10.1093/gbe/evy036

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa
Cited by: 33
Author(s): Germain Chevignon, Bret M. Boyd, Jayce W. Brandt, Kerry M. Oliver, Michael R. Strand
Software Mentions: 2
Published: over 8 years ago

10.1093/gbe/evz072

Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship
Cited by: 20
Author(s): Trestan Pillonel, Claire Bertelli, Sébastien Aeby, Marie de Barsy, Nicolas Jacquier, Carole Kebbi-Beghdadi, Linda Mueller, Manon Vouga, Gilbert Greub
Software Mentions: 2
Published: over 7 years ago

10.1186/s13073-014-0088-0

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity
Cited by: 90
Author(s): Barbara Hrdličková, Vinod Kumar, Kartiek Kanduri, Daria V. Zhernakova, Subhash Tripathi, Juha Karjalainen, Riikka Lund, Yang Li, Ubaid Ullah, Rutger Modderman, Wayel H. Abdulahad, Harri Lähdesmäki, Lude Franke, Riitta Lahesmaa, Cisca Wijmenga, Sebo Withoff
Software Mentions: 2
Published: almost 12 years ago

10.1186/2047-217X-3-1

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
Cited by: 67
Author(s): Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster, Andrew Stubbs
Software Mentions: 2
Published: over 12 years ago

10.1093/gigascience/giy046

Chromosome-scale assembly of the Monopterus genome
Cited by: 28
Author(s): Xueya Zhao, Majing Luo, Zhigang Li, Zhong Pei, Yang Cheng, Fengling Lai, Xin Wang, Min Jiang, Mingzhou Bai, Yulan Yang, Hanhua Cheng, Rongjia Zhou
Software Mentions: 2
Published: over 8 years ago

10.1093/gigascience/giz108

High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
Cited by: 35
Author(s): Andreas J. Stroehlein, Pasi K. Korhonen, Teik Min Chong, Yan Lue Lim, Kok‐Gan Chan, Bonnie L. Webster, David Rollinson, Paul J. Brindley, Robin B. Gasser, Neil D. Young
Software Mentions: 2
Published: about 7 years ago

10.1093/gigascience/giaa065

Galactic Circos: User-friendly Circos plots within the Galaxy platform
Cited by: 26
Author(s): Helena Rasche, Saskia Hiltemann
Software Mentions: 2
Published: over 6 years ago

10.1093/gigascience/giaa069

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
Cited by: 5
Author(s): Morteza Roodgar, Afshin Babveyh, Linh P. Nguyen, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, Mohan Avula, Lihua Jiang, Ruiqi Jian, Ho-Yong Lee, Giltae Song, Hassan Chaı̈b, Irving Weissman, Serafim Batzoglou, Susan Holmes, David Glenn Smith, Joseph L. Mankowski, Stefan Prost, M Snyder
Software Mentions: 2
Published: over 6 years ago

10.1038/s41437-020-00365-x

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population
Cited by: 24
Author(s): Yanhua Zhang, Yuzhe Wang, Yiyi Li, Jun Wu, Xinlei Wang, Cheng Bian, Yadong Tian, Guirong Sun, Ruili Han, Xiaojun Liu, Ruirui Jiang, Yanbin Wang, Guoxi Li, Wenting Li, Xiaoxiang Hu, Xin Kang
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-020-0308-2

A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination
Cited by: 4
Author(s): Thomas M. Davis, Yayuan Yang, Lise L. Mahoney, Daniel C. Frailey
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-021-00565-4

The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis
Cited by: 30
Author(s): Xiaoyang Xu, Yuan Huang, Xiaqing Yu, Shihua Huang, Yuming Sun, Ting Zhang, Qingquan Liu, Haiying Tong, Yongxia Zhang, Yinjie Wang, Chunxiao Liu, Lei Wu, Menglan Hou, Yongheng Yang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-021-00559-2

