Ecosyste.ms: Papers

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.1186/1475-2859-6-29

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
Cited by: 107
Author(s): L.M. Serrano, Douwe Molenaar, Michiel Wels, Bas Teusink, Peter A. Bron, Willem M. de Vos, Eddy J. Smid
Software Mentions: 4
Published: about 17 years ago

10.1186/s12864-021-07666-3

Re-examination of two diatom reference genomes using long-read sequencing
Cited by: 19
Author(s): Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-020-00827-8

Disentangling the mechanisms shaping the surface ocean microbiota
Cited by: 131
Author(s): Ramiro Logares, Ina Maria Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas Sebastian Benedikt Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz‐González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol, Ramón Massana
Software Mentions: 4
Published: over 4 years ago

10.1111/1751-7915.12006

Tips and tricks for the assembly of aCorynebacterium pseudotuberculosisgenome using a semiconductor sequencer
Cited by: 12
Author(s): Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Siomar de Castro Soares, Anderson Santos, Síntia Almeida, Luís Carlos Guimarães, Flávia Figueira, Eudes Guilherme Vieria Barbosa, Andreas Tauch, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 4
Published: almost 12 years ago

10.3389/fcimb.2021.652837

Potential Roles of Oral Microbiota in the Pathogenesis of Immunoglobin A Nephropathy
Cited by: 6
Author(s): Jiawei He, Xu‐Jie Zhou, Ping Hou, Yan-Na Wang, Tao Gan, Yang Li, Yang Liu, Lijun Liu, Sufang Shi, Li Zhu, Jicheng Lv, Hong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1111/1751-7915.13496

Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state‐associated and mobile multidrug resistance‐carrying bacteria
Cited by: 15
Author(s): Dorota A. Dobrzanska, Matthew T F Lamaudière, Jess Rollason, Lauren Acton, Michael Duncan, Sharon Compton, John Simms, Gareth D. Weedall, Igor Y. Morozov
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-015-1799-3

RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress
Cited by: 67
Author(s): Longxing Hu, Huiying Li, Liang Chen, Yanhong Lou, Erick Amombo, Jinmin Fu
Software Mentions: 4
Published: over 9 years ago

10.1186/s13072-020-00368-2

Chromatin accessibility dynamics of Chlamydia-infected epithelial cells
Cited by: 4
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry S. A. Myers
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.118.200677

Genotype-by-Environment-by-Environment Interactions in the <i>Saccharomyces cerevisiae</i> Transcriptomic Response to Alcohols and Anaerobiosis
Cited by: 5
Author(s): Maria Sardi, Molly Krause, Justin Heilberger, Audrey P. Gasch
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000297

Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids
Cited by: 16
Author(s): Raymond Kiu, Shabhonam Caim, Anaïs Painset, Derek Pickard, Craig Swift, Gordon Dougan, Alison E. Mather, Corinne Amar, Lindsay J. Hall
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.3302

Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans
Cited by: 19
Author(s): Alizé Lacoste Jeanson, Ján Dupej, Chiara Villa, Jaroslav Brůžek
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.7071

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
Cited by: 1
Author(s): Jakub Hynšt, Karla Plevová, Lenka Radová, Vojtěch Bystrý, Karol Pál, Šárka Pospı́šilová
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-019-0306-9

Mechanistic insights into the evolution of DUF26-containing proteins in land plants
Cited by: 67
Author(s): Aleksia Vaattovaara, Benjamin Brandt, Sitaram Rajaraman, Omid Safronov, Andres Veidenberg, Markéta Luklová, Jaakko Kangasjärvi, Ari Löytynoja, Michael Hothorn, Jarkko Salojärvi, Michael Wrzaczek
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSystems.00127-17

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts
Cited by: 2
Author(s): Xiaoyun Ren, David Eccles, Gabrielle Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul Geeleher, Joanna K. MacKichan
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13046-020-1541-0

