Ecosyste.ms: Papers

10.1371/journal.pgen.1006466

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets
Cited by: 39
Author(s): Mark P. Keller, Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, Ning Leng, Christopher Brandon, Elias Chaibub Neto, Christopher L. Plaisier, Shane P. Simonett, Melkam A. Kebede, Gloria Sheynkman, Milton M. Klein, Nitin S. Baliga, Lloyd M. Smith, Karl W. Broman, Brian S. Yandell, Christina Kendziorski, Alan D. Attie
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13059-021-02454-4

Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus
Cited by: 35
Author(s): Silva Kasela, Zharko Daniloski, Sailalitha Bollepalli, Tristan X. Jordan, Benjamin R. tenOever, Neville E. Sanjana, Tuuli Lappalainen
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pgen.1004277

DNA Repair Pathway Selection Caused by Defects in TEL1, SAE2, and De Novo Telomere Addition Generates Specific Chromosomal Rearrangement Signatures
Cited by: 19
Author(s): Christopher D. Putnam, Katielee Pallis, Tikvah K. Hayes, Richard D. Kolodner
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1000598

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Cited by: 773
Author(s): Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1003030

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
Cited by: 61
Author(s): Recep Çolak, TaeHyung Kim, Magali Michaut, Mark Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pcbi.1002779

Bioinformatics for the Human Microbiome Project
Cited by: 74
Author(s): Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis Huttenhower
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-018-4838-z

Genome sequencing analysis of Streptomyces coelicolor mutants that overcome the phosphate-depending vancomycin lethal effect
Cited by: 20
Author(s): Fernando Santos-Beneit
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-3869-1

Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing
Cited by: 89
Author(s): Minmin Liu, Huiyang Yu, Gangjun Zhao, Qiufeng Huang, Yongen Lu, Bo Ouyang
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1006472

Ten quick tips for sharing open genomic data
Cited by: 8
Author(s): Anne V. Brown, Jacqueline Campbell, Teshale Assefa, David Grant, Rex T. Nelson, Nathan T. Weeks, Steven B. Cannon
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1005480

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
Cited by: 35
Author(s): Mikhail Shugay, Andrew R. Zaretsky, Dmitry A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrey Shelenkov, Mikhail Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1004491

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Cited by: 12
Author(s): Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Yi Zheng, Colin N. Dewey, Sündüz Keleş
Software Mentions: 1
Published: about 9 years ago

10.1186/gm403

HLA typing from RNA-Seq sequence reads
Cited by: 193
Author(s): Sebastian Boegel, Martin Löwer, Michael K. E. Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguérin, Özlem Türeci, Mustafa Diken, John C. Castle, Uğur Şahin
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pbio.2006459

A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
Cited by: 80
Author(s): William J. Fitzsimmons, Robert J. Woods, John McCrone, Andrew Woodman, Jamie J. Arnold, Madhumita Yennawar, Richard P. Evans, Craig Ε. Cameron, Adam S. Lauring
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.3000289

Resolving noise–control conflict by gene duplication
Cited by: 47
Author(s): Michal Chapal, Sefi Mintzer, Sagie Brodsky, Miri Carmi, Naama Barkai
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pbio.2004526

Zbtb7a is a transducer for the control of promoter accessibility by NF-kappa B and multiple other transcription factors
Cited by: 35
Author(s): José M. Ramos Pittol, Agata Oruba, Gerhard Mittler, Simona Saccani, Dominic van Essen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.1000523

Control of Transcription by Cell Size
Cited by: 108
Author(s): Chia-Yung Wu, P. Alexander Rolfe, David K. Gifford, Gerald R. Fink
Software Mentions: 1
Published: about 14 years ago

10.1186/s13073-021-00932-9

Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
Cited by: 23
Author(s): Indhu‐Shree Rajan‐Babu, Junran J. Peng, Readman Chiu, Patricia Birch, Madeline Couse, Colleen Guimond, Anna Lehman, Jill Mwenifumbo, Clara van Karnebeek, Jan M. Friedman, Shelin Adam, Christèle du Souich, Alison M Elliott, Anna Lehman, Jill Mwenifumbo, Tanya N. Nelson, Clara van Karnebeek, Jan M. Friedman, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, İnanç Birol, Jan M. Friedman
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-021-07481-w