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis
Cited by: 22
Author(s): Da-Xia Chen, Yuan Pan, Yu Wang, Yanze Cui, Yingjun Zhang, Rangyu Mo, Xiaoli Wu, Jun Tan, Jian Zhang, Lianan Guo, Zhao Xiao, Wenkai Jiang, Tsieh Sun, Xiaodi Hu, Longyun Li
Software Mentions: 2
Published: over 5 years ago

10.1038/hortres.2016.52

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array
Cited by: 38
Author(s): M. Vukosavljev, Paul Arens, Roeland E. Voorrips, Wendy Pc van ‘t Westende, G. Esselink, Peter M. Bourke, Peter Cox, Eric van de Weg, R.G.F. Visser, Chris Maliepaard, M.J.M. Smulders
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41438-020-00435-5

Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis
Cited by: 19
Author(s): Pei Li, Baishi Wang, Jian Ye, Xiaodi Hu, Lihong Fu, Kui Li, Zhiyu Ni, Zhenlong Wang, Yujie Wei, Luye Shi, Ying Zhang, Xue Bai, Mengwan Jiang, Shuhui Wang, Chunling Ma, Shujin Li, Kaihui Liu, Wanshui Li, Bin Cong
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-020-00399-6

The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis)
Cited by: 20
Author(s): Yue Gao, Shengnan Huang, Gaoyang Qu, Wei Fu, Meidi Zhang, Zhiyong Liu, Hui Feng
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-020-00409-7

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset
Cited by: 8
Author(s): Kiflu Tesfamicael, Endale Gebre, Timothy J. March, Beata Sznajder, D. E. Mather, Carlos M. Rodríguez López
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-019-0202-y

A high-quality Actinidia chinensis (kiwifruit) genome
Cited by: 89
Author(s): Haolin Wu, Tao Ma, Minghui Kang, Fandi Ai, Junlin Zhang, Guanyong Dong, Jianquan Liu
Software Mentions: 2
Published: about 7 years ago

10.1038/hortres.2017.79

Divergent evolutionary patterns of the MAPK cascade genes in Brassica rapa and plant phylogenetics
Cited by: 20
Author(s): Peng Wu, Wenli Wang, Ying Liu, Xilin Hou
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41438-020-00373-2

Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits
Cited by: 2
Author(s): Yufang Guo, Ryan M. Warner
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-019-0191-x

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
Cited by: 37
Author(s): Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Hazem Hassan, Bihong Feng, Nathan K Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
Software Mentions: 2
Published: about 7 years ago

10.1038/s41438-020-0261-0

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander
Cited by: 31
Author(s): Xiaoming Song, Fulei Nie, Wei Chen, Xiao Ma, Ke Gong, Qing Yang, Jinpeng Wang, Nan Li, Pengchuan Sun, Qiaoying Pei, Tong Yu, Jingjing Hu, Xinyu Li, Tong Wu, Shuyan Feng, Xiuqing Li, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0253-0

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization
Cited by: 37
Author(s): Xiaoming Song, Jinpeng Wang, Pengchuan Sun, Xiao Ma, Qing Yang, Jingjing Hu, Shiqun Sun, Yuxian Li, Jigao Yu, Shuyan Feng, Qiaoying Pei, Tong Yu, Ning Yang, Yinzhe Liu, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0333-1

High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.)
Cited by: 25
Author(s): Xueqin Song, Yuhui Xu, Guolian Kang, Guangxun Fan, Fan Zhang, Chengyan Deng, Silan Dai, Hua He, Huaigen Xin, Yingying Li
Software Mentions: 2
Published: over 6 years ago

10.1016/j.meegid.2016.07.010

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus
Cited by: 16
Author(s): David J. King, Graham Freimanis, Richard Orton, Ryan Waters, Daniel T. Haydon, Donald P. King
Software Mentions: 2
Published: about 10 years ago