FKBP9 promotes the malignant behavior of glioblastoma cells and confers resistance to endoplasmic reticulum stress inducers
Cited by: 16
Author(s): Huizhe Xu, Peng Liu, Yumei Yan, Kun Fang, Dapeng Liang, Yangcheng Liu, Xiaohong Zhang, Songyan Wu, Jin Ma, Ruoyu Wang, Tao Li, Haozhe Piao, Meng Shao
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-87759-x

SIRT1 promotes lipid metabolism and mitochondrial biogenesis in adipocytes and coordinates adipogenesis by targeting key enzymatic pathways
Cited by: 58
Author(s): Yasser Majeed, Najeeb Halabi, Aisha Madani, Rudolf Engelke, Aditya Bhagwat, Houari Abdesselem, Maha Victor Agha, Muneera Vakayil, Raphael Jean Courjaret, Neha Goswami, Hisham Ben Hamidane, Mohamed A. Elrayess, Arash Rafii, Johannes Graumann, Frank Schmidt, Nayef Mazloum
Software Mentions: 4
Published: over 3 years ago

10.1002/cti2.1087

Rapid sequencing‐based diagnosis of infectious bacterial species from meningitis patients in Zambia
Cited by: 26
Author(s): So Nakagawa, Shigeaki Inoue, Kirill Kryukov, Junya Yamagishi, Ayumu Ohno, Kyoko Hayashida, Ruth Nakazwe, Mox Kalumbi, Darlington Mwenya, Nana Asami, Chihiro Sugimoto, Mable Mutengo, Tadashi Imanishi
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.66014

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses
Cited by: 18
Author(s): Stephan Wilmes, Polly-Anne Jeffrey, Jonathan Martínez-Fábregas, Maximillian Hafer, Paul K. Fyfe, Elizabeth Pöhler, Silvia Gaggero, Martín López‐García, Grant Lythe, Charles Taylor, Thomas Guerrier, David Launay, Suman Mitra, Jacob Piehler, Carmen Molina-Parı́s, Ignacio Moraga
Software Mentions: 4
Published: over 3 years ago

10.1098/rsob.200052

Bioinformatical dissection of fission yeast DNA replication origins
Cited by: 1
Author(s): Koji Masuda, Claire Renard-Guillet, Katsuhiko Shirahige, Takashi Sutani
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-19684-5

Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
Cited by: 23
Author(s): Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Alves Campos, Rony Swennen, Sébastien Carpentier
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0109262

De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
Cited by: 48
Author(s): Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Software Mentions: 4
Published: about 10 years ago

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: over 5 years ago

10.1038/s41438-018-0073-7

Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV
Cited by: 39
Author(s): Tian Wang, Zhiqi Deng, Xi Zhang, Hongzheng Wang, Yu Wang, Xiuying Liu, Songyu Liu, Feng Xu, Tao Li, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 4
Published: about 6 years ago

10.1155/2017/7210463

Comparison of Attenuated Total Reflectance Mid-Infrared, Near Infrared, and ¹H-Nuclear Magnetic Resonance Spectroscopies for the Determination of Coffee’s Geographical Origin
Cited by: 27
Author(s): Jéssica Medina, Diana Caro Rodríguez, Victoria A. Arana, Andrés Bernal, Pierre Esseiva, Julien Wist
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0104355

Copy Number Variation in Thai Population
Cited by: 25
Author(s): Bhoom Suktitipat, Chaiwat Naktang, Wuttichai Mhuantong, Tularak Thitima, Paramita Artiwet, Pasomsap Ekawat, Wallaya Jongjaroenprasert, Suthat Fuchareon, Surakameth Mahasirimongkol, Wasun Chantratita, Boonsit Yimwadsana, Varodom Charoensawan, Natini Jinawath
Software Mentions: 4
Published: over 10 years ago

10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)
Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: about 5 years ago

