pypi: Circos | Projects | Ecosyste.ms: Papers

10.1186/s12859-016-1055-0

DensityMap: a genome viewer for illustrating the densities of features
Cited by: 13
Author(s): Sébastien Guizard, Benoît Piégu, Yves Bigot
Software Mentions: 4
Published: about 8 years ago

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

10.3389/fmicb.2018.00063

Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level
Cited by: 47
Author(s): Michael Schmid, Jonathan Muri, Damianos P. Melidis, Adithi R. Varadarajan, Vincent Somerville, Adrian Wicki, Aline Moser, M Bourqui, Claudia Wenzel, Elisabeth Eugster‐Meier, Juerg E. Frey, Stefan Irmler, Christian H. Ahrens
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-12-402

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Cited by: 2,222
Author(s): Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. Beatson
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12864-017-3800-9

A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M
Cited by: 12
Author(s): Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu, Wei Chen
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-018-5157-0

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)
Cited by: 39
Author(s): Rui Hu, Jie Xiao, Tao Gu, Xiao‐Lan Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-15-198

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: almost 10 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1825-5

Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates
Cited by: 124
Author(s): Nan Zhang, Dongqing Yang, Dandan Wang, Youzhi Miao, Jiahui Shao, Xuan Zhou, Zhihui Xu, Qing Li, Haichao Feng, Shuqing Liu, Qirong Shen, Ruifu Zhang
Software Mentions: 4
Published: over 8 years ago

10.3390/cancers12123738

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients
Cited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: over 3 years ago

10.1155/2014/264519

A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Cited by: 6
Author(s): Preston Leung, Rowena A. Bull, Andrew R. Lloyd, Fabio Luciani
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-016-3070-y

The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Cited by: 27
Author(s): Pablo Ivan Pereira Ramos, Márlon Grégori Flores Custódio, Guadalupe del Rosario Quispe Saji, Thiago Bérgamo Cardoso, Gisele Lucchetti da Silva, Graziela Braun, Willames M. B. S. Martins, Raquel Girardello, Ana Tereza Ribeiro de Vasconcelos, Elmer Fernández, Ana Cristina Gales, Marisa Fabiana Nicolás
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: about 3 years ago

10.1186/s12977-015-0148-6

An integrated map of HIV genome-wide variation from a population perspective
Cited by: 83
Author(s): Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-14-244

RCircos: an R package for Circos 2D track plots
Cited by: 425
Author(s): Hongen Zhang, Paul S. Meltzer, Sean Davis
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12870-016-0788-2

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
Cited by: 33
Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0255822

Evaluation of the severity of nonalcoholic fatty liver disease through analysis of serum exosomal miRNA expression
Cited by: 5
Author(s): Jeong‐An Gim, Soo Min Bang, Young‐Sun Lee, Sun Young Yim, Young Kul Jung, Hayeon Kim, Baek-hui Kim, Ji Hoon Kim, Yeon Seok Seo, Hyung Joon Yim, Jong Eun Yeon, Soon Ho Um, Kwan Soo Byun
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0146916

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
Cited by: 15
Author(s): Sophie Weiss, Thomas J. Mansell, Pooneh Mortazavi, Rob Knight, Ryan T. Gill
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-5444-4

The plastid and mitochondrial genomes of Eucalyptus grandis
Cited by: 31
Author(s): Desré Pinard, Alexander Andrew Myburg, Eshchar Mizrachi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-021-03057-8

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper
Cited by: 4
Author(s): Myung-Shin Kim, Geun Young Chae, Soohyun Oh, Jihyun Kim, Hyunggon Mang, Seungill Kim, Doil Choi
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12870-019-1708-z

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
Cited by: 30
Author(s): Ming Li, Songtao Yang, Wei Xü, Zhien Pu, Jiayi Feng, Zhangying Wang, Cong Zhang, Peng Ma, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yán Li, Huan Yang, Anzhong Liao, Wei Song, Zhongren Zhang, Ji Li, Kai Wang, Yizheng Zhang, Hao Lin, Jinbo Zhang, Wen-Fang Tan
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2502-z

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
Cited by: 71
Author(s): Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian Foley, Leonard A. Smith, Rafael Fernández, Miia Lindström, Hannu Korkeala, Paul Keim, Jeffrey T. Foster, Karen K. Hill
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: almost 11 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
Cited by: 14
Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: about 10 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms22041811

