuda, Tatsuhiro Kojima, Akira Yajima, Y. Hashiyada, Masahiro Kaneda, Kei Sato, Kyoichi Imai, Kentaro Tanemura, Takahiro Arima, Robert B. Gilchrist
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-08256-8
Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification
Cited by: 22
Author(s): Jianjian Lv, Bingbo Gao, Ping Liu, Jian Li, Xianliang Meng
Software Mentions: 2
Published: over 7 years ago
10.1534/g3.120.401361
Completed Genomic Sequence of<i>Bacillus thuringiensis</i>HER1410 Reveals a<i>Cry</i>-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
10.1038/s41598-017-11466-9
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
Cited by: 19
Author(s): Lior David, Xavier Grau‐Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0121846
Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes
Cited by: 6
Author(s): Avinash M. Veerappa, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Megha Murthy, Raviraj V. Suresh, Dinesh S. Manjegowda, Nallur B. Ramachandra
Software Mentions: 2
Published: over 9 years ago
10.1093/g3journal/jkaa007
Genomic analyses of two Italian oyster mushroom <i>Pleurotus pulmonarius</i> 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
10.1371/journal.pone.0074825
CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data
Cited by: 19
Author(s): Rocco Piazza, Vera Magistroni, Alessandra Pirola, Sara Redaelli, Roberta Spinelli, Serena Redaelli, Marta Galbiati, Simona Valletta, Giovanni Giudici, Giovanni Cazzaniga, Carlo Gambacorti‐Passerini
Software Mentions: 2
Published: about 11 years ago
10.1038/s41598-017-13513-x
Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera
Cited by: 16
Author(s): Yingying Gao, Yi Wang, H. P. Xin, Shaohua Li, Zhenchang Liang
Software Mentions: 2
Published: about 7 years ago
10.1093/g3journal/jkab209
Transcriptomic and photosynthetic responses to grafting of the <i>Nod1</i> 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/ijms19103246
Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses
Cited by: 19
Author(s): Jianbo Li, Jin Zhang, Huixia Jia, Zhiqiang Yue, Mengzhu Lu, Xuebing Xin, Jianjun Hu
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0134824
Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis
Cited by: 9
Author(s): Jun Duan, Tim R. Ladd, Daniel Doucet, Michel Cusson, Kees vanFrankenhuyzen, Omprakash Mittapalli, Peter J. Krell, Guoxing Quan
Software Mentions: 2
Published: over 9 years ago
10.3390/ijms20010152
Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat
Cited by: 24
Author(s): Jie Tang, Lianming Du, Yuanmei Liang, Maurycy Daroch
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0043192
Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing
Cited by: 60
Author(s): Winnie S. Liang, David W. Craig, John D. Carpten, Mitesh J. Borad, Michael J. Demeure, Glen J. Weiss, Tyler Izatt, Shripad Sinari, Alexis Christoforides, Jessica Aldrich, Ahmet Kurdoglu, Michael T. Barrett, L Taylor Phillips, Hollie Benson, Waibhav Tembe, Esteban Braggio, Jeffrey Kiefer, Christophe Legendre, Richard G. Posner, Galen Hostetter, Angela Baker, Jan B. Egan, Haiyong Han, Douglas F. Lake, Edward C. Stites, Ramesh K. Ramanathan, Rafaël Fonseca, A. Keith Stewart, Daniel D. Von Hoff
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0090002
Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
Cited by: 33
Author(s): Lien Spans, Christine Helsen, Liesbeth Clinckemalie, Thomas Van den Broeck, Stefan Prekovic, Steven Joniau, Evelyne Lerut, Frank Claessens
Software Mentions: 2
Published: over 10 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
10.1371/journal.pone.0072361
PhenoTimer: Software for the Visual Mapping of Time-Resolved Phenotypic Landscapes
Cited by: 1
Author(s): Maria Secrier, Reinhard Schneider
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0079475
The Transcriptional Landscape of Campylobacter jejuni under Iron Replete and Iron Limited Growth Conditions
Cited by: 41
Author(s): James Butcher, Alain Stintzi
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0197392
Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium
Cited by: 12
Author(s): Jun Yan, Guilin Li, Xingqi Guo, Yang Li, Xiaohong Cao
Software Mentions: 2
Published: over 6 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
10.3390/ijms20194864
Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum
Cited by: 15
Author(s): Liang Yang, Mingjun Miao, Hongjun Lyu, Xue Cao, Ju Li, Li YueJian, Zhi Li, Wei Chang
Software Mentions: 2
Published: about 5 years ago
10.3390/ijms20215311
Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton
Cited by: 25
Author(s): Muhammad Imran, Sarfraz Shafiq, Muhammad Farooq, Muhammad Kashif Naeem, Émilie Widemann, Ali Bakhsh, Kevin B. Jensen, Richard R.‐C. Wang
Software Mentions: 2
Published: about 5 years ago
10.3390/ijms20225796
Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco
Cited by: 24
Author(s): Qianqian Zhou, Qingchang Li, Peng Li, Songtao Zhang, Che Liu, Jingjing Jin, Peijian Cao, Yongxia Yang
Software Mentions: 2
Published: about 5 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/ijms21010351
Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis
Cited by: 24
Author(s): Liru Cao, Pengyu Zhang, LU Xin-shi, Guorui Wang, Zhenhua Wang, Qianjin Zhang, Xin Zhang, Xin Wei, Fujian Mei, Wei Li, Tongchao Wang
Software Mentions: 2
Published: almost 5 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
10.1371/journal.pone.0216126
New framework for automated article selection applied to a literature review of Enhanced Biological Phosphorus Removal
Cited by: 6
Author(s): Minh Nguyen Quang, Tim Rogers, Jan Hofman, Ana Lanham
Software Mentions: 2
Published: over 5 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
10.1371/journal.pone.0091776
Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana
Cited by: 145
Author(s): Kenlee Nakasugi, Ross N. Crowhurst, Julia Bally, Peter M. Waterhouse
Software Mentions: 2
Published: over 10 years ago
10.3390/ijms21072580
A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)
Cited by: 4
Author(s): Katarzyna B. Czyż, Michał Książkiewicz, Grzegorz Koczyk, Anna Szczepaniak, Jan Podkowiński, B. Naganowska
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21083015
Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat (Triticum aestivum L.)