10.1016/j.ajhg.2015.07.007

Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability
Cited by: 51
Author(s): Stephen R.F. Twigg, Jennifer Forecki, Jacqueline A.C. Goos, Ivy C.A. Richardson, A. Jeannette M. Hoogeboom, Ans M.W. van den Ouweland, Sigrid Swagemakers, Maarten H. Lequin, Daniel Van Antwerp, Simon J. McGowan, Isabelle Westbury, Kerry A. Miller, Steven A. Wall, Peter J. van der Spek, Irene M.J. Mathijssen, Erwin Pauws, Christa Merzdorf, Andrew O.M. Wilkie
Software Mentions: 4
Published: about 9 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/8162524

High-Throughput Sequencing and Exploration of the lncRNA-circRNA-miRNA-mRNA Network in Type 2 Diabetes Mellitus
Cited by: 39
Author(s): Fang Yang, Chen Yang, Zhiqiang Xue, Yaogai Lv, Ли Шен, Kexin Li, Pingping Zheng, Pan Pan, Tianyu Feng, Lina Jin, Yan Yao
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-016-1428-4

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Cited by: 45
Author(s): Roberto A. Barrero, Kathryn R. Napier, J. H. Cunnington, L. W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13073-020-00824-4

The identification of novel immunogenic antigens as potential Shigella vaccine components
Cited by: 8
Author(s): Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner, Stephen Baker
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-59549-4

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
Cited by: 7
Author(s): Katrine Højholt Iversen, Louise Rasmussen, Kosai Al-Nakeeb, José Juan Almagro Armenteros, Christian Salgård Jensen, Rimtas Dargis, Oksana Lukjancenko, Ulrik Stenz Justesen, Claus Moser, Flemming Schønning Rosenvinge, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Simon Rasmussen
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0124671

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Cited by: 158
Author(s): Dáithí C. Murray, Megan L. Coghlan, Michael Bunce
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-015-0848-1

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling
Cited by: 59
Author(s): J. David Barrass, Jane E. A. Reid, Yuanhua Huang, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs, Sander Granneman
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-13-136

A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica
Cited by: 60
Author(s): S. Ueno, Yoshinari Moriguchi, Kentaro Uchiyama, Tokuko Ujino‐Ihara, Norihiro Futamura, Tetsuya Sakurai, Kenji Shinohara, Yoshihiko Tsumura
Software Mentions: 4
Published: almost 13 years ago

10.1534/genetics.118.301515

PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in <i>Arabidopsis thaliana</i>
Cited by: 17
Author(s): Tohru Kanno, Peter Venhuizen, Wen Teng, Wen-Dar Lin, Phebe Chiou, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0208641

Use of a sequential high throughput screening assay to identify novel inhibitors of the eukaryotic SRP-Sec61 targeting/translocation pathway
Cited by: 5
Author(s): W. Klein, Claudia Rutz, Jamina Eckhard, Becky Provinciael, Edgar Specker, Martin Neuenschwander, Gunnar Kleinau, Patrick Scheerer, Jens-Peter von Kries, Marc Nazaré, Kurt Vermeire, Ralf Schülein
Software Mentions: 4
Published: almost 6 years ago

10.3390/genes12010044

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data
Cited by: 12
Author(s): Claudio Cucini, Pietro Paolo Fanciulli, Francesco Frati, Peter Convey, Francesco Nardi, Antonio Carapelli
Software Mentions: 4
Published: almost 4 years ago

10.1186/gb-2013-14-12-r146

Lsh regulates LTR retrotransposon repression independently of Dnmt3b function
Cited by: 53
Author(s): Donncha S. Dunican, Hazel A Cruickshanks, Masako Suzuki, Colin A. Semple, Tracey Davey, Robert J. Arceci, John M. Greally, Ian R. Adams, Richard R. Meehan
Software Mentions: 4
Published: almost 12 years ago

10.1186/s13059-020-02235-5

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
Cited by: 36
Author(s): José Antonio Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, M. Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel, Korbinian Schneeberger
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40168-017-0301-7

Environmental drivers of viral community composition in Antarctic soils identified by viromics
Cited by: 87
Author(s): Evelien M. Adriaenssens, Rolf Kramer, Marc W. Van Goethem, Thulani P. Makhalanyane, Ian D. Hogg, Don A. Cowan
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-020-3386-0