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses
Cited by: 10
Author(s): Paweł Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech M. Karłowski, Przemysław Nuc, Zofia Szweykowska-Kulińska, Andrzej Pacak
Software Mentions: 1
Published: over 3 years ago

10.3390/plants9030362

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis
Cited by: 6
Author(s): Yan Liu, Wenrui Gao, Shizhou Wu, Lu Lu, Yaqiu Chen, Jinxin Guo, Shuzhen Men, Xiaoming Zhang
Software Mentions: 1
Published: over 4 years ago

10.1186/s13742-015-0068-3

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Cited by: 129
Author(s): Yong Hou, Kui Wu, Shi Xiao-li, Fuqiang Li, Liying Song, Huawei Wu, Michael Dean, Guibo Li, Shirley Tsang, Runze Jiang, Xiaolong Zhang, Bo Li, Geng Li, Niharika Bedekar, Na Lü, Guoyun Xie, Han Liang, Liao Chang, Ting Wang, Jianghao Chen, Yingrui Li, Xiuqing Zhang, Huanming Yang, Xun Xu, Ling Wang, Jun Wang
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-271

SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways
Cited by: 36
Author(s): Juan Yu, Zhenhai Zhang, Jiangang Wei, Yi Ling, Wenying Xu, Zhen Su
Software Mentions: 1
Published: over 10 years ago

10.1093/gigascience/giy053

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries
Cited by: 12
Author(s): Fu-Hao Lu, Neil McKenzie, George Kettleborough, Darren Heavens, Matt Clark, Michael W. Bevan
Software Mentions: 1
Published: over 6 years ago

10.1007/s11103-017-0679-4

Structure, target-specificity and expression of PN_LNC_N13, a long non-coding RNA differentially expressed in apomictic and sexual Paspalum notatum
Cited by: 13
Author(s): Ana Claudia Ochogavía, Giulio Galla, Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Claudia Pessino
Software Mentions: 1
Published: about 7 years ago

10.1111/pbi.13049

Impact of differential<scp>DNA</scp>methylation on transgene expression in cotton<i>(Gossypium hirsutum L.)</i>events generated by targeted sequence insertion
Cited by: 3
Author(s): Aurine Verkest, Stephane Bourout, Jurgen Debaveye, Kristine Reynaert, Bernadette Saey, Ilse van den Brande, Kathleen D’Halluin
Software Mentions: 1
Published: almost 6 years ago

10.1111/pbi.12701

Spearmint R2R3‐<scp>MYB</scp> transcription factor Ms<scp>MYB</scp> negatively regulates monoterpene production and suppresses the expression of geranyl diphosphate synthase large subunit (<i>Ms<scp>GPPS</scp></i>.<i><scp>LSU</scp></i>)
Cited by: 83
Author(s): Vaishnavi Amarr Reddy, Qian Wang, Niha Dhar, Nitin Kumar, Prasanna Nori Venkatesh, Chakravarthy Rajan, Deepa Panicker, Vishweshwaran Sridhar, Hui-Zhu Mao, Rajani Sarojam
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-019-6433-3

A crustacean annotated transcriptome (CAT) database
Cited by: 12
Author(s): Wenyan Nong, Zacary Y. H. Chai, Xiaoying Jiang, Jing Qin, Ka Yan, King Ming Chan, Ting Fung Chan, Billy K. C. Chow, Hoi Shan Kwan, Chris K C Wong, Jian‐Wen Qiu, Jerome H.L. Hui, Ka Hou Chu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-6580-6

Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide
Cited by: 8
Author(s): Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, Srinivas Kethavath, Monika Dass, Harpreet Singh, Rakhee Nayak, Sreenivasulu Kurukuti, Kuljeet Singh Sandhu
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-016-2822-z

Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development
Cited by: 6
Author(s): Devi Krishna Priya Karunakaran, Sahar Al Seesi, Abdul Rouf Banday, Marybeth Baumgartner, Anouk M. Olthof, Christopher Lemoine, Ion Măndoiu, Rahul N. Kanadia
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1835-3

MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae
Cited by: 11
Author(s): Bernarda Calla, Scott M. Geib
Software Mentions: 1
Published: about 9 years ago

10.1186/s43008-019-0002-x

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
Cited by: 118
Author(s): Peter R. Johnston, Luis Quijada, Chris Smith, Hans-Otto Baral, Tsuyoshi Hosoya, Christiane Baschien, Kadri Pärtel, Wen-Ying Zhuang, Danny Haelewaters, Park DuckChul, Steffen Carl, Francesc López-Giráldez, Zheng Wang, Jeffrey P. Townsend
Software Mentions: 1
Published: over 5 years ago

10.3390/insects11030161

First Report of Aleurocanthus spiniferus on Ailanthus altissima: Profiling of the Insect Microbiome and MicroRNAs
Cited by: 10
Author(s): Giovanni Bubici, Maria Isabella Prigigallo, Francesca Garganese, Francesco Nugnes, M. G. M. Jansen, Francesco Porcelli
Software Mentions: 1
Published: over 4 years ago

10.3390/insects12060533

Male-Biased microRNA Discovery in the Pea Aphid
Cited by: 3
Author(s): Xiaomi Liu, Erica L. Culbert, Jennifer A. Brisson
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-018-4600-6

RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages
Cited by: 57
Author(s): Arunasalam Naguleswaran, Nicholas Doiron, Isabel Roditi
Software Mentions: 1
Published: over 6 years ago

10.1098/rstb.2018.0319

A gossypol biosynthetic intermediate disturbs plant defence response
Cited by: 13
Author(s): Xiu Tian, Xin Fang, Jin-Quan Huang, Ling-Jian Wang, Ying‐Bo Mao, Xiao‐Ya Chen
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11079

Characterization of the first vaginal <i>Lactobacillus crispatus</i> genomes isolated in Brazil
Cited by: 3
Author(s): Marcelle Oliveira de Almeida, Rodrigo Dias de Oliveira Carvalho, Flávia Figueira Aburjaile, Fábio Miranda, Janaína Canário Cerqueira, Bertram Brenig, Preetam Ghosh, Rommel Thiago Jucá Ramos, Rodrigo Bentes Kato, Siomar de Castro Soares, Artur M. S. Silva, Vasco Azevedo, Marcus Vinícius Canário Viana
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100566

Nutrient availability regulates proline/alanine transporters in Trypanosoma brucei
Cited by: 5
Author(s): Alexander C. Haindrich, Viona Ernst, Arunasalam Naguleswaran, Quentin-Florian Oliveres, Isabel Roditi, Doris Rentsch
Software Mentions: 1
Published: almost 4 years ago

10.1111/jcmm.14252

5‐Hydroxymethylcytosine profiling from genomic and cell‐free DNA for colorectal cancers patients
Cited by: 17
Author(s): Ping Gao, Shengli Lin, Ming‐Yan Cai, Yan Zhu, Yanqun Song, Yi Sui, Jing Lin, Jiaxiuyu Liu, Xingyu Lu, Yun‐Shi Zhong, Yuehong Cui, Ping‐Hong Zhou
Software Mentions: 1
Published: over 5 years ago

10.1111/jcmm.15828

Decreased long non‐coding RNA lincFOXF1 indicates poor progression and promotes cell migration and metastasis in osteosarcoma
Cited by: 4
Author(s): Shu-Li Yang, Jian Chen, Bin Lv, Jun Zhang, Deli Li, Meng‐Yuan Huang, Yuan Li, Guoyong Yin
Software Mentions: 1
Published: about 4 years ago

10.1242/jcs.208066

Phosphorylation of the RNA binding protein Zfs1 modulates sexual differentiation in fission yeast
Cited by: 9
Author(s): Francisco J. Navarro, Probir Chakravarty, Paul Nurse
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.7930