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes
Cited by: 15
Author(s): Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Software Mentions: 4
Published: over 3 years ago

10.1186/s12951-021-00916-2

Silicon dioxide nanoparticles induced neurobehavioral impairments by disrupting microbiota–gut–brain axis
Cited by: 23
Author(s): Jun Diao, Yinyin Xia, Xuejun Jiang, Jingfu Qiu, Shuqun Cheng, Junhao Su, Xinhao Duan, Min Gao, Xia Qin, Jun Zhang, Jie Fan, Zhen Zou, Chengzhi Chen
Software Mentions: 4
Published: almost 3 years ago

10.1093/bioinformatics/btt294

SVGenes: a library for rendering genomic features in scalable vector graphic format
Cited by: 2
Author(s): Graham J. Etherington, Dan MacLean
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12870-020-02744-2

Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions
Cited by: 6
Author(s): Xuan Wang, Fei Shen, Yuan Gao, Kun Wang, Ruiting Chen, Jun Luo, Lili Yang, Xi Zhang, Changwei Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Cong Peng, Zhenhai Han, Xinzhong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-4708-8

Small RNA-based prediction of hybrid performance in maize
Cited by: 20
Author(s): Felix Seifert, Alexander Thiemann, Tobias A. Schrag, Dominika Rybka, Albrecht E. Melchinger, Matthias Frisch, Stefan Scholten
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-016-0933-y

Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico
Cited by: 39
Author(s): Andréa Garavito, Christophe Montagnon, Romain Guyot, Benoît Bertrand
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-015-0818-3

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Cited by: 11
Author(s): Xiao Zhu, Ho-fung Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms22041539

Non-Coding RNAs in the Transcriptional Network That Differentiates Skeletal Muscles of Sedentary from Long-Term Endurance- and Resistance-Trained Elderly
Cited by: 13
Author(s): Paola De Sanctis, Giuseppe Filardo, Provvidenza Maria Abruzzo, Annalisa Astolfi, Alessandra Bolotta, Valentina Indio, Alessandro Di Martino, Christian Höfer, Helmut Kern, Stefan Löefler, Maurilio Marcacci, Marina Marini, Sandra Zampieri, Cinzia Zucchini
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12866-019-1500-0

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Cited by: 101
Author(s): Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey, Christian H. Ahrens
Software Mentions: 4
Published: almost 5 years ago

10.1111/jpy.13079

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
Cited by: 20
Author(s): Antoine Fort, Marcus McHale, Kévin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-57546-1

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

10.1038/s41598-020-61633-8

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

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pntd.0008237

Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms
Cited by: 20
Author(s): Jayden Logan, Mark S. Pearson, Srikanth S. Manda, Young Jun Choi, Matthew A. Field, Ramon M. Eichenberger, Jason Mulvenna, Shivashankar H. Nagaraj, Ricardo Toshio Fujiwara, Pedro Henrique Gazzinelli-Guimarães, Lilian Lacerda Bueno, Vitor Luís Tenório Mati, Jeffrey M. Bethony, Makedonka Mitreva, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1005954

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
Cited by: 102
Author(s): Shubha Vij, Heiner Kuhl, Irina M. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, K. Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James Drake, Matthew Boitano, Richard J. Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, G. Gopikrishna, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1008452

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania
Cited by: 12
Author(s): Megan A. Sloan, Karen Brooks, Thomas D. Otto, Mandy Sanders, James A. Cotton, Petros Ligoxygakis
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pntd.0009719

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Cited by: 6
Author(s): Luisa Berná, Gonzalo Greif, Sebastián Pita, Paula Faral-Tello, Florencia Díaz-Viraqué, Rita de Cássia Moreira de Souza, Gustavo Adolfo Vallejo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 4
Published: over 2 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1000832

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Cited by: 238
Author(s): Michael J. Clark, Nils Homer, Brian D. O’Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson
Software Mentions: 4
Published: over 14 years ago

10.1186/s12864-020-06820-7

Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Cited by: 6
Author(s): Clemens L. Weiß, Marie-Theres Gansauge, Ayinuer Aximu‐Petri, Matthias Meyer, Hernán A. Burbano
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-11327-5

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea
Cited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-49915-2

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

10.1038/srep18616

Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer
Cited by: 15
Author(s): Ning An, Xue Yang, Shujun Cheng, Guiqi Wang, Kaitai Zhang
Software Mentions: 4
Published: over 8 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-020-06871-w