10.1128/IAI.00041-18

Adipocyte Model of Mycobacterium tuberculosis Infection Reveals Differential Availability of Iron to Bacilli in the Lipid-Rich Caseous Environment
Cited by: 10
Author(s): Aditya Nandy, Anupam Mondal, Rajesh Pandey, Prakash Arumugam, Stanzin Dawa, Neetika Jaisinghani, Vittal Rao, Debasis Dash, Sheetal Gandotra
Software Mentions: 2
Published: over 8 years ago

10.3390/insects11040232

Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)
Cited by: 17
Author(s): Nan Zhou, Yanling Dong, Pingping Qiao, Zhaofu Yang
Software Mentions: 2
Published: over 6 years ago

10.1093/jac/dkv119

Within-host diversity of MRSA antimicrobial resistances
Cited by: 51
Author(s): Kinga I. Stańczak-Mrozek, Anusha Manne, Gwenan M. Knight, Katherine A. Gould, Adam A. Witney, Jodi A. Lindsay
Software Mentions: 2
Published: over 11 years ago

10.1111/jcmm.16358

Analysis of T‐cell receptor repertoire in peripheral blood of patients with pancreatic cancer and other pancreatic diseases
Cited by: 2
Author(s): Hui Wang, Yue Yuan, Chunfeng Lu, Siqi Zhou, Yixuan Zhang, Jing Zhao, Chenghu Xu, Jie Yang, Haochen Su, Borui Li, Xi-Han Li, Pin Wang, Guifang Xu, Lei Wang, Xiaoping Zou, Shanshan Bao, Shu Zhang, Ying Lv
Software Mentions: 2
Published: over 5 years ago

10.1093/jxb/erv203

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening
Cited by: 166
Author(s): Bin Zhu, Yanmin Yang, Ran Li, Daqi Fu, Liwei Wen, Yunbo Luo, Hongliang Zhu
Software Mentions: 2
Published: over 11 years ago

10.1093/jxb/erx336

A disulfide bond A-like oxidoreductase is a strong candidate gene for self-incompatibility in apricot (Prunus armeniaca) pollen
Cited by: 20
Author(s): Juan Vicente Muñoz-Sanz, Elena Zuriaga, M. L. Badenes, Carlos Romero
Software Mentions: 2
Published: about 9 years ago

10.1093/jxb/erx384

Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula
Cited by: 74
Author(s): Tianzuo Wang, Mingfeng Zhao, Xiuxiu Zhang, Min Liu, Chen-ge Yang, Yuhui Chen, Rujin Chen, Jiangqi Wen, Kirankumar S. Mysore, Wenhao Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1093/jxb/erz541

Mutations of two FERONIA-like receptor genes enhance rice blast resistance without growth penalty
Cited by: 35
Author(s): Zhuhong Yang, Junjie Xing, Long Wang, Yue Liu, Jianing Qu, Yang Tan, Xiqin Fu, Qinlu Lin, Huafeng Deng, Feng Yu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1004744

Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk
Cited by: 122
Author(s): Sebastian Schulz, Denitsa Eckweiler, Agata Bielecka, Tanja Nicolai, Raimo Franke, Andreas Dötsch, Klaus Hornischer, Sebastian Bruchmann, Juliane Düvel, Susanne Häußler
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1006582

Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing
Cited by: 53
Author(s): A.T. Shenoy, Terry Brissac, Ryan P. Gilley, Nikhil Kumar, Yong Wang, Norberto González-Juarbe, Whitney S. Hinkle, Sean C. Daugherty, Amol C. Shetty, Sandra Ott, Luke J. Tallon, Jessy Deshane, Hervé Tettelin, Carlos J. Orihuela
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1007461

The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence
Cited by: 30
Author(s): Indu Warrier, Nikhil Ram-Mohan, Zeyu Zhu, Ariana Hazery, Haley Echlin, Jason Rosch, Michelle M. Meyer, Tim van Opijnen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1009447

A heterochromatin inducing protein differentially recognizes self versus foreign genomes
Cited by: 7
Author(s): Eric Burton, Ibukun A. Akinyemi, Tiffany R. Frey, Huanzhou Xu, Xiaofan Li, Lai Jing Su, Jizu Zhi, Michael T. McIntosh, Sumita Bhaduri‐McIntosh
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009886

