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

10.1038/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
10.3390/ijms19092525
Opposite Polarity Monospore Genome De Novo Sequencing and Comparative Analysis Reveal the Possible Heterothallic Life Cycle of Morchella importuna
Cited by: 28
Author(s): Wei Liu, LianFu Chen, Yingli Cai, Qianqian Zhang, Yinbing Bian
Software Mentions: 3
Published: about 6 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
10.1186/s12864-021-07378-8
Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Cited by: 19
Author(s): Dou Liu, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Hǎihóng Shāng, Hongbin Li, Gao Xiao
Software Mentions: 3
Published: almost 4 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
10.1186/s12864-019-6319-4
Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Cited by: 14
Author(s): Jing Li, Xiaotong Gao, Shiye Sang, Changning Liu
Software Mentions: 3
Published: almost 5 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
10.1038/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/s41598-019-52139-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
10.1186/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
10.1038/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: about 5 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
10.1111/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/s41598-019-50624-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/s41598-018-33744-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
10.1038/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
10.1186/1471-2164-13-545
Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
Cited by: 98
Author(s): Jihye Park, Ying Zhang, Anne M. Buboltz, Xuqing Zhang, Stephan C. Schuster, Umesh Ahuja, Minghsun Liu, Jeff F. Miller, Mohammed Sebaihia, Stephen D. Bentley, Julian Parkhill, Eric T. Harvill
Software Mentions: 3
Published: about 12 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
10.1038/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
10.1186/1471-2164-14-617
Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
Cited by: 99
Author(s): Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: about 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/acel.13357
Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 3 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/s41598-018-37792-0
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
10.1038/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/s41598-017-17484-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/s41598-018-21560-1
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: almost 7 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/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/s41598-018-22237-5
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
10.1038/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
10.1093/gigascience/giy044
Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant
Cited by: 9
Author(s): Chien‐Yueh Lee, Ping-Han Hsieh, Li-Mei Chiang, Amrita Chattopadhyay, Kuanyi Li, Yi-Fang Lee, Tzu-Pin Lu, Liang‐Chuan Lai, Eric S. Lin, Hsinyu Lee, Shih‐Torng Ding, Mong‐Hsun Tsai, Chien‐Yu Chen, Eric Y. Chuang
Software Mentions: 3
Published: over 6 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
10.1186/s12859-014-0422-y
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: almost 10 years ago
10.7717/peerj.1310
Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: about 9 years ago
10.1093/gigascience/giaa148
Chromosome-level reference genome of the European wasp spider<i>Argiope bruennichi</i>: a resource for studies on range expansion and evolutionary adaptation
Cited by: 29
Author(s): Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuß, Lars Riff Jensen, C. J. Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
