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: over 11 years ago

10.1186/s12870-020-02809-2

Tight association of genome rearrangements with gene expression in conifer plastomes
Cited by: 5
Author(s): Ching‐Yi Wu, Edi Sudianto, Shu‐Miaw Chaw
Software Mentions: 3
Published: almost 5 years ago

10.3390/biology9090295

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Cited by: 33
Author(s): Girum Fitihamlak Ejigu, Jaehee Jung
Software Mentions: 3
Published: about 5 years ago

10.1038/s42003-020-1096-9

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Cited by: 27
Author(s): Austin B. Mudd, Jessen V. Bredeson, Rachel Baum, Dirk Hockemeyer, Daniel S. Rokhsar
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-021-03078-3

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)
Cited by: 17
Author(s): Bin Huang, Zhinuo Huang, Ruifang Ma, Muthusamy Ramakrishnan, Jialu Chen, Zhijun Zhang, Kim Yrjälä
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-5485-8

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
Cited by: 51
Author(s): Rick E. Masonbrink, Tom Maier, Usha Muppirala, Arun S. Seetharam, Étienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nia Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves‐van den Akker, Matthew E. Hudson, Andrew J. Severin, Thomas J. Baum
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.5991

New genome assembly of the barn owl (<i>Tyto alba alba</i>)
Cited by: 8
Author(s): Anne‐Lyse Ducrest, Samuel Neuenschwander, Emanuel Schmid‐Siegert, Marco Pagni, Clément Train, David Dylus, Yannis Nevers, Alex Warwick Vesztrocy, Luis M. San‐Jose, Mélanie Dupasquier, Christophe Dessimoz, Ioannis Xénarios, Alexandre Roulin, Jérôme Goudet
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-018-5041-y

Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)
Cited by: 30
Author(s): Chongjing Xia, Meinan Wang, Chuntao Yin, Omar E. Cornejo, Scot H. Hulbert, X. M. Chen
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0184119

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome
Cited by: 25
Author(s): Sarah M. Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W. Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 3
Published: about 8 years ago

10.1155/2018/5206758

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in<i>Brassica rapa</i>
Cited by: 8
Author(s): Nadeem Khan, Chunmei Hu, Waleed Amjad Khan, Emal Naseri, Koeun Han, Hansong Dong, Xilin Hou
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: almost 12 years ago

10.3389/fnagi.2017.00249

DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment
Cited by: 48
Author(s): Lara Ianov, Alberto Riva, Ashok Kumar, Thomas C. Foster
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0125964

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species
Cited by: 34
Author(s): S. P. Singh, Suresh Chand, Nagendra Singh, Tilak Raj Sharma
Software Mentions: 3
Published: over 10 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 7 years ago

10.7554/eLife.19084

Two subunits of human ORC are dispensable for DNA replication and proliferation
Cited by: 32
Author(s): Etsuko Shibata, Manjari Kiran, Yoshiyuki Shibata, Samarendra Kumar Singh, Shashi Kiran, Anindya Dutta
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.22152

Mapping the function of neuronal ion channels in model and experiment
Cited by: 32
Author(s): William F Podlaski, Alexander Seeholzer, Lukas N. Groschner, Gero Miesenböck, Rajnish Ranjan, Tim P. Vogels
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-06877-4

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max
Cited by: 4
Author(s): Kai Fan, Yunrui Chen, Zhijun Mao, Fang Yao, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-018-1386-2

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time
Cited by: 23
Author(s): Gilad Gabay, Yardena Dahan, Yacov Izhaki, Adi Faigenboim, Giora Ben-Ari, Yonatan Elkind, Moshe A. Flaishman
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0118528

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination
Cited by: 73
Author(s): Kristen L. Hoek, Parimal Samir, Leigh M. Howard, Xinnan Niu, Nripesh Prasad, Allison C. Galassie, Qi Liu, Tara M. Allos, Kyle A. Floyd, Yan Guo, Yu Shyr, Shawn Levy, Sebastian Joyce, Kathryn M. Edwards, Andrew J. Link
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-019-2122-2

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties
Cited by: 29
Author(s): Heshan Du, Jingjing Yang, Bin Chen, Xiaofen Zhang, Jian Zhang, Kun Yang, Sansheng Geng, Changlong Wen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-016-3336-4

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance
Cited by: 53
Author(s): William T. Molin, Alice A. Wright, Amy Lawton‐Rauh, Christopher Saski
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12866-020-01737-3

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Cited by: 7
Author(s): Jiaokun Li, Tianyuan Gu, Liangzhi Li, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, Guanzhou Qiu, Weimin Zeng
Software Mentions: 3
Published: over 5 years ago

