10.3390/jof6010007

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1
Cited by: 5
Author(s): Ling Peng, Liangwei Li, Xiaochuan Liu, Jianwei Chen, Chengcheng Shi, Wenjie Guo, Qiwu Xu, Guangyi Fan, Xin Liu, Dehai Li
Software Mentions: 3
Published: almost 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

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 10 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

10.1155/2016/1562041

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

10.7554/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

10.1007/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

10.1007/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

10.7150/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

10.1038/s41598-017-15363-z

LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets
Cited by: 45
Author(s): Zhixu Ni, Georgia Angelidou, Ralf Hoffmann, Maria Fedorova
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-09680-6

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
Cited by: 10
Author(s): Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-017-10434-7

The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants
Cited by: 32
Author(s): Kamil Myszczyński, Alina Bączkiewicz, Katarzyna Buczkowska, Monika Ślipiko, Monika Szczecińska, Jakub Sawicki
Software Mentions: 3
Published: about 8 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 4 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

10.1186/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

10.1186/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

10.1186/1471-2164-15-773

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

10.1111/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

10.1111/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

10.1038/srep28851

Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules
Cited by: 17
Author(s): Isar Nassiri, Rosario Lombardo, Mario Lauria, Melissa J. Morine, Petros Moyseos, Vijayalakshmi Varma, Greg T. Nolen, Bridgett Knox, Daniel T. Sloper, Jim Kaput, Corrado Priami
Software Mentions: 3
Published: over 9 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: about 9 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

10.1111/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/s41598-017-03528-9

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations
Cited by: 8
Author(s): Yufang Guo, Wei Kuang Lin, Qiuxia Chen, Verónica Vallejo, Ryan M. Warner
Software Mentions: 3
Published: over 8 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

10.1111/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/srep20957

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Cited by: 9
Author(s): Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe, Tim De Meyer
Software Mentions: 3
Published: over 9 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: about 12 years ago

10.1038/srep25107

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Cited by: 27
Author(s): Weike Duan, Zhinan Huang, Xiaoming Song, Tongkun Liu, Hailong Liu, Xilin Hou, Ying Liu
Software Mentions: 3
Published: over 9 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: almost 5 years ago

10.1073/pnas.2005536117

Molecular causes of an evolutionary shift along the parasitism–mutualism continuum in a bacterial symbiont
Cited by: 12
Author(s): Paul Herrera, Lisa N Schuster, Cécilia Wentrup, Lena König, Thomas Kempinger, Hyunsoo Na, Jasmin Schwarz, Stephan Köstlbacher, Florian Wascher, Markus Zojer, Thomas Rattei, Matthias Horn
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-019-0014-9

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Cited by: 14
Author(s): Xiaoyong Li, Geng Tian, Yue Zhao, Ji Wu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0129396

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome
Cited by: 26
Author(s): Ching-Ping Lin, Chih‐Yuan Ko, Ching-I Kuo, Mao-Sen Liu, Roland Schafleitner, Long-Fang Oliver Chen
Software Mentions: 3
Published: over 10 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

10.1093/pcmedi/pbab012

Spaceflight decelerates the epigenetic clock orchestrated with a global alteration in DNA methylome and transcriptome in the mouse retina
Cited by: 7
Author(s): Zhong Chen, Seta Stanbouly, Nina C. Nishiyama, Xin Chen, Michael D. Delp, Hongyu Qiu, Xiao Wen Mao, Charles Wang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41597-019-0291-3

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: almost 6 years ago

10.3390/genes12030417

Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)
Cited by: 9
Author(s): Fulei Mo, Nian Zhang, Yefeng Qiu, Lingjun Meng, Mozhen Cheng, Jiayin Liu, Lanning Yao, Rui Lv, Yuxin Liu, Yao Zhang, Xiuling Chen, Aoxue Wang
Software Mentions: 3
Published: over 4 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

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 4 years ago

10.1093/g3journal/jkab002

<i>De novo</i>whole-genome assembly and resequencing resources for the roan (<i>Hippotragus equinus</i>), an iconic African antelope
Cited by: 4
Author(s): Margarida Gonçalves, Hans R. Siegismund, Bettine Jansen van Vuuren, Klaus‐Peter Koepfli, Nathalie Ferrand, Raquel Godinho
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes10070544

Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment
Cited by: 18
Author(s): Tasuku Ito, Hiroaki Nishio, Yoshiaki Tarutani, Naoko Emura, Mie N. Honjo, Atsushi Toyoda, Asao Fujiyama, Tetsuji Kakutani, Hiroshi Kudoh
Software Mentions: 3
Published: over 6 years ago

10.1093/jxb/erz256

Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice
Cited by: 24
Author(s): Gopal Misra, Roslen Anacleto, Saurabh Badoni, Vito M. Butardo, Lilia Molina, Andreas Graner, Matty Demont, Matthew K. Morell, Nese Sreenivasulu
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 11 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

10.1534/g3.116.037150

The Long Noncoding RNA Transcriptome of<i>Dictyostelium discoideum</i>Development
Cited by: 8
Author(s): Rafael D. Rosengarten, Balaji Santhanam, Janez Kokošar, Gad Shaulsky
Software Mentions: 3
Published: almost 9 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