Software Mentions: 3
Published: almost 4 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
10.1016/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
10.1038/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
10.7717/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.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
10.1186/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
10.1093/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
10.1093/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
10.1186/1471-2105-13-S8-S8
An eQTL biological data visualization challenge and approaches from the visualization community
Cited by: 10
Author(s): Christopher W. Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts, William C. Ray
Software Mentions: 3
Published: over 12 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/s13059-019-1631-5
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
10.3892/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
10.1186/s13068-020-1651-0
Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742
Cited by: 6
Author(s): Youzhi Miao, Xing Chen, Tuo Li, Han Zhu, Tang Si-yu, Dongyang Liu, Qirong Shen
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13068-017-0885-y
Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
Cited by: 23
Author(s): Man Zhou, Peng Guo, Tao Wang, Limin Gao, Hang Yin, Cheng Cai, Jie Gu, Xin Lü
Software Mentions: 3
Published: over 7 years ago
10.1186/1754-6834-7-66
The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
Cited by: 55
Author(s): Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, Erik Böer, Toni Gabaldón, José Almeida Cruz, Emmanuel Talla, Christian Marck, André Goffeau, Valérie Barbe, Philippe Baret, Keith Baronian, Sebastian Beier, Claudine Bleykasten, R. Bode, Serge Casarégola, Laurence Despons, Cécile Fairhead, Martin Giersberg, Przemysław Piotr Gierski, Urs Hähnel, Anja Hartmann, Dagmara Jankowska, Claire Jubin, Paul P. Jung, Ingrid Lafontaine, Véronique Leh-Louis, Marc Lemaire, Marina Marcet‐Houben, Martin Mascher, Guillaume Morel, Guy‐Franck Richard, Jan Riechen, Christine Sacerdot, Anasua Sarkar, Guilhem Savel, Joseph Schacherer, David James Sherman, Nils Stein, Marie Laure Straub, Agnès Thierry, Anke Trautwein-Schult, Benoît Vacherie, Éric Westhof, Sebastian Worch, Bernard Dujon, Jean Luc Souciet, Patrick Wincker, Uwe Scholz, Cécile Neuvéglise
Software Mentions: 3
Published: almost 11 years ago
10.1038/s42003-021-02559-3
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 3 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/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
10.1038/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/s13059-014-0408-0
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
Cited by: 159
Author(s): Shaoke Lou, Heung‐Man Lee, Hao Qin, Jing‐Woei Li, Zhibo Gao, Xin Liu, Landon L. Chan, Vincent K. Lam, Wing‐Yee So, Ying Wang, Si Lok, Jun Wang, Ronald Cw, Stephen Kwok‐Wing Tsui, Juliana C.N. Chan, Ting-Fung Chan, Kevin Y. Yip
Software Mentions: 2
Published: over 10 years ago
10.1186/gb-2013-14-6-r64
A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Cited by: 45
Author(s): Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Frédéric Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M. Martis, Klaus Mayer, Abraham B. Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet
Software Mentions: 2
Published: over 11 years ago
10.1186/s13059-015-0648-7
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
Cited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 9 years ago
10.1186/gb-2013-14-11-r129
Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12864-019-6146-7
DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
Cited by: 15
Author(s): Haoling Huang, Ping Wu, Shaolun Zhang, Qi Shang, Haotong Yin, Qirui Hou, Jinbo Zhong, Xijie Guo
Software Mentions: 2