A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road
Cited by: 7
Author(s): Xutong Wu, Chao Ning, Felix M. Key, Aida Andrades Valtueña, Aditya Kumar Lankapalli, Shizhu Gao, Yang Xuan, Fan Zhang, Linlin Liu, Zhongzhi Nie, Jian Ma, Johannes Krause, Alexander Herbig, Yinqiu Cui
Software Mentions: 2
Published: about 5 years ago

10.1186/1742-4690-11-17

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB
Cited by: 35
Author(s): Matthew S. Dahabieh, Marcel Ooms, Chanson J. Brumme, Jeremy M. G. Taylor, P. Richard Harrigan, Viviana Simon, Ivan Sadowski
Software Mentions: 2
Published: over 12 years ago

10.1186/1742-4690-10-126

Functional conservation of HIV-1 Gag: implications for rational drug design
Cited by: 56
Author(s): Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12284-019-0270-5

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection
Cited by: 8
Author(s): Zhenhui Zhong, Lian‐Yu Lin, Meilian Chen, Lili Lin, Xiaofeng Chen, Yunzhi Lin, Xi Chen, Zonghua Wang, Justice Norvienyeku, Huakun Zheng
Software Mentions: 2
Published: over 7 years ago

10.1126/sciadv.abh3032

Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies
Cited by: 26
Author(s): Namshik Han, Woochang Hwang, Konstantinos Tzelepis, Patrick Schmerer, Eliza Yankova, Méabh MacMahon, Winnie Lei, Nicholas M Katritsis, Anika Liu, Ulrike Felgenhauer, Alison Schuldt, Robert G. Harris, Kathryn Chapman, Frank McCaughan, Friedemann Weber, Tony Kouzarides
Software Mentions: 2
Published: over 5 years ago

10.1038/sdata.2015.72

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus
Cited by: 50
Author(s): Thomas Schmutzer, Birgit Samans, Emmanuelle Dyrszka, Chris Ulpinnis, Stéphan Weise, Doreen Stengel, Christian Colmsee, Denis Lespinasse, Zeljko Micic, Stefan Abel, Peter Duchscherer, Frank Breuer, Amine Abbadi, Gunhild Leckband, Rod J. Snowdon, Uwe Scholz
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep14941

Profiling RNA editing in human tissues: towards the inosinome Atlas
Cited by: 187
Author(s): Ernesto Picardi, Caterina Manzari, Francesca Mastropasqua, Italia Aiello, Anna Maria D’Erchia, Graziano Pesole
Software Mentions: 2
Published: about 11 years ago

10.1038/srep15443

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: about 11 years ago

10.1038/srep18227

MycoCAP - Mycobacterium Comparative Analysis Platform
Cited by: 4
Author(s): Siew Woh Choo, Mia Yang Ang, Avirup Dutta, Shi Tan, Cheuk Chuen Siow, Hamed Heydari, Naresh V.R. Mutha, Wei Yee Wee, George T.F. Wong
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep20650

Feature co-localization landscape of the human genome
Cited by: 11
Author(s): Siu-Kin Ng, Taobo Hu, Xi Long, Colin Chan, Suk Ying Tsang, Hong Xue
Software Mentions: 2
Published: over 10 years ago

10.1038/srep24501

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts
Cited by: 84
Author(s): Chao Bian, Yinchang Hu, Vydianathan Ravi, Irina M. Kuznetsova, Xueyan Shen, Xuemei Mu, Yu Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon-Hui Tay, Natascha May Thevasagayam, Aleksey Komissarov, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Jingjing Luo, Yi Liu, Hongmei Song, Chao Liu, Xuejie Wang, Donghong Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojie Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gaosi Xu, Pao Xu, Junmin Xu, Stephen J. O’Brien, László Orbán, Byrappa Venkatesh, Qiong Shi
Software Mentions: 2
Published: over 10 years ago