Detection of disease in <i>Cucurbita maxima</i> Duch. ex Lam<i>.</i> caused by a mixed infection of <i>Zucchini yellow mosaic virus</i>, <i>Watermelon mosaic virus</i>, and <i>Cucumber mosaic virus</i> in Southeast China using a novel small RNA sequencing method
Cited by: 2
Author(s): Yi Wang, Ping Zhu, Qin Zhou, Xiaojun Zhou, Zeqing Guo, Linrun Cheng, Liyan Zhu, Xiaochan He, Yidan Zhu, Huanming Yang
Software Mentions: 1
Published: about 5 years ago

10.1186/2043-9113-2-21

Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays
Cited by: 2
Author(s): Subhashini Srinivasan, Arun H. Patil, Mohit Verma, Jonathan Bingham, Srivatsan Raghunathan
Software Mentions: 1
Published: almost 13 years ago

10.3390/jcm4091798

Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets
Cited by: 18
Author(s): Wei‐Ting Kuo, Ming-Wei Su, Yungling Leo Lee, Chien-Hsiun Chen, Chew-Wun Wu, Wen‐Liang Fang, Kai Huang, Wen-Chiao Lin
Software Mentions: 1
Published: about 9 years ago

10.1128/JCM.00104-18

Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline
Cited by: 11
Author(s): David Wyllie, Nicholas D. Sanderson, Richard Myers, Tim Peto, Esther Robinson, Derrick W. Crook, E. Grace Smith, A Sarah Walker
Software Mentions: 1
Published: over 6 years ago

10.1128/JCM.00683-19

Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen
Cited by: 21
Author(s): Xuebing Wang, Haijian Zhou, Dongke Chen, Pengcheng Du, Ruiting Lan, Xiaotong Qiu, Xuexin Hou, Zhiguo Liu, Lina Sun, Shuai Xu, Xingzhao Ji, Heqiao Li, Dan Li, Jingshan Zhang, Hui Zeng, Zhenjun Li
Software Mentions: 1
Published: about 5 years ago

10.1093/jxb/eru193

Was low CO2 a driving force of C4 evolution: Arabidopsis responses to long-term low CO2 stress
Cited by: 51
Author(s): Yuanyuan Li, Jiajia Xu, Noor ul Haq, Hui Zhang, Xin‐Guang Zhu
Software Mentions: 1
Published: over 10 years ago

10.1093/jxb/erx117

Enhancing faba bean (Vicia faba L.) genome resources
Cited by: 33
Author(s): James W. Cooper, Michael Wilson, Martijn F.L. Derks, Sandra Smit, K. Kunert, Christopher A. Cullis, Christine H. Foyer
Software Mentions: 1
Published: over 7 years ago

10.1093/aobpla/ply077

Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice
Cited by: 4
Author(s): Imdad Ullah Zaid, Weijie Tang, Jianbo He, Sana Ullah Khan, Delin Hong
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.ppat.1004130

Cathepsin-L Can Resist Lysis by Human Serum in Trypanosoma brucei brucei
Cited by: 31
Author(s): Sam Alsford, Rachel B. Currier, José Afonso Guerra-Assunção, Taane G. Clark, David Horn
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1004230

A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission
Cited by: 276
Author(s): Eugene V. Ryabov, Graham R. Wood, Jessica Fannon, Jonathan D. Moore, James C. Bull, Dave Chandler, Andrew Mead, Nigel John Burroughs, David J. Evans
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-14-168

De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatumand grapefruit peel
Cited by: 66
Author(s): Vera Hershkovitz, Noa Sela, Leena Taha-Salaime, Jia Liu, G. Rafael, Clarita Kessler, Radi Aly, Maggie Levy, Michael Wisniewski, Samir Droby
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1004653

Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing
Cited by: 75
Author(s): Friederike S. Rossmann, Tomáš Raček, Dominique Wobser, Jacek Puchałka, Elaine M. Rabener, Matthias Reiger, Antoni P. A. Hendrickx, Ann Kristin Diederich, Kirsten Jung, Christoph Klein, Johannes Hüebner
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-942

Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets
Cited by: 36
Author(s): Scott M. Geib, Bernarda Calla, Brian E. Hall, Shaobin Hou, Nicholas C. Manoukis
Software Mentions: 1
Published: almost 11 years ago

10.1523/JNEUROSCI.1821-20.2020

<i>Tet1</i>Isoforms Differentially Regulate Gene Expression, Synaptic Transmission, and Memory in the Mammalian Brain
Cited by: 19
Author(s): Celeste B. Greer, Jeffrey G. Wright, Joscha Weiss, Roman M. Lazarenko, Sean P. Moran, Junqin Zhu, Keagan S. Chronister, Aiwu Jin, Andrew Kennedy, J. David Sweatt, Garrett A. Kaas
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-14-404

Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients
Cited by: 14
Author(s): Sarbashis Das, Tanmoy Roychowdhury, Pravin Kumar, Anil Kumar, Priya Kalra, Jitendra Singh, Sarman Singh, H. K. Prasad, Alok Bhattacharya
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1005856

The Mutational Robustness of Influenza A Virus
Cited by: 79
Author(s): Elisa Visher, Shawn E. Whitefield, John McCrone, William J. Fitzsimmons, Adam S. Lauring
Software Mentions: 1
Published: about 8 years ago

10.1186/s12863-016-0364-7

Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet
Cited by: 53
Author(s): Yongqiang Wang, Li Lin, Sha Tang, Jianguang Liu, Hanshuang Zhang, Hui Zhi, Guanqing Jia, Xianmin Diao
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.2861

Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia
Cited by: 6
Author(s): Scott William Roy
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-96425-1

Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean
Cited by: 9
Author(s): Dipak Kumar Sahoo, Anindya Bijoy Das, Xiaoqiu Huang, Silvia R. Cianzio, Madan K. Bhattacharyya
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.ppat.1006756

A role for small RNA in regulating innate immunity during plant growth
Cited by: 71
Author(s): Yadong Deng, Jubin Wang, Jeffrey J. Tung, Dan Liú, Yingjia Zhou, Shan He, Yunlian Du, Barbara Baker, Feng Li
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.ppat.1007156

Identification of virus-encoded microRNAs in divergent Papillomaviruses
Cited by: 26
Author(s): Rachel Chirayil, Rodney P. Kincaid, Christine Dahlke, Chad V. Kuny, Nicole Dälken, Michael Spohn, Becki Lawson, Adam Grundhoff, Christopher S. Sullivan
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-015-0656-1

Extracellular Onchocerca-derived small RNAs in host nodules and blood
Cited by: 98
Author(s): Juan F. Quintana, Benjamin L. Makepeace, Simon A. Babayan, Alasdair Ivens, Kenneth Pfarr, Mark Blaxter, Alexander Yaw Debrah, Samuel Wanji, Henrietta F. Ngangyung, Germanus S. Bah, Vincent N. Tanya, David W. Taylor, Achim Hoerauf, Amy H. Buck
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1007534

Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms
Cited by: 72
Author(s): Youxin Yang, Tingli Liu, Danyu Shen, Jinyan Wang, Xitie Ling, Zhongze Hu, Tianzi Chen, Jieli Hu, J.Y. Huang, Wenbao Yu, Daolong Dou, Ming-Bo Wang, Baolong Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41392-020-00238-z

Novel insights into stress-induced susceptibility to influenza: corticosterone impacts interferon-β responses by Mfn2-mediated ubiquitin degradation of MAVS
Cited by: 14
Author(s): Zhi-Pu Luo, Lifang Liu, Yingnan Jiang, Lu-Ping Tang, Wen Li, Shu-Hua Ouyang, Long-Fang Tu, Yanping Wu, Haibiao Gong, Chang-Yu Yan, Shan Jiang, Yuhui Lu, Tongzheng Liu, Zhuhua Jiang, Hiroshi Kojima, Yang Yu, Xin‐Sheng Yao, Yi-Fang Li, Rong‐Rong He
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.ppat.1007817