10.3390/ijerph17031009

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China
Cited by: 15
Author(s): Shengnan Chen, Hao He, Rongrong Zong, Kaiwen Liu, Miaomiao Yan, Lei Xu, Yutian Miao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12866-020-02024-x

High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis
Cited by: 15
Author(s): Yunfeng Luo, Zhongke Wang, Ya-Ling He, Guifang Li, Xinhua Lv, Zhuang Li
Software Mentions: 3
Published: about 5 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12920-017-0245-6

Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer
Cited by: 17
Author(s): Shirley Pepke, Greg Ver Steeg
Software Mentions: 3
Published: over 8 years ago

10.3390/ijerph15040708

Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China
Cited by: 29
Author(s): Xiaojuan Wang, Jie Gu, Hua Gao, Xiaoqing Qian, Haichao Li
Software Mentions: 3
Published: over 7 years ago

10.1155/2021/6289174

Comparative Analysis of the Glutathione S-Transferase Gene Family of Four Triticeae Species and Transcriptome Analysis of GST Genes in Common Wheat Responding to Salt Stress
Cited by: 24
Author(s): Yongchao Hao, Shoushen Xu, Zhongfan Lyu, Hong Wei Wang, Lingrang Kong, Silong Sun
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-016-2736-9

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family
Cited by: 42
Author(s): Fengya Zheng, Haiyang Wu, Rongzhi Zhang, Shiming Li, Weiming He, Fuk‐Ling Wong, Genying Li, Shancen Zhao, Hon‐Ming Lam
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0218938

Genome-wide comparative analysis of RNA-binding Glycine-rich protein family genes between Gossypium arboreum and Gossypium raimondii
Cited by: 11
Author(s): Yang Wei, Min Yu, Changsong Zou, Changming Lu, Daoqian Yu, Hongyan Cheng, Pengfei Jiang, Feng Xu, Youping Zhang, Qiaolian Wang, Hong Zhang, Guoli Song, Zhuqing Zhou
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01399-18

<i>Leishmania</i> Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification
Cited by: 76
Author(s): Giovanni Bussotti, Evi Gouzelou, Mariana Côrtes Boité, Ihcene Kherachi Djenad, Zoubir Harrat, Naouel Eddaikra, Jeremy C. Mottram, Μαρία Αντωνίου, Vasiliki Christodoulou, Aymen Bali, Fatma Z. Guerfali, Dhafer Laouini, M. Shahid Mukhtar, Franck Dumetz, Jean‐Claude Dujardin, Despina Smirlis, Pierre Lechat, Pascale Pescher, Adil El Hamouchi, Meryem Lemrani, Carmen Chicharro, Ivonne Pamela Llanes-Acevedo, Laura Botana, Israel Cruz, Javier Moreno, Fakhri Jeddi, Abdul Karim, A. Bouratbine, Elisa Cupolillo, Gérald F. Späth
Software Mentions: 3
Published: almost 7 years ago

10.7150/thno.53737

Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: almost 5 years ago

10.1007/s00122-016-2762-7

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat
Cited by: 51
Author(s): Huihuang Yan, Wubishet A. Bekele, Charlene P. Wight, Yuanying Peng, Tim Langdon, Robert G. Latta, Yong‐Bi Fu, Axel Diederichsen, Catherine Howarth, Eric N. Jellen, Brian Boyle, Yuming Wei, Nicholas A. Tinker
Software Mentions: 3
Published: about 9 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: over 5 years ago

10.1007/s00122-019-03517-8

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
Cited by: 22
Author(s): Beatrice Corsi, Lawrence Percival‐Alwyn, Rowena Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn &amp; Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-89146-y

Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-6416-4

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line
Cited by: 10
Author(s): Shumin Zhou, Jinpeng Zhang, Hongyu Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li, Lihui Li
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pbio.2003769

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Cited by: 88
Author(s): Eleni Gentekaki, Bruce A. Curtis, Courtney W. Stairs, Vladimír Klimeš, Marek Eliáš, Dayana E. Salas‐Leiva, Emily K. Herman, Laura Eme, María Cecilia Arias, Bernard Henrissat, Frédérique Hilliou, Mary J. Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolísko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger
Software Mentions: 3
Published: about 8 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 6 years ago

10.1111/tpj.14115

High intraspecific diversity of <i>Restorer‐of‐fertility‐like</i> genes in barley
Cited by: 21
Author(s): Joanna Melonek, Ruonan Zhou, Philipp E. Bayer, David Edwards, Nils Stein, Ian Small
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-69389-x