Cited by: 10
Author(s): Cai'e Zhou, Zhaonian Dong, Ting Zhang, Jianhui Wu, Shizhou Yu, Qingdong Zeng, Dejun Han, Wei Tong
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21114022
Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma
Cited by: 10
Author(s): Hatem Zayed
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21144905
Genome-Wide Identification and Expression Profile Analysis of the PHT1 Gene Family in Gossypium hirsutum and Its Two Close Relatives of Subgenome Donor Species
Cited by: 4
Author(s): Sheng Cai, Fujie Liu, Baoliang Zhou
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21155305
The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia
Cited by: 11
Author(s): Martina Wahlund, Indranil Sinha, Kristina Broliden, Shanie Saghafian–Hedengren, Anna Nilsson, Anna Berggren
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21175987
Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa
Cited by: 3
Author(s): Weike Duan, Zhinan Huang, Ying Liu, Xiaoming Song, Xiaochuan Sun, Can Jin, Yunpeng Wang, Jizhong Wang
Software Mentions: 2
Published: over 4 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
10.1371/journal.pone.0107497
visPIG - A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data
Cited by: 38
Author(s): Matthew Scales, Roland Jäger, G Migliorini, Richard S. Houlston, Marc Henrion
Software Mentions: 2
Published: about 10 years ago
10.3390/ijms21218100
Genotypic and Phenotypic Changes in Candida albicans as a Result of Cold Plasma Treatment
Cited by: 5
Author(s): Ewa Tyczkowska-Sieroń, Tadeusz Kałużewski, Magdalena Grabiec, Bogdan Kaƚużewski, J. Tyczkowski
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms21217934
Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq
Cited by: 12
Author(s): Thiago Mateus Rosa-Santos, Renan Gonçalves da Silva, Poornasree Kumar, Pratibha Kottapalli, Chiquito J. Crasto, Kameswara Rao Kottapalli, Suzelei C. França, Sônia Marli Zingaretti
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0151673
Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle
Cited by: 14
Author(s): Krysty Munns, Rahat Zaheer, Yong Xu, Kim Stanford, Chad R. Laing, Victor P. J. Gannon, L.B. Selinger, Tim A. McAllister
Software Mentions: 2
Published: over 8 years ago
10.3390/ijms22031044
Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase (CDPK) and CDPK-Related Kinase (CRK) Gene Families in Medicago truncatula
Cited by: 16
Author(s): Peng Zhao, Huan Liu, Weiyi Kong, Jiayi Ji, Tianyu Cai, Zhenfei Guo
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms22031146
Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation
Cited by: 1
Author(s): Reinhard Ullmann, B Becker, Simone Rothmiller, Annette Schmidt, Horst Thiermann, Hanns Leonhard Kaatsch, Gerrit Schrock, J. W. Müller, Julia Jakobi, Richard Obermair, Matthias Port, Harry Scherthan
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms22052665
A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini
Cited by: 6
Author(s): Anastasia Samsonova, Alexander Kanapin, Mikhail Bankin, Anton Logachev, Maria Gretsova, Tatiana A. Rozhmina, Maria Samsonova
Software Mentions: 2
Published: over 3 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
10.3390/ijms22105291
Genome-Wide Analysis of nsLTP Gene Family and Identification of SiLTPs Contributing to High Oil Accumulation in Sesame (Sesamum indicum L.)
Cited by: 17
Author(s): Shengnan Song, Jun You, Lisong Shi, Sheng Chen, Wangyi Zhou, Senouwa Segla Koffi Dossou, Komivi Dossa, Linhai Wang
Software Mentions: 2
Published: over 3 years ago