Schistosoma japonicum extracellular vesicle miRNA cargo regulates host macrophage functions facilitating parasitism
Cited by: 78
Author(s): Juntao Liu, Lihui Zhu, Jianbin Wang, Lin Qiu, Yongjun Chen, Richard E. Davis, Guofeng Cheng
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1008030

Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival
Cited by: 54
Author(s): Liang Wei Wang, Zhonghao Wang, Ina Ersing, Luis Nobre, Rui Guo, Sizun Jiang, Stephen J. Trudeau, Bo Zhao, Michael P. Weekes, Benjamin E. Gewurz
Software Mentions: 1
Published: about 5 years ago

10.1186/s13071-015-0863-9

Small mosquitoes, large implications: crowding and starvation affects gene expression and nutrient accumulation in Aedes aegypti
Cited by: 54
Author(s): David Price, Faye Schilkey, Alexander Ulanov, Immo A. Hansen
Software Mentions: 1
Published: over 9 years ago

10.1186/s13015-019-0148-5

Prefix-free parsing for building big BWTs
Cited by: 31
Author(s): Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun
Software Mentions: 1
Published: over 5 years ago

10.3390/v8050120

Characterization of a Novel Polerovirus Infecting Maize in China
Cited by: 62
Author(s): Sha Chen, Guangzhuang Jiang, Ji Wu, Yong Liu, Yajuan Qian, Xueping Zhou
Software Mentions: 1
Published: over 8 years ago

10.1080/21505594.2020.1856560

The novel outer membrane protein from OprD/Occ family is associated with hypervirulence of carbapenem resistant Acinetobacter baumannii ST2/KL22
Cited by: 6
Author(s): Mingxi Hua, Jingyuan Liu, Pengcheng Du, Xinzhe Liu, Min Li, Huizhu Wang, Chen Chen, Xinmin Xu, Jiang Yu, Yajie Wang, Hui Zeng, Ang Li
Software Mentions: 1
Published: almost 4 years ago

10.1080/21505594.2018.1475797

Eicosanoid biosynthesis influences the virulence of <i>Candida parapsilosis</i>
Cited by: 16
Author(s): T. Chakraborty, Ernst Thuer, Marieke Heijink, Renáta Tóth, László Bodai, Csaba Vágvölgyi, Martin Giera, Toni Gabaldón, Attila Gácser
Software Mentions: 1
Published: over 6 years ago

10.1186/s12985-021-01500-8

Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers
Cited by: 3
Author(s): Anneth-Mwasi Tumbo, Tobias Schindler, Jean-Pierre Dangy, Nina Orlova-Fink, Jose Raso Bieri, Maximillian Mpina, Florence A. Milando, Omar Juma, Ally Hamad, Elizabeth Nyakarungu, Mwajuma Chemba, Ali Mtoro, Kamaka Ramadhan, Ally Olotu, Damas Makweba, Stephen Mgaya, Kenneth Stuart, Matthieu Perreau, Jack T. Stapleton, Said Jongo, Stephen L. Hoffman, Marcel Tanner, Salim Abdulla, Claudia Daubenberger
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12985-018-1014-7

NS3 Protein from Rice stripe virus affects the expression of endogenous genes in Nicotiana benthamiana
Cited by: 8
Author(s): Gentu Wu, Guixian Zheng, Qiao Hu, Mingge Ma, Mingjun Li, Xihuan Sun, Fei Yan, Ling Qing
Software Mentions: 1
Published: over 6 years ago

10.1186/s12985-017-0803-8

The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome
Cited by: 14
Author(s): Lindani Moyo, S. V. Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, H. R. Pappu
Software Mentions: 1
Published: over 7 years ago

10.1098/rspb.2015.2733

A gene associated with social immunity in the burying beetle <i>Nicrophorus vespilloides</i>
Cited by: 37
Author(s): William J. Palmer, Ana Duarte, Matthew Schrader, Jonathan P. Day, Rebecca M. Kilner, Francis M. Jiggins
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12985-016-0663-7

RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis
Cited by: 22
Author(s): Feng Sun, Fang Peng, Juan Li, Linlin Du, Ying Lan, Tong Zhou, Yanting Fan, Wenbiao Shen, Yijun Zhou
Software Mentions: 1
Published: almost 8 years ago

10.7554/eLife.55612

Establishment of H3K9me3-dependent heterochromatin during embryogenesis in Drosophila miranda
Cited by: 19
Author(s): Kevin H.-C. Wei, Carolus Chan, Doris Bachtrog
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.14243

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex
Cited by: 63
Author(s): Michael Tramantano, Lu Sun, Christy Au, Daniel F Labuz, Zhimin Liu, Mindy Chou, Chen Shen, Ed Luk
Software Mentions: 1
Published: over 8 years ago

10.15252/msb.20167028

Metabolic constraints on the evolution of antibiotic resistance
Cited by: 125
Author(s): Mattia Zampieri, Tim N. Enke, Victor Chubukov, Vito Ricci, Laura J. V. Piddock, Uwe Sauer
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.10501

Egr-5 is a post-mitotic regulator of planarian epidermal differentiation
Cited by: 92
Author(s): Kimberly C. Tu, Li-Chun Cheng, Hanh Thi-Kim Vu, Jeffrey J. Lange, Sean A. McKinney, Chris Seidel, Alejandro Sánchez Alvarado
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.17820

The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains
Cited by: 216
Author(s): Erin G. Conlon, Lei Lü, Aarti Sharma, Takashi Yamazaki, Timothy Tang, Neil A. Shneider, James L. Manley
Software Mentions: 1
Published: about 8 years ago

10.1186/s13756-018-0363-8

Whole genome sequence revealed the fine transmission map of carbapenem-resistant Klebsiella pneumonia isolates within a nosocomial outbreak
Cited by: 23
Author(s): Wenjun Sui, Haijian Zhou, Pengcheng Du, Lijun Wang, Tian Qin, Mei Wang, Hao Ren, Yue Huang, Jing Hou, Chen Chen, Xinxin Lu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12876-020-01460-3

Effects of proton pump inhibitor use on the esophageal microbial community
Cited by: 8
Author(s): Sadia Tasnim, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Richard B. Pyles, Ikenna Okereke
Software Mentions: 1
Published: about 4 years ago

10.1530/REP-17-0592

Identification and verification of potential piRNAs from domesticated yak testis
Cited by: 16
Author(s): Jishang Gong, Quanwei Zhang, Qi Wang, Youji Ma, Jiaxiang Du, Yong Zhang, Xingxu Zhao
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-12-440

Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes
Cited by: 10
Author(s): Tobias Mourier
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-15-583

Transcriptional landscape of repetitive elements in normal and cancer human cells
Cited by: 232
Author(s): Steven W. Criscione, Yue Zhang, W. T. Thompson, John M. Sedivy, Nicola Neretti
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms18040723

Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin-Based Dilated Cardiomyopathy
Cited by: 10
Author(s): Qifeng Zhou, Johannes-Martin Hahn, Balram Neupane, Parwez Aidery, Siegfried Labeit, Meinrad Gawaz, Michael Gramlich
Software Mentions: 1
Published: over 7 years ago

10.1002/mgg3.251

hg19K: addressing a significant lacuna in hg19-based variant calling
Cited by: 4
Author(s): Savita Karthikeyan, Pushpinder Bawa, Subhashini Srinivasan
Software Mentions: 1
Published: about 8 years ago

10.1098/rsob.190116

Biochemical analysis of nucleosome targeting by Tn5 transposase
Cited by: 9
Author(s): Shoko Sato, Yasuhiro Arimura, Tomoya Kujirai, Akihito Harada, Kazuhira Maehara, Jumpei Nogami, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/8845520

Changes in the Small RNA Expression in Endothelial Cells in Response to Inflammatory Stimulation
Cited by: 1
Author(s): Peixi Liu, Lingli Hu, Yuan Shi, Yingjun Liu, Guangrong Yu, Yingjie Zhou, Qingzhu An, Wei Zhu
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules23071604