GsmPlot: a web server to visualize epigenome data in NCBI
Cited by: 2
Author(s): Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12870-019-1708-z

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

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in <i>Arabidopsis thaliana</i>
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: over 4 years ago

10.1534/g3.120.401578

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of <i>Dictyostelium discoideum</i>
Cited by: 8
Author(s): Sibel Küçükyıldırım, Megan G Behringer, Way Sung, Debra A. Brock, Thomas G. Doak, Hatıce Mergen, David C. Queller, Joan E. Strassmann, Michael Lynch
Software Mentions: 4
Published: about 4 years ago

10.1093/molbev/msz063

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana
Cited by: 16
Author(s): Reetu Tuteja, Peter C. McKeown, Paraic C. Ryan, Claire C. Morgan, Mark T.A. Donoghue, Tim Downing, Mary J. O’Connell, Charles Spillane
Software Mentions: 4
Published: over 5 years ago

10.1111/mec.12521

Population genomic footprints of selection and associations with climate in natural populations of <i>Arabidopsis halleri</i> from the Alps
Cited by: 89
Author(s): Martin C. Fischer, Christian Rellstab, Andrew Tedder, Stefan Zoller, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer
Software Mentions: 4
Published: about 11 years ago

10.1186/s13073-021-00853-7

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis
Cited by: 20
Author(s): Damian R. Plichta, Juhi Somani, Matthieu Pichaud, Zachary S Wallace, Ana D. Fernandes, Cory A. Perugino, Harri Lähdesmäki, John H. Stone, Hera Vlamakis, Daniel C. Chung, Dinesh Khanna, Shiv Pillai, Ramnik J. Xavier
Software Mentions: 4
Published: over 3 years ago

10.1186/s12870-014-0306-3

Increased sucrose levels mediate selective mRNA translation in Arabidopsis
Cited by: 22
Author(s): Magdalena Gamm, Alessia Peviani, Anne Honsel, Berend Snel, Sjef Smeekens, Johannes Hanson
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0098404

Deep Sequencing Reveals New Aspects of Progesterone Receptor Signaling in Breast Cancer Cells
Cited by: 12
Author(s): Anastasia Kougioumtzi, Panayiotis Tsaparas, Angeliki Magklara
Software Mentions: 4
Published: over 10 years ago

10.1093/g3journal/jkaa042

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant
Cited by: 2
Author(s): Qian Zhu, Warwick N. Stiller, Philippe Moncuquet, Stuart Gordon, Yuman Yuan, Scott Barnes, Iain W. Wilson
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-016-2457-0

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster
Cited by: 18
Author(s): Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-Chung Tung, Kwei-Yan Liu, Hsueh‐Tzu Shih, Yi-Jyun Chen, Yen‐Ting Lin, Li‐Ting Ma, Jun Huang, Po-Chun Wu, Hong Mei, Fang-Hua Chu, June‐Tai Wu, Wen-Hsiung Li, Chien‐Yu Chen
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0043554

A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata
Cited by: 17
Author(s): Erica Lasek‐Nesselquist
Software Mentions: 3
Published: about 12 years ago

10.1186/s12870-020-02450-z

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars
Cited by: 21
Author(s): Heng Zhou, Ying He, Yu Cheng Zhu, Meiyu Li, Shuang Song, Wenhao Bo, Yingyue Li, Xiaoming Pang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0041389

Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux
Cited by: 42
Author(s): Erin Lynch, Morgan G. I. Langille, Aaron E. Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen, Marc T. Facciotti
Software Mentions: 3
Published: over 12 years ago

10.1186/s12870-020-02673-0

Resistance analysis of cherry rootstock ‘CDR-1’ (Prunus mahaleb) to crown gall disease
Cited by: 5
Author(s): Chengcheng Liang, Tian Wang, Rendun Wu, Mei Zhao, Yong Zhao, Yuliang Cai
Software Mentions: 3
Published: about 4 years ago