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Cited by: 29
Author(s): Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus, Eva H. Stukenbrock
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: over 3 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
Cited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.ppat.1008334

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

10.1186/s12864-015-1233-x

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: almost 3 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: almost 3 years ago

10.3390/genes9080379

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Cited by: 22
Author(s): George C. diCenzo, Klaudia Dębiec, Jan Krzysztoforski, Witold Uhrynowski, Alessio Mengoni, Camilla Fagorzi, Adrian Górecki, Łukasz Dziewit, Tomasz Bajda, Grzegorz Rzepa, Łukasz Drewniak
Software Mentions: 4
Published: almost 6 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: over 8 years ago

10.1186/s12915-020-00802-7

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

10.1534/g3.116.037556

Construction of a High-Density American Cranberry (Vaccinium macrocarponAit.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
Cited by: 27
Author(s): Brandon Schlautman, Giovanny Covarrubias‐Pazaran, Luis Diaz‐Garcia, Massimo Iorizzo, James J. Polashock, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
Software Mentions: 4
Published: about 7 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-13-202

Comparing thousands of circular genomes using the CGView Comparison Tool
Cited by: 234
Author(s): Jason R. Grant, Adriano S. Arantes, Paul Stothard
Software Mentions: 4
Published: almost 12 years ago

10.1534/g3.120.401550

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

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-14-918

POMO - Plotting Omics analysis results for Multiple Organisms
Cited by: 3
Author(s): Jake Lin, Richard Kreisberg, Aleksi Kallio, Andrew T. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, Reija Autio
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 11 years ago

10.1093/bioinformatics/btw116

Goldilocks: a tool for identifying genomic regions that are ‘just right’
Cited by: 2
Author(s): Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
Software Mentions: 4
Published: about 8 years ago

10.7717/peerj.3162

The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: almost 3 years ago

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: almost 7 years ago

10.3390/genes7040013

Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms22010347

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
Cited by: 8
Author(s): Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak
Software Mentions: 4
Published: over 3 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: about 5 years ago

10.3389/fpls.2016.01857

Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula
Cited by: 10
Author(s): David J. Burks, Rajeev K. Azad
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.640163

A 598-bp InDel Variation in the Promoter Region of Bna.SOC1.A05 Is Predominantly Present in Winter Type Rapeseeds
Cited by: 1
Author(s): Sarah Matar, Siegbert Melzer
Software Mentions: 3
Published: about 3 years ago

10.3389/fpls.2020.545042

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

10.3389/fpls.2021.721253

Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat (Triticum aestivum L.)
Cited by: 12
Author(s): Zhenyu Wang, Ruoyu Zhang, Yue Cheng, Pengzheng Lei, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 3
Published: over 2 years ago

10.3389/fpls.2018.00771

Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection
Cited by: 28
Author(s): Paulo A. Zaini, Rafael Nascimento, Hossein Gouran, Dario Cantu, Sandeep Chakraborty, My L. Phu, Luíz Ricardo Goulart, Abhaya M. Dandekar
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpls.2015.01238

The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots
Cited by: 45
Author(s): Nanette Christie, Peri A Tobias, Sanushka Naidoo, Carsten Külheim
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2018.00183

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Cited by: 8
Author(s): Anne Steininger, Grit Ebert, B Becker, Chalid Assaf, Markus Möbs, Christian A. Schmidt, Piotr Grabarczyk, Lars Riff Jensen, Grzegorz K. Przybylski, Matthias Port, Andreas W. Kuß, Reinhard Ullmann
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-15-331

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Cited by: 40
Author(s): Suhn Kyong Rhie, Dennis J. Hazelett, Simon Coetzee, Chunli Yan, Houtan Noushmehr
Software Mentions: 3
Published: about 10 years ago

10.1007/s00401-013-1168-8

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Cited by: 162
Author(s): Katja Kobow, Antony Kaspi, K N Harikrishnan, K. Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El‐Osta, Ingmar Blümcke
Software Mentions: 3
Published: over 10 years ago

10.3389/fonc.2021.669270

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

10.3389/fonc.2021.591893

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

10.3389/fpls.2015.01247

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula
Cited by: 84
Author(s): Yongjun Shu, Ying Liu, Jun Zhang, Lili Song, Changhong Guo
Software Mentions: 3
Published: over 8 years ago

Projects: pypi: Circos

Papers Mentioning Circos 2,252