10.1534/g3.115.026666

The <i>HIST1</i> Locus Escapes Reprogramming in Cloned Bovine Embryos
Cited by: 5
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Kyuheum Jeon, Yong‐Kook Kang
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2019.00586

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis
Cited by: 27
Author(s): Marco Kreuzer, Caroline Howard, Bhim Adhikari, Colin A. Pendry, Julie A. Hawkins
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01083

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2021.684619

Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)
Cited by: 4
Author(s): Tingting Li, Wenqiu Pan, Yiyuan Yuan, Ying Liu, Yihan Li, Xiaoyu Wu, Fei Wang, Licao Cui
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 5 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

10.3389/fpls.2016.01186

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2021.633310

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum
Cited by: 27
Author(s): Luis Díaz-Garcia, Luis Fernando García-Ortega, María González-Rodriguez, Luis Delaye, Massimo Iorizzo, Juan Zalapa
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2019.00918

A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus
Cited by: 10
Author(s): Diego Zappacosta, Jimena Gallardo, José Luís Carballo, M Meier, Juan Manuel Rodrigo, Cristian Gallo, Juan Pablo Selva, Juliana Stein, Juan Pablo Amelio Ortiz, Emidio Albertini, Viviana Echenique
Software Mentions: 3
Published: over 6 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: over 4 years ago

10.3389/fpls.2018.01332

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family
Cited by: 28
Author(s): Yueying Li, Liangliang He, Jing Li, Jianghua Chen, Changning Liu
Software Mentions: 3
Published: about 7 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

10.3389/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: almost 9 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: about 5 years ago

10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants
Cited by: 23
Author(s): Gangyi Yang, Wenlong Luo, Jian Zhang, Xian-cheng Yan, Yuguo Du, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1008337

Comprehensive analysis of iron utilization by Mycobacterium tuberculosis
Cited by: 52
Author(s): Lei Zhang, R. Curtis Hendrickson, Virginia Meikle, Elliot J. Lefkowitz, Thomas R. Ioerger, Michael Niederweis
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-3852-x

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida
Cited by: 97
Author(s): Anna Faddeeva-Vakhrusheva, Ken Kraaijeveld, Martijn F.L. Derks, Seyed Yahya Anvar, Valeria Agamennone, Wouter Suring, Andries A. Kampfraath, Jacintha Ellers, Giang Le Ngoc, Cornelis A.M. van Gestel, Janine Mariën, Sandra Smit, Nico M. van Straalen, Dick Roelofs
Software Mentions: 3
Published: over 8 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

10.3389/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: almost 10 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: over 7 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: almost 10 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: about 4 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: over 4 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: over 6 years ago

10.1186/s12864-016-2967-9

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

10.3389/fnins.2017.00358

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study
Cited by: 7
Author(s): Edgar Guevara, Wyston C. Pierre, Camille Tessier, Luis Akakpo, Irène Londono, Frédéric Lesage, Gregory A. Lodygensky
Software Mentions: 3
Published: over 8 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: about 7 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: about 4 years ago

10.3389/fmicb.2021.674952

Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals
Cited by: 19
Author(s): Syed Mashab Ali Shah, Moein Khojasteh, Qi Wang, S. Mohsen Taghavi, Zhi-Hong Xu, Pejman Khodaygan, Lifang Zou, Sedighe Mohammadikhah, Gongyou Chen, Ebrahim Osdaghi
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000265

Insertion sequences drive the emergence of a highly adapted human pathogen
Cited by: 18
Author(s): Erwin Sentausa, Pauline Basso, Alice Berry, Annie Adrait, Gwendoline Bellement, Yohann Couté, Stephen Lory, Sylvie Elsen, Ina Attrée
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2017.01009

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.01930

New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: about 5 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

10.1099/mgen.0.000154

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 10 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

10.1111/1751-7915.13655

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: about 5 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 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

10.1038/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 5 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

10.1038/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 7 years ago

10.3389/fneur.2020.00184

Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke
Cited by: 13
Author(s): Yanfei Zhang, Ling‐Bing Meng, Meng-lei Hao, Jiao Yang, Tong Zou
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.682356

Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH
Cited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2014.00789

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
Cited by: 38
Author(s): Vikash Singh, Mukesh Jain, Rohini Garg
Software Mentions: 3
Published: almost 11 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

10.3389/fmicb.2019.01325

Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Cited by: 29
Author(s): Aniela B. Mundinger, Christopher E. Lawson, Mike S. M. Jetten, Hanna Koch, Sebastian Lücker
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.01448

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Cited by: 33
Author(s): Jade L. L. Teng, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Samson S. Y. Wong, Pak C. Sham, Susanna K. P. Lau, Patrick C. Y. Woo
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2019.01446

Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia
Cited by: 13
Author(s): Bryan Naidenov, Alexander Lim, Karyn Willyerd, Nathanial Torres, William L. Johnson, Hong Jin Hwang, Peter R. Hoyt, John E. Gustafson, Charles Chen
Software Mentions: 3
Published: over 6 years ago