10.1038/srep29017

Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry
Cited by: 64
Author(s): Charles Hawkins, Julie Caruana, Erin Schiksnis, Zhongchi Liu
Software Mentions: 2
Published: over 10 years ago

10.1038/srep30158

The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features
Cited by: 28
Author(s): Songtao Gui, Zhihua Wu, Hongyuan Zhang, Yinzhen Zheng, Zhixuan Zhu, Dequan Liang, Yi Ding
Software Mentions: 2
Published: over 10 years ago

10.1038/srep30135

Full transcription of the chloroplast genome in photosynthetic eukaryotes
Cited by: 46
Author(s): Chao Shi, Shuo Wang, Enhua Xia, Jianjun Jiang, Fan-Chun Zeng, Li‐Zhi Gao
Software Mentions: 2
Published: about 10 years ago

10.1038/srep31209

Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: about 10 years ago

10.1038/srep32013

Evolutionary and Expression Analysis Provides Evidence for the Plant Glutamate-like Receptors Family is Involved in Woody Growth-related Function
Cited by: 13
Author(s): Jianqing Chen, Yinghui Jing, Xinyue Zhang, Leiting Li, Peng Wang, Shaoling Zhang, Hongsheng Zhou, Juyou Wu
Software Mentions: 2
Published: about 10 years ago

10.1038/srep28594

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Cited by: 91
Author(s): Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu‐Chien, Minami Matsui
Software Mentions: 2
Published: over 10 years ago

10.1038/srep32598

Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)
Cited by: 2
Author(s): Xu Zhang, Zhilin Qu, Bing Su
Software Mentions: 2
Published: about 10 years ago

10.1038/srep40579

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts
Cited by: 160
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep41124

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)
Cited by: 49
Author(s): Kazuki Mori, Kenta Shirasawa, Hitoshi Nogata, Chiharu Hirata, Kosuke Tashiro, Toshiyuki Habu, Sangwan Kim, Shuichi Himeno, Satoru Kuhara, Hiroyasu Ikegami
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-01446-4

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment
Cited by: 38
Author(s): Hongwei Fang, Yishan Chen, Lei Huang, Guojian He
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-03445-x

Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors
Cited by: 26
Author(s): Ramon M. Eichenberger, Chandra Ramakrishnan, Giancarlo Russo, Peter Deplazes, Adrian B. Hehl
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-03923-2

Nitric oxide mediated transcriptional modulation enhances plant adaptive responses to arsenic stress
Cited by: 82
Author(s): Pradyumna Kumar Singh, Yuvraj Indoliya, Abhisekh Singh Chauhan, Surendra Singh, Amit Singh, Sanjay Dwivedi, Rudra Deo Tripathi, Debasis Chakrabarty
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-05312-1

Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber
Cited by: 44
Author(s): Gang Yang, Mo Peng, Xiangli Tian, Shuanglin Dong
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-07039-5

Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence
Cited by: 22
Author(s): Satoshi Sugimura, Norio Kobayashi, Hiroaki Okae, T. Yamanouchi, Hideo Matsuda, Tatsuhiro Kojima, Akira Yajima, Y. Hashiyada, Masahiro Kaneda, Kei Sato, Kyoichi Imai, Kentaro Tanemura, Takahiro Arima, Robert B. Gilchrist
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-08256-8

Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification
Cited by: 22
Author(s): Jianjian Lv, Bingbo Gao, Ping Liu, Jian Li, Xianliang Meng
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-11466-9

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
Cited by: 19
Author(s): Lior David, Xavier Grau‐Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-13513-x

Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera
Cited by: 16
Author(s): Yingying Gao, Yi Wang, H. P. Xin, Shaohua Li, Zhenchang Liang
Software Mentions: 2
Published: about 9 years ago

10.1186/s40793-017-0274-y

First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Cited by: 7
Author(s): Emilie Muller, Shaman Narayanasamy, Myriam Zeimes, Cédric Christian Laczny, Laura Lebrun, Malte Herold, Nathan D. Hicks, John D. Gillece, James M. Schupp, Paul Keim, Paul Wilmes
Software Mentions: 2
Published: about 9 years ago