Transcriptomic Analysis of the Candidate Genes Related to Aroma Formation in Osmanthus fragrans
Cited by: 22
Author(s): Xia Yang, Haiyan Li, Yuanzheng Yue, Wenjie Ding, Chen Xu, Tingting Shi, Gongwei Chen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12284-019-0287-9

Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae
Cited by: 28
Author(s): Lei Tian, Chunguang Chang, Lina Ma, Fahad Nasir, Jianfeng Zhang, Weiqiang Li, Lam-Son Phan Tran, Chunjie Tian
Software Mentions: 1
Published: over 5 years ago

10.1093/molbev/msab188

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication
Cited by: 8
Author(s): Oscar Alejandro Pérez‐Escobar, Sidonie Bellot, Natalia A. S. Przelomska, Jonathan M. Flowers, Mark Nesbitt, Philippa Ryan, Rafał M. Gutaker, Muriel Gros-Balthazard, Tom Wells, Benedikt G. Kuhnhäuser, Rowan J. Schley, Diego Bogarín, Steven Dodsworth, Rudy Diaz, Manuela Lehmann, Peter Petoe, Wolf L. Eiserhardt, Michaela Preick, Michael Hofreiter, Irka Hajdas, Michael D. Purugganan, Alexandre Antonelli, Barbara Gravendeel, Ilia J. Leitch, María Fernanda Torres Jiménez, Alexander S. T. Papadopulos, Guillaume Chomicki, Susanne S. Renner, William J. Baker
Software Mentions: 1
Published: over 3 years ago

10.1093/molbev/msx175

Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment
Cited by: 14
Author(s): Oliver Smith, Sarah Palmer, A. R. Clapham, Pamela Rose, Yuan Liu, Jun Wang, Robin G. Allaby
Software Mentions: 1
Published: over 7 years ago

10.1093/molbev/msab133

Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses
Cited by: 8
Author(s): Minkyu Park, Pascal‐Antoine Christin, Jeffrey L. Bennetzen
Software Mentions: 1
Published: over 3 years ago

10.1038/sdata.2019.13

MicroRNA expression profiles across blood and different tissues in cattle
Cited by: 26
Author(s): Hui-Zeng Sun, Yanhong Chen, Le Luo Guan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13229-015-0040-1

Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex
Cited by: 82
Author(s): Michal Mor, Stefano Nardone, Dev Sharan Sams, Evan Elliott
Software Mentions: 1
Published: over 9 years ago

10.1186/s12862-018-1274-2

Diverse RNA interference strategies in early-branching metazoans
Cited by: 20
Author(s): Andrew Calcino, Selene L. Fernández-Valverde, Ryan J. Taft, Bernard M. Degnan
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-016-2493-9

Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology
Cited by: 20
Author(s): Kailai Wang, Carmelo S. del Castillo, Matthieu Le Corre, Emmanuelle Pales Espinosa, Bassem Allam
Software Mentions: 1
Published: over 8 years ago

10.1080/23802359.2019.1679677

The complete mitochondrial genome of soft coral <i>Sarcophyton trocheliophorum</i> (Cnidaria: Anthozoa) using next-generation sequencing
Cited by: 4
Author(s): Chengji Shen, Ya-Ting Dan, Alireza Asem, Pei-Zheng Wang, Wei Xue, Xiao-Bo Tong, Weidong Li
Software Mentions: 1
Published: over 5 years ago

10.1080/23802359.2017.1325343

The complete mitochondrial genome of the Egyptian honey bee, <i>Apis mellifera lamarckii</i> (Insecta: Hymenoptera: Apidae)
Cited by: 17
Author(s): Amin Eimanifar, Rebecca T. Kimball, Edward L. Braun, Dahi M. Moustafa, Nizar Haddad, Stefan Fuchs, Bernd Grünewald, Jamie Ellis
Software Mentions: 1
Published: almost 8 years ago