10.3389/fphar.2018.00912

Investigating the Molecular Mechanism of Aqueous Extract of Cyclocarya paliurus on Ameliorating Diabetes by Transcriptome Profiling
Cited by: 7
Author(s): Jing Li, Mei Luo, Minghua Hu, An‐Yuan Guo, Xiangliang Yang, Qiong Zhang, Yanhong Zhu
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.720800

Disruption of Photomorphogenesis Leads to Abnormal Chloroplast Development and Leaf Variegation in Camellia sinensis
Cited by: 7
Author(s): Xizhi Gao, Chenyu Zhang, Cui Lu, Minghan Wang, Nianci Xie, Jianjiao Chen, Yunfei Li, Jiahao Chen, Chengwen Shen
Software Mentions: 3
Published: about 3 years ago

10.1186/s12870-021-03051-0

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique
Cited by: 3
Author(s): Huangwei Zhang, Meng Li, Min Jung Kong, Jim M. Dunwell, Yuyan Zhang, Chao Yue, Juyou Wu, Shaoling Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.00060

Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors
Cited by: 5
Author(s): Ricardo Ulloa, Ana Moya-Beltrán, Camila Rojas-Villalobos, Harold Núñez, P. Chiacchiarini, Edgardo R. Donati, Alejandra Giaveno, Raquel Quatrini
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmolb.2020.00040

Computational Investigation of Voltage-Gated Sodium Channel β3 Subunit Dynamics
Cited by: 4
Author(s): William G. Glass, Anna L. Duncan, Philip C. Biggin
Software Mentions: 3
Published: over 4 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 7 years ago

10.3389/fnins.2017.00709

Multi-modal Brain MRI in Subjects with PD and iRBD
Cited by: 12
Author(s): Silvia Mangia, Alena Svátková, Daniele Mascali, Mikko J. Nissi, Philip Burton, Petr Bednařík, Edward J. Auerbach, Federico Giove, Lynn E. Eberly, Michael J. Howell, Igor Nestrašil, Paul Tuite, Shalom Michaeli
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1009686

A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing
Cited by: 11
Author(s): Akihiro Nita, Akinobu Matsumoto, Ronghao Tang, Chisa Shiraishi, Kazuya Ichihara, Daisuke Saito, Mikita Suyama, Tomoharu Yasuda, Gaku Tsuji, Masutaka Furue, Bunpei Katayama, Toshiyuki Ozawa, Takaho Murata, Teruki Dainichi, Kenji Kabashima, Atsushi Hatano, Masaki Matsumoto, Keiichi I. Nakayama
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0094270

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-3684-8

Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth
Cited by: 8
Author(s): Lydgia A. Jackson, Michael Day, Jennie Allen, Edgar J. Scott, David W. Dyer
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.660002

Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900Insertions Reveals Strain Type-Specific Modalities
Cited by: 6
Author(s): Cyril Condé, Marian Price-Carter, Thierry Cochard, Maxime Branger, Karen Stevenson, Richard J. Whittington, John P. Bannantine, Franck Biet
Software Mentions: 3
Published: over 3 years ago

10.3389/fvets.2021.644474

Identification of Photoperiod-Induced LncRNAs and mRNAs in Pituitary Pars Tuberalis of Sheep
Cited by: 10
Author(s): Qing Xia, Mingxing Chu, Xiaoyun He, Qiuyue Liu, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Ran Di
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006382

Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin
Cited by: 18
Author(s): Ryosuke Kita, Hunter B. Fraser
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.02411

A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein
Cited by: 12
Author(s): Zhanming Fan, Shangxin Song, Yafang Ma, Xinglian Xu
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2021.714920

Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems
Cited by: 2
Author(s): Michael Hoffert, Rika E. Anderson, Julie Réveillaud, Leslie G. Murphy, Ramunas Stepanauskas, J. A. Huber
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2018.00332

A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen
Cited by: 17
Author(s): Stephen J. Goodswen, Paul J. Kennedy, John Ellis
Software Mentions: 3
Published: over 6 years ago