10.1007/s00122-019-03311-6

A reference high-density genetic map of greater yam (Dioscorea alata L.)
Cited by: 51
Author(s): Fabien Cormier, Floriane Lawac, Erick Malédon, Marie-Claire Gravillon, Elie Nudol, Pierre Mournet, Hélène Vignes, Gemma Arnau
Software Mentions: 2
Published: over 7 years ago

10.1007/s00122-019-03503-0

Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype
Cited by: 14
Author(s): Shantel A. Martinez, Oluwayesi Shorinola, Samantha Conselman, Deven R. See, Daniel Z. Skinner, Cristóbal Uauy, Camille M. Steber
Software Mentions: 2
Published: over 6 years ago

10.7150/thno.51243

Utilization of circulating cell-free DNA profiling to guide first-line chemotherapy in advanced lung squamous cell carcinoma
Cited by: 5
Author(s): Tao Jiang, Liyan Jiang, Xiaorong Dong, Kai Gu, Yueyin Pan, Qianling Shi, Guojun Zhang, Huijuan Wang, Xiaochun Zhang, Nong Yang, Yuping Li, Jianping Xiong, Tienan Yi, Min Peng, Yong Song, Yun Fan, Jiuwei Cui, Gongyan Chen, Wei Tan, Aimin Zang, Qisen Guo, Genming Zhao, Ziping Wang, Jianxing He, Wenxiu Yao, Xiaohong Wu, Kai Chen, Xiaohua Hu, Chunhong Hu, Lu Yue, Da Jiang, Guangfa Wang, Junfeng Liu, Guohua Yang, Junling Li, Henghui Zhang, Lihong Wu, Fang Lü, Dandan Liang, Yang Zhao, Weihong Zhao, Wenmin Xie, Shengxiang Ren, Caicun Zhou
Software Mentions: 2
Published: almost 6 years ago

10.1038/tp.2015.214

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns
Cited by: 129
Author(s): José Vicente Sánchez-Mut, Holger Heyn, Enrique Vidal, Sebastian Morán, Sergi Sayols, Raúl Delgado-Morales, Matthew D. Schultz, Belén Ansoleaga, Paula Garcia‐Esparcia, Meritxell Pons-Espinal, María Martínez de Lagrán, Joaquín Dopazo, Alberto Rábano, Jesús Ávila, Mara Dierssen, Ira T. Lott, Isidre Ferrer, Joseph R. Ecker, Manel Esteller
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41398-020-00879-2

Mapping PTSD symptoms to brain networks: a machine learning study
Cited by: 23
Author(s): Amin Zandvakili, Jennifer Barredo, Hannah Swearingen, Emily Aiken, Yosef A. Berlow, Benjamin D. Greenberg, Linda L. Carpenter, Noah S. Philip
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.01630-17

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes
Cited by: 87
Author(s): Margaret I. Steele, Waldan K. Kwong, Marvin Whiteley, Nancy A. Moran
Software Mentions: 2
Published: almost 9 years ago

10.1128/mBio.00097-18

Phosphotyrosine-Mediated Regulation of Enterohemorrhagic <i>Escherichia coli</i> Virulence
Cited by: 6
Author(s): Colin D. Robertson, Tracy H. Hazen, James B. Kaper, David A. Rasko, Anders Højgaard Hansen
Software Mentions: 2
Published: over 8 years ago

10.1128/mBio.02899-18

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes
Cited by: 30
Author(s): Ankita Kothari, Yu Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Dominique C. Joyner, Terry C. Hazen, Steven W. Singer, Aindrila Mukhopadhyay
Software Mentions: 2
Published: over 7 years ago