Published: about 5 years ago
10.1186/gb-2014-15-2-r40
Genome-wide discovery and characterization of maize long non-coding RNAs
Cited by: 385
Author(s): Liang-In Lin, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng‐Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Evans Mulenga, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C.P. Timmermans, Nathan M. Springer, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-019-6388-4
Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome
Cited by: 24
Author(s): Konstantin V. Kuleshov, Gabriele Margos, Volker Fingerle, Joris Koetsveld, Irina A. Goptar, Mikhail L. Markelov, Nadezhda M. Kolyasnikova, Denis S. Sarksyan, Nina P. Kirdyashkina, German A. Shipulin, Joppe W. Hovius, Alexander E. Platonov
Software Mentions: 2
Published: almost 5 years ago
10.1128/AEM.01911-20
Critical Role of MetR/MetB/MetC/MetX in Cysteine and Methionine Metabolism, Fungal Development, and Virulence of Alternaria alternata
Cited by: 13
Author(s): Yunpeng Gai, Lei Li, Hongshen Ma, Brendan K. Riely, Bing Liu, Hongye Li
Software Mentions: 2
Published: almost 4 years ago
10.1186/gb-2010-11-10-r104
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Cited by: 141
Author(s): Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stéphane Terry, David Z. Chen, Joel Rozowsky, Ashutosh Tewari, Naoki Kitabayashi, Benjamin Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark Gerstein
Software Mentions: 2
Published: about 14 years ago
10.1186/s12864-021-07958-8
Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues
Cited by: 10
Author(s): Jiecuo Duo, Huan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang, Ran Duan
Software Mentions: 2
Published: about 3 years ago
10.3389/fpls.2018.01127
QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus
Cited by: 39
Author(s): Nadia Raboanatahiry, Hongbo Chao, Dalin Hou, Shi Pu, Wei Yan, Liang Yu, Baoshan Wang, Maoteng Li
Software Mentions: 2
Published: over 6 years ago
10.1186/gb-2011-12-10-r103
Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Cited by: 176
Author(s): Wigard P. Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S.P. Vermaat, Markus J. van Roosmalen, Stef van Lieshout, Isaäc J Nijman, Wijnand M. Roessingh, Ruben van ‘t Slot, José van de Belt, Victor Guryev, Marco J. Koudijs, Emile E. Voest, Edwin Cuppen
Software Mentions: 2
Published: almost 14 years ago
10.1186/s13059-015-0849-0
Circlator: automated circularization of genome assemblies using long sequencing reads
Cited by: 715
Author(s): Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 2
Published: almost 9 years ago
10.1155/2014/396727
Gender-Specific DNA Methylome Analysis of a Han Chinese Longevity Population
Cited by: 9
Author(s): Liang Sun, Jie Lin, Hongwu Du, Chengping Hu, Zezhi Huang, Zhen Lv, Chenguang Zheng, Xiaoyi Shi, Yan Zhang, Ze Yang
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-019-6133-z
Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya
Cited by: 15
Author(s): Gang Wang, Jingxian Lin, Yang Shi, Xiaoguang Chang, Yuanyuan Wang, Lin Guo, Wenhui Wang, Meijie Dou, Youjin Deng, Ray Ming, Jisen Zhang
Software Mentions: 2
Published: about 5 years ago
10.3389/fpls.2015.00910
Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling
Cited by: 69
Author(s): Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Rohit Khandelwal, Jananee Jaishankar, Shweta Shweta, Kashif Nawaz
Software Mentions: 2
Published: about 9 years ago
10.3389/fpls.2021.702243
Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective
Cited by: 5
Author(s): Seong-Min Hong, Yong Pyo Lim, Suk‐Yoon Kwon, Ah-Young Shin, Yongmin Kim
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2020.00406
Genome-Wide Identification of Peanut KCS Genes Reveals That AhKCS1 and AhKCS28 Are Involved in Regulating VLCFA Contents in Seeds
Cited by: 18