A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Cited by: 22
Author(s): Honghao Lv, Yong Wang, Fengqing Han, Jialei Ji, Zhiyuan Fang, Mu Zhuang, Zhansheng Li, Yangyong Zhang, Limei Yang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-017-1653-5

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 8 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: about 11 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 6 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 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: almost 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 6 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 7 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: over 6 years ago

10.1038/s41598-018-33744-w

Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube
Cited by: 42
Author(s): Zhijun Zhong, Xingang Li
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-39286-z

Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)
Cited by: 41
Author(s): Dahe Qiao, Chun Yang, Juan Chen, Yan Guo, Yán Li, Suzhen Niu, Kemei Cao, Zhengwu Chen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-30583-7

The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: about 7 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 7 years ago

10.1038/s41598-018-31770-2

Characterisation and functional predictions of canine long non-coding RNAs
Cited by: 24
Author(s): Céline Le Béguec, Valentin Wucher, Laëtitia Lagoutte, Édouard Cadieu, Nadine Botherel, Benoît. Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte
Software Mentions: 3
Published: about 7 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: over 7 years ago

10.1038/s41598-017-17203-6

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-6404-8

EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis
Cited by: 0
Author(s): Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao‐Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung‐Yen Lin
Software Mentions: 3
Published: over 5 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 5 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 8 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 7 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 6 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 4 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 5 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 9 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2164-14-S1-S5

Genomic differences between cultivated soybean, G. max and its wild relative G. soja
Cited by: 31
Author(s): Trupti Joshi, Babu Valliyodan, J. G. Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen
Software Mentions: 3
Published: almost 13 years ago

10.7717/peerj.3134

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Cited by: 44
Author(s): Sean P. Jungbluth, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.3406

MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing
Cited by: 25
Author(s): Koji Ishiya, Shintaroh Ueda
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 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 7 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: almost 11 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 11 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 6 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 7 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 6 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 6 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-017-3499-7

Visualization of consensus genome structure without using a reference genome
Cited by: 3
Author(s): Isao Tada, Yasuhiro Tanizawa, Masanori Arita
Software Mentions: 3
Published: over 8 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 5 years ago

10.1093/gbe/evt189

The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution
Cited by: 27
Author(s): Bram Verhelst, Yves Van de Peer, Pierre Rouzé
Software Mentions: 3
Published: almost 12 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: over 10 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-018-1552-8

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Cited by: 56
Author(s): Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David J. Miller
Software Mentions: 3
Published: about 7 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 7 years ago

10.1186/s12864-015-2233-6

Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress
Cited by: 66
Author(s): Xiaosan Huang, Kongqing Li, Xiaogang Xu, Zhenghong Yao, Can Jin, Shaoling Zhang
Software Mentions: 3
Published: almost 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 6 years ago

10.1186/s13059-015-0837-4

Genomic legacy of the African cheetah, Acinonyx jubatus
Cited by: 159
Author(s): Pavel Dobrynin, Shi Ping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergei Kliver, Anne Schmidt‐Küntzel, Klaus‐Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel García-Pérez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alex Makunin, Vladimir Brukhin, Wei‐Lin Qiu, Long Zhang, Fang Li, Jine Yi, Carlos A. Driscoll, Agostinho Antunes, Tarás K. Oleksyk, Eduardo Eizirik, Polina L. Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomàs Marquès‐Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O’Brien
Software Mentions: 3
Published: almost 10 years ago

10.1093/molbev/msaa109

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Cited by: 12
Author(s): Bryan D. Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez‐Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Minjun Shi, Christine Hein Vu, Shu Dan Yeh, Laura Fanti, Xiao Qin Xia, Julio Rozas, José M. Ranz
Software Mentions: 3
Published: over 5 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 10 years ago

10.1186/s12864-016-2967-9

Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection
Cited by: 44
Author(s): Stanford Kwenda, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: about 9 years ago

10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 14 years ago

10.1186/gb-2014-15-2-r39

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Cited by: 226
Author(s): Linhai Wang, Shanlin Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Liu S, Rajeev K. Varshney, Jun Wang, Xiurong Zhang
Software Mentions: 3
Published: almost 12 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 11 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms8070981

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
Cited by: 15
Author(s): Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen, Yuxin Yang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.668623

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns
Cited by: 16
Author(s): Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Cláudio Benício Cardoso-Silva, Melina Cristina Mancini, Danilo Augusto Sforça, Lucas Borges dos Santos, James Shiniti Nagai, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Monalisa Sampaio Carneiro, Thiago Willian Almeida Balsalobre, Marcos G. Quiles, Welison Andrade Pereira, Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza
Software Mentions: 3
Published: over 4 years ago