10.1128/mBio.00764-19

Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to <i>Cryptococcus</i> Pathogens
Cited by: 32
Author(s): Andrew Ryan Passer, Marco A. Coelho, R. Blake Billmyre, Minou Nowrousian, Moritz Mittelbach, Andrey Yurkov, Anna Floyd Averette, Christina A. Cuomo, Sheng Sun, Joseph Heitman
Software Mentions: 2
Published: over 7 years ago

10.1128/mBio.00254-21

Accessory Genome Dynamics and Structural Variation of <i>Shigella</i> from Persistent Infections
Cited by: 7
Author(s): Rebecca J. Bengtsson, Timothy J. Dallman, Hester Allen, P Malaka De Silva, George E. Stenhouse, Caisey V Pulford, Rebecca J. Bennett, Claire Jenkins, Kate S. Baker
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00102-17

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2 ^T Using Transcriptomics
Cited by: 9
Author(s): Tom Berben, Cherel Balkema, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: almost 9 years ago

10.1128/mSystems.00867-20

Insights into the Metabolism and Evolution of the Genus <i>Acidiphilium</i> , a Typical Acidophile in Acid Mine Drainage
Cited by: 24
Author(s): Liangzhi Li, Zhenghua Liu, Min Zhang, Delong Meng, Xueduan Liu, Pei Wang, Xiu-Tong Li, Zhen Jiang, Shuiping Zhong, Cheng‐Ying Jiang, Huaqun Yin
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12960-020-0463-4

Gender imbalance in executive management positions at the Mexican National Institutes of Health
Cited by: 9
Author(s): Lucero Soledad Rivera-Romano, Cristóbal Fresno, Enrique Hernández‐Lemus, Mireya Martínez-García, Maité Vallejo
Software Mentions: 2
Published: over 6 years ago

10.1038/ismej.2016.192

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system
Cited by: 157
Author(s): Laura A. Sauder, Mads Albertsen, Katja Engel, Jasmin Schwarz, Per Halkjær Nielsen, Michael Wagner, Josh D. Neufeld
Software Mentions: 2
Published: over 9 years ago

10.1038/s41396-020-00827-4

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
Cited by: 95
Author(s): Dimitra Sakoula, Hanna Koch, J. Howard Frank, Mike S. M. Jetten, Maartje A. H. J. van Kessel, Sebastian Lücker
Software Mentions: 2
Published: almost 6 years ago

10.3390/jof7050384

Differential Expression of Amanitin Biosynthetic Genes and Novel Cyclic Peptides in Amanita molliuscula
Cited by: 3
Author(s): Yunjiao Lüli, Shengwen Zhou, Xuan Li, Zuohong Chen, Zhu‐Liang Yang, Hong Luo
Software Mentions: 2
Published: over 5 years ago

10.1155/2013/678969

Conservation, Divergence, and Genome-Wide Distribution of<i>PAL</i>and<i>POX A</i>Gene Families in Plants
Cited by: 29
Author(s): Hukam C. Rawal, Nisha Singh, Tilak Raj Sharma
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13045-017-0465-4

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets
Cited by: 36
Author(s): Katherine E. Hill, Andrew D. Kelly, Marieke L. Kuijjer, William T. Barry, Ahmed Rattani, Cassandra Garbutt, Haydn Kissick, Katherine A. Janeway, Antonio R. Perez–Atayde, Jeffrey D. Goldsmith, Mark C. Gebhardt, Mohamed S. Arredouani, Greg Cote, Francis J. Hornicek, Edwin Choy, Zhenfeng Duan, John Quackenbush, Benjamin Haibe‐Kains, Dimitrios Spentzos
Software Mentions: 2
Published: over 9 years ago

10.3390/ijerph16142474

Implications of Soil Pollution with Diesel Oil and BP Petroleum with ACTIVE Technology for Soil Health
Cited by: 33
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.40655

Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis
Cited by: 64
Author(s): Leonardo Furci, Ritushree Jain, Joost H. M. Stassen, Oliver Berkowitz, James Whelan, David Roquis, Victoire Baillet, Vincent Colot, Frank Johannes, Jurriaan Ton
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.62474