Author(s): Dongxin Huai, Xiaomeng Xue, Yang Li, Peng Wang, Jianguo Li, Liying Yan, Yuning Chen, Xin Wang, Nian Liu, Yanping Kang, Zhihui Wang, Yi Huang, Huifang Jiang, Yong Lei, Boshou Liao
Software Mentions: 2
Published: over 4 years ago
10.3389/fpls.2020.00650
Genome-Wide Analysis of Basic Helix-Loop-Helix Transcription Factors to Elucidate Candidate Genes Related to Fruit Ripening and Stress in Banana (Musa acuminata L. AAA Group, cv. Cavendish)
Cited by: 15
Author(s): Zhuo Wang, Caihong Jia, Jingyi Wang, Hongxia Miao, Juhua Liu, Cui Chen, Haiyuan Yang, Biao Xu, Zhiqiang Jin
Software Mentions: 2
Published: over 4 years ago
10.3389/fpls.2017.00140
Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection
Cited by: 31
Author(s): Qinhu Wang, Cong Jiang, Chenfang Wang, Changjun Chen, Jin‐Rong Xu, Huiquan Liu
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12864-018-4511-6
Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family
Cited by: 65
Author(s): Man Zhang, Qing Liu, Hongbo Shi, Mingliang Guo, Mengnan Chai, Qing-Yu He, Mei Yan, Du Cao, Lihua Zhao, Hanyang Cai, Yuan Qin
Software Mentions: 2
Published: almost 7 years ago
10.1093/bioinformatics/btv433
ClicO FS: an interactive web-based service of Circos
Cited by: 78
Author(s): Wei-Hien Cheong, Yung-Chie Tan, Soon-Joo Yap, Kee-Peng Ng
Software Mentions: 2
Published: over 9 years ago
10.3389/fpls.2021.707496
Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress
Cited by: 5
Author(s): Jirui Gong, Tianlong Shi, Yuke Li, Han-Cheng Wang, Fēi Li
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-016-0948-6
Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
Cited by: 55
Author(s): Alice M. Walsh, John W. Whitaker, Chaohua Huang, Yauheniya Cherkas, S. Lamberth, Carrie Brodmerkel, Mark Curran, Radu Dobrin
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2164-14-573
Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)
Cited by: 160
Author(s): Xiaoming Song, Ying Liu, Xilin Hou
Software Mentions: 2
Published: over 11 years ago
10.1186/s13104-020-05169-0
Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast
Cited by: 12
Author(s): William T. Molin, Allison Yaguchi, Mark Blenner, Christopher A. Saski
Software Mentions: 2
Published: over 4 years ago
10.3389/fpls.2018.01565
Detection of T. urartu Introgressions in Wheat and Development of a Panel of Interspecific Introgression Lines
Cited by: 22
Author(s): Surbhi Grewal, Stella Hubbart‐Edwards, Caiyun Yang, Duncan Scholefield, Stephen Ashling, Amanda Burridge, Paul Wilkinson, Ian P. King, Julie King
Software Mentions: 2
Published: about 6 years ago
10.3389/fpls.2021.672017
Identification of Glutathione S-Transferase Genes in Hami Melon (Cucumis melo var. saccharinus) and Their Expression Analysis Under Cold Stress
Cited by: 12
Author(s): Wen Song, Fake Zhou, Chunhui Shan, Qin Zhang, Ming Ning, Xiumin Liu, Xinxin Zhao, Wenchao Cai, Xinquan Yang, Guangfei Hao, Fengxian Tang
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2016.00007
Genome-Wide Identification and Comparative Analysis of Cytosine-5 DNA Methyltransferase and Demethylase Families in Wild and Cultivated Peanut
Cited by: 25
Author(s): Pengfei Wang, Chao Gao, Xiaotong Bian, Shuzhen Zhao, Chuanzhi Zhao, Han Xia, Hui Song, Lei Hou, Shungang Wan, Xingjun Wang
Software Mentions: 2
Published: almost 9 years ago
10.3389/fpls.2021.721558
Genome-Wide Comparative Analysis of R2R3 MYB Gene Family in Populus and Salix and Identification of Male Flower Bud Development-Related Genes
Cited by: 16
Author(s): Fangwei Zhou, Ying-Nan Chen, Huaitong Wu, Tongming Yin
Software Mentions: 2
Published: about 3 years ago
10.3389/fpls.2017.01644
RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat
Cited by: 16
Author(s): Shumin Zhou, Baiqiang Yan, Fĕi Li, Jinpeng Zhang, Jing Zhang, Huihui Ma, Weihua Liu, Yuqing Lu, Xinming Yang, Xiuquan Li, Xu Liu, Lihui Li
Software Mentions: 2