10.3389/fnhum.2014.00625

A single session of exercise increases connectivity in sensorimotor-related brain networks: a resting-state fMRI study in young healthy adults
Cited by: 63
Author(s): A. Saeed Rajab, David Crane, Laura Middleton, Andrew D. Robertson, Michelle Hampson, Bradley J. MacIntosh
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2016.01342

Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios
Cited by: 55
Author(s): Samantha M. Gromek, Andrea M. Suria, Matthew S. Fullmer, Jillian L. Garcia, J. Peter Gogarten, Spencer V. Nyholm, Marcy J. Balunas
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pcbi.1008939

How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
Cited by: 22
Author(s): Fan Jin, Frauke Gräter
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00659

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements
Cited by: 8
Author(s): Iliyas Rashid, Ajey Kumar Pathak, Ravindra Kumar, Prachi Srivastava, Mahender Singh, S. Murali, Basdeo Kushwaha
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.01040

Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat
Cited by: 10
Author(s): Yinghui Ling, Qi Zheng, Yunsheng Li, Menghua Sui, Hao Wu, Yunhai Zhang, Mingxing Chu, Yuehui Ma, Fugui Fang, Lei Xu
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2014.00150

Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing—the FRAGMENT approach
Cited by: 8
Author(s): Chang Sun, Thomas McAndrew, Benjamin Smith, Zigui Chen, Marina Frimer, Robert D. Burk
Software Mentions: 3
Published: over 10 years ago

10.3389/fchem.2020.598710

Discovery of 5,5′-Methylenedi-2,3-Cresotic Acid as a Potent Inhibitor of the Chemotactic Activity of the HMGB1·CXCL12 Heterocomplex Using Virtual Screening and NMR Validation
Cited by: 3
Author(s): Federica De Leo, Giacomo Quilici, Francesco De Marchis, Malisa Vittoria Mantonico, Marco E. Bianchi, Giovanna Musco
Software Mentions: 3
Published: almost 4 years ago

10.3389/fendo.2021.600682

Whole Genome Sequencing Prioritizes CHEK2, EWSR1, and TIAM1 as Possible Predisposition Genes for Familial Non-Medullary Thyroid Cancer
Cited by: 11
Author(s): Aayushi Srivastava, Sara Galimberti, Diamanto Skopelitou, Benchun Miao, Nagarajan Paramasivam, Chiara Diquigiovanni, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1007293

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
Cited by: 20
Author(s): Fábio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark Gerstein
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2017.00205

Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals
Cited by: 29
Author(s): Ran Tian, Daiqing Yin, Yanzhi Liu, Inge Seim, Shixia Xu
Software Mentions: 3
Published: almost 7 years ago

10.3389/fcell.2021.706375

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development
Cited by: 19
Author(s): Muhammad Muzammal Adeel, Hao Jiang, Yibeltal Arega, Kai Cao, Dazhen Lin, Canhui Cao, Gang Cao, Peng Wu, Guoliang Li
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00652

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes
Cited by: 25
Author(s): Bin Zeng, Ting Chen, Junyi Luo, Mei-Ying Xie, Limin Wei, Qianyun Xi, Jiajie Sun, Yongliang Zhang
Software Mentions: 3
Published: over 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 7 years ago

10.34133/2019/5809404

Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean
Cited by: 45
Author(s): Kyle A. Parmley, Koushik Nagasubramanian, Soumik Sarkar, Baskar Ganapathysubramanian, Asheesh K. Singh
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12863-017-0584-5

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
Cited by: 20
Author(s): Adugna Abdi Woldesemayat, Peter van Heusden, Bongani K. Ndimba, Alan Christoffels
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pbio.3001026

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
Cited by: 66
Author(s): Alexander Kloosterman, Peter Cimermančič, E. A. Aboutabl, Congcong Du, Michalis Hadjithomas, Mohamed S. Donia, Michael A. Fischbach, Gilles P. van Wezel, Marnix H. Medema
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13072-015-0028-2