Integron activity accelerates the evolution of antibiotic resistance
Cited by: 39
Author(s): Célia Souque, José Antonio Escudero, R. Craig MacLean
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.09214

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma
Cited by: 112
Author(s): Ana Rita Grosso, Ana Paula Leite, Sílvia Carvalho, Maria Margarida Nunes Gaspar de Matos, Filipa Martins, Alexandra C Vítor, Joana Desterro, Maria Carmo‐Fonseca, Sérgio Fernandes de Almeida
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.53886

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Cited by: 68
Author(s): Daniel R. Evans, M. Patrick Griffith, Alexander Sundermann, Kathleen A. Shutt, Melissa Saul, Mustapha M. Mustapha, Jane W. Marsh, Vaughn S. Cooper, Lee H. Harrison, Daria Van Tyne
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.26036

Dynamics of genomic innovation in the unicellular ancestry of animals
Cited by: 113
Author(s): Xavier Grau‐Bové, Guifré Torruella, Stuart P. Donachie, Hiroshi Suga, Guy Leonard, Thomas A. Richards, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms160922258

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae
Cited by: 24
Author(s): Monika Szczecińska, Jakub Sawicki
Software Mentions: 2
Published: about 11 years ago

10.3390/ijms161125951

Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)
Cited by: 26
Author(s): Jingqun Ao, Jia Li, Xinxin You, Yinnan Mu, Yang Ding, Kaiqiong Mao, Chao Bian, Pengfei Mu, Qiong Shi, Xinhua Chen
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms18081734

Genome-Wide Organization and Expression Profiling of the SBP-Box Gene Family in Chinese Jujube (Ziziphus jujuba Mill.)
Cited by: 25
Author(s): Shuang Song, Heng Zhou, Songbai Sheng, Mengshu Cao, Yingyue Li, Xiaoming Pang
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms19020550

Expression of Pluripotency Genes in Chondrocyte-Like Cells Differentiated from Human Induced Pluripotent Stem Cells
Cited by: 5
Author(s): Ewelina Stelcer, Katarzyna Kulcenty, Marcin Ruciński, Karol Jopek, Tomasz Trzeciak, Magdalena Richter, Joanna Wróblewska, Wiktoria Maria Suchorska
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms19103246

Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses
Cited by: 19
Author(s): Jianbo Li, Jin Zhang, Huixia Jia, Zhiqiang Yue, Mengzhu Lu, Xuebing Xin, Jianjun Hu
Software Mentions: 2
Published: about 8 years ago

10.3390/ijms20010152

Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat
Cited by: 24
Author(s): Jie Tang, Lianming Du, Yuanmei Liang, Maurycy Daroch
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms20194864

Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum
Cited by: 15
Author(s): Liang Yang, Mingjun Miao, Hongjun Lyu, Xue Cao, Ju Li, Li YueJian, Zhi Li, Wei Chang
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms20215311

Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton
Cited by: 25
Author(s): Muhammad Imran, Sarfraz Shafiq, Muhammad Farooq, Muhammad Kashif Naeem, Émilie Widemann, Ali Bakhsh, Kevin B. Jensen, Richard R.‐C. Wang
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms20225796

Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco
Cited by: 24
Author(s): Qianqian Zhou, Qingchang Li, Peng Li, Songtao Zhang, Che Liu, Jingjing Jin, Peijian Cao, Yongxia Yang
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms21010351

Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis
Cited by: 24
Author(s): Liru Cao, Pengyu Zhang, LU Xin-shi, Guorui Wang, Zhenhua Wang, Qianjin Zhang, Xin Zhang, Xin Wei, Fujian Mei, Wei Li, Tongchao Wang
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms21072580

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)
Cited by: 4
Author(s): Katarzyna B. Czyż, Michał Książkiewicz, Grzegorz Koczyk, Anna Szczepaniak, Jan Podkowiński, B. Naganowska
Software Mentions: 2
Published: over 6 years ago