Published: about 7 years ago
10.3389/fphar.2020.620724
Gut Microbiota and Related Metabolites Were Disturbed in Ulcerative Colitis and Partly Restored After Mesalamine Treatment
Cited by: 16
Author(s): Liang Dai, Yiming Tang, Wenjun Zhou, Yanqi Dang, Qian Sun, Zhipeng Tang, Meizhen Zhu, Guang Ji
Software Mentions: 2
Published: almost 4 years ago
10.3389/fonc.2019.01305
Expanding the Transcriptome of Head and Neck Squamous Cell Carcinoma Through Novel MicroRNA Discovery
Cited by: 14
Author(s): Leigha D. Rock, Brenda C. Minatel, Erin A. Marshall, Florian Guisier, Adam P. Sage, Mateus Camargo Barros-Filho, Greg L. Stewart, Cathie Garnis, Wan L. Lam
Software Mentions: 2
Published: almost 5 years ago
10.3389/fphys.2017.00253
Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica
Cited by: 41
Author(s): Shiliang Fan, Dong Zhang, Giampiero Cai, Ming Zhao, Haiqin Wu, Youmei Li, Yongming Shen, Mingyu Han
Software Mentions: 2
Published: over 7 years ago
10.3389/fpls.2021.629859
The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum
Cited by: 3
Author(s): Yiping Cui, Bo Wu, Aitian Peng, Xiaobing Song, Xia Chen
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2164-14-397
Web-based visual analysis for high-throughput genomics
Cited by: 44
Author(s): Jeremy Goecks, Carl Eberhard, Tomithy Too, Anton Nekrutenko, James Taylor
Software Mentions: 2
Published: over 11 years ago
10.1186/s12864-015-1988-0
Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes
Cited by: 40
Author(s): Mingyong Tang, Zhiwen Chen, Corrinne E. Grover, Yumei Wang, Shuangshuang Li, Guozheng Liu, Zhiying Ma, Jonathan F. Wendel, Jinping Hua
Software Mentions: 2
Published: about 9 years ago
10.3389/fnins.2020.582279
Phenotypic Resemblance to Neuropsychiatric Disorder and Altered mRNA Profiles in Cortex and Hippocampus Underlying IL15Rα Knockout
Cited by: 2
Author(s): Yi He, Yuxin Yu, Yanan Li, Weicheng Duan, Zuoli Sun, Jian Yang, Abba J. Kastin, Weihong Pan, Yan Zhang, Kang Wang
Software Mentions: 2
Published: almost 4 years ago
10.3389/fneur.2014.00240
Subject–Motion Correction in HARDI Acquisitions: Choices and Consequences
Cited by: 12
Author(s): Shireen Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana R. Leppert, G. Bruce Pike, Guido Gerig
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12870-021-02941-7
Genetic control of flowering in greater yam (Dioscorea alata L.)
Cited by: 10
Author(s): Fabien Cormier, Guillaume Martin, Hélène Vignes, Laurie Lachman, Denis Cornet, Yoana Faure, Erick Malédon, Pierre Mournet, Gemma Arnau, Hâna Chaïr
Software Mentions: 2
Published: over 3 years ago
10.3389/fneur.2017.00741
Spontaneous Recovery from Unresponsive Wakefulness Syndrome to a Minimally Conscious State: Early Structural Changes Revealed by 7-T Magnetic Resonance Imaging
Cited by: 9
Author(s): Xiaoxiao Tan, Jian Gao, Zhen Zhou, Rui-Li Wei, Ting Gong, Yuqin Wu, Kehong Liu, Fangping He, Junyang Wang, Jingqi Li, Xiaolin Zhang, Gang Pan, Benyan Luo
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2164-13-505
Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma
Cited by: 31
Author(s): Jared J. Gartner, Sean Davis, Xiaomu Wei, Jimmy C. Lin, Niraj Trivedi, Jamie K. Teer, Paul S. Meltzer, Steven A. Rosenberg, Yardena Samuels
Software Mentions: 2
Published: about 12 years ago
10.1186/s12870-017-0979-5
Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa
Cited by: 58
Author(s): Md. Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Manosh Kumar Biswas, Hoy‐Taek Kim, Ill–Sup Nou
Software Mentions: 2
Published: almost 8 years ago
10.3389/fmicb.2019.00966
Comparative Genomics Reveals the High Copy Number Variation of a Retro Transposon in Different Magnaporthe Isolates
Cited by: 7
Author(s): Pankaj Kumar Singh, Ajay Kumar Mahato, Priyanka Jain, Rajeev Rathour, Vinay Sharma, Tilak Raj Sharma
Software Mentions: 2
Published: over 5 years ago