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates
Cited by: 16
Author(s): Parameswaran Ramachandran, Gareth Palidwor, Theodore J. Perkins
Software Mentions: 3
Published: about 9 years ago

10.1002/ece3.4688

High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (<i>Canis latrans</i> ) populations
Cited by: 20
Author(s): Elizabeth Heppenheimer, Kristin E. Brzeski, Joseph W. Hinton, Brent R. Patterson, Linda Y. Rutledge, Alexandra L. DeCandia, Tyler Wheeldon, Steven R. Fain, Paul A. Hohenlohe, Roland Kays, Bradley N. White, Michael J. Chamberlain, Bridgett M. vonHoldt
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41426-018-0097-y

The concordance between upper and lower respiratory microbiota in children with <i>Mycoplasma pneumoniae</i> pneumonia
Cited by: 22
Author(s): Wenkui Dai, Heping Wang, Qian Zhou, Xin Feng, Zhiwei Lü, Dongfang Li, Zhenyu Yang, Yanhong Liu, Yinhu Li, Guoli Xie, Kunling Shen, Yonghong Yang, Yuejie Zheng, Shuai Cheng Li
Software Mentions: 3
Published: over 6 years ago

10.15252/emmm.201708515

<scp>PATL</scp> 2 is a key actor of oocyte maturation whose invalidation causes infertility in women and mice
Cited by: 52
Author(s): Marie Christou‐Kent, Zine‐Eddine Kherraf, Amir Amiri‐Yekta, Emilie Le Blévec, Thomas Karaouzène, Béatrice Conne, Jessica Escoffier, Saïd Assou, Audrey Guttin, Emeline Lambert, Guillaume Martinez, Magalie Boguenet, Sélima Fourati Ben Mustapha, Isabelle Cédrin Durnerin, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Charles Coutton, Nicolas Thierry‐Mieg, Serge Nef, Serge P. Bottari, Raoudha Zouari, Jean-Paul Issartel, Pierre F. Ray, Christophe Arnoult
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-019-3261-z

Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens)
Cited by: 12
Author(s): Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li, Xinchun Lin
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pbio.3000421

Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy
Cited by: 44
Author(s): Reshef Tal, Shafiq Shaikh, Pallavi Pallavi, Aya Tal, Francesc López-Giráldez, Fang Lyu, Yuanyuan Fang, Shruti Chinchanikar, Ying Liu, Harvey J. Kliman, Myles H. Alderman, Nicola Pluchino, Jehanzeb Kayani, Ramanaiah Mamillapalli, Diane S. Krause, Hugh S. Taylor
Software Mentions: 3
Published: about 5 years ago

10.1186/s13072-019-0312-7

Folate deficiency induced H2A ubiquitination to lead to downregulated expression of genes involved in neural tube defects
Cited by: 16
Author(s): Pei Pei, Xiyue Cheng, Jianhua Yu, Jinying Shen, Xue Li, Jianxin Wu, Shan Wang, Ting Zhang
Software Mentions: 3
Published: about 5 years ago

10.1111/pbi.12940

Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor <i>Triticum dicoccoides</i>
Cited by: 27
Author(s): Bala Anı Akpınar, Sezgi Biyiklioglu, Burcu Alptekin, M. Havránková, Jan Vrána, Jaroslav Doležel, Assaf Distelfeld, Pilar Hernández, Hikmet Budak
Software Mentions: 3
Published: over 6 years ago

10.1016/j.csbj.2016.07.002

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction
Cited by: 10
Author(s): Ying Huang, Shiyi Chen, Feilong Deng
Software Mentions: 3
Published: almost 9 years ago

10.3390/v13050836

Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain)
Cited by: 12
Author(s): Carlos S. Casimiro-Soriguer, Javier Pérez-Florido, Jose L. Fernández-Rueda, Irene Pedrosa-Corral, Vicente Guillot-Sulay, Nicola Lorusso, Luis Javier Martínez-González, José María Navarro-Marí, Joaquı́n Dopazo, Sara Sanbonmatsu‐Gámez
Software Mentions: 3
Published: over 3 years ago