bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1038/srep40618

Identification of misexpressed genetic elements in hybrids between Drosophila-related species
Cited by: 27
Author(s): Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron, Claudia M. A. Carareto, Cristina Vieira
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2021.695242

PD-L1 Dysregulation in COVID-19 Patients
Cited by: 49
Author(s): Francesco Sabbatino, Valeria Conti, Gianluigi Franci, Carmine Sellitto, Valentina Manzo, Pasquale Pagliano, Emanuela De Bellis, Alfonso Masullo, Francesco Antonio Salzano, Alessandro Caputo, Ilaria Peluso, Pio Zeppa, Giosuè Scognamiglio, Giovanna Greco, Carla Zannella, Michele Ciccarelli, Claudia Cicala, Carmine Vecchione, Amelia Filippelli, Stefano Pepe
Software Mentions: 1
Published: over 5 years ago

10.14814/phy2.14381

Altered proteomics profile in the amnion of patients with oligohydramnios
Cited by: 2
Author(s): Cecilia Y. Cheung, Robert A. Brace
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.01246

Fifteen Years of Sm-p80-Based Vaccine Trials in Nonhuman Primates: Antibodies From Vaccinated Baboons Confer Protection in vivo and in vitro From Schistosoma mansoni and Identification of Putative Correlative Markers of Protection
Cited by: 17
Author(s): Weidong Zhang, Liu Le, Gufran Ahmad, Adebayo J. Molehin, Arif Jamal Siddiqui, Workineh Torben, Souvik Karmakar, Juan U. Rojo, Souad R. Sennoune, Samara Lazarus, Sabiha Khatoon, Jasmin Freeborn, Justin Sudduth, Ashraf F. Rezk, David Carey, Roman F. Wolf, James F. Papin, Ray Damian, Sean A. Gray, Florian Marks, Darrick Carter, Afzal A. Siddiqui
Software Mentions: 1
Published: over 6 years ago

10.1038/srep41063

Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites
Cited by: 30
Author(s): Simone Pelliciari, Eva Pinatel, Andrea Vannini, Clelia Peano, Simone Puccio, Gianluca De Bellis, Alberto Danielli, Vincenzo Scarlato, Davide Roncarati
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21249641

Titration of SF3B1 Activity Reveals Distinct Effects on the Transcriptome and Cell Physiology
Cited by: 2
Author(s): Karen S. Kim Guisbert, Isiah Mossiah, Eric Guisbert
Software Mentions: 1
Published: almost 6 years ago

10.3390/pathogens9020099

Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.
Cited by: 4
Author(s): Laura C. Miller, Damarius S. Fleming, Kelly M. Lager
Software Mentions: 1
Published: over 6 years ago

10.3390/pathogens10040470

Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection
Cited by: 9
Author(s): Min Zhang, Hongyuan Zhang, Jie Tan, Shuping Huang, Xia Chen, Dàohóng Jiāng, Xiangyu Xiao
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10010063

Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves
Cited by: 10
Author(s): Birgit Wassermann, Lisé Korsten, Gabriele Berg
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10091179

Intestinal Transcriptomic and Histologic Profiling Reveals Tissue Repair Mechanisms Underlying Resistance to the Parasite Ceratonova shasta
Cited by: 8
Author(s): Damien Barrett, Itziar Estensoro, Ariadna Sitjà‐Bobadilla, Jerri L. Bartholomew
Software Mentions: 1
Published: about 5 years ago

10.1186/s12866-021-02257-4

Regulation of virulence and β-lactamase gene expression in Staphylococcus aureus isolates: cooperation of two-component systems in bloodstream superbugs
Cited by: 7
Author(s): Sanaz Dehbashi, Hamed Tahmasebi, Behrouz Zeyni, Mohammad Reza Arabestani
Software Mentions: 1
Published: about 5 years ago

10.3390/pathogens7040092

Relation between Biofilm and Virulence in Vibrio tapetis: A Transcriptomic Study
Cited by: 13
Author(s): Sophie Rodrigues, Christine Paillard, Sabine van Dillen, Ali Tahrioui, Jean‐Marc Berjeaud, Alain Dufour, Alexis Bazire
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12866-021-02304-0

The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response
Cited by: 3
Author(s): Xiaohong Chen, Aiqi Hu, Qian Zou, Sha Luo, Hetao Wu, Chunxiao Yan, Tao Liu, Donglan He, Xiaohua Li, Guyue Cheng
Software Mentions: 1
Published: about 5 years ago

10.3390/pathogens9060479

Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells
Cited by: 5
Author(s): Jin He, Chaoliang Leng, Jiazhen Pan, Aoqi Li, Hua Zhang, Cong Feng, Huanan Wang
Software Mentions: 1
Published: over 6 years ago

10.20411/pai.v3i2.250

Fecal Host Transcriptomics for Non-invasive Human Mucosal Immune Profiling: Proof of Concept in Clostridium difficile Infection
Cited by: 8
Author(s): Robert Salais, Amanda Barrett, Kornelia Edes, Michael C. Graves, Litty Paul, Jenna Rychert, Bert K. Lopansri, Daniel T. Leung
Software Mentions: 1
Published: about 8 years ago

10.1038/s41388-018-0197-0

LMTK3 confers chemo-resistance in breast cancer
Cited by: 29
Author(s): Justin Stebbing, Kalpit Shah, Lei Cheng Lit, Teresa Gagliano, Angeliki Ditsiou, Tingting Wang, Franz Wendler, Thomas R. Simon, Krisztián Szabó, Timothy O’Hanlon, Michael Dean, April Camilla Roslani, Swee Hung Cheah, Soo‐Chin Lee, Georgios Giamas
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.10529

Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage
Cited by: 8
Author(s): Yueqi Li, Wudi Wei, Sanqi An, Junjun Jiang, Jinhao He, Hong Zhang, Gang Wang, Jing Han, Bingyu Liang, Ye Li, Hao Liang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-021-02295-y

Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice
Cited by: 5
Author(s): Veronica Moskovicz, Rina T. Greenblatt Ben-El, Guy Horev, Boaz Mizrahi
Software Mentions: 1
Published: about 5 years ago

10.1186/s12866-017-0966-x

Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Cited by: 12
Author(s): Vijay Kumar Sharma, Darrell O. Bayles, David P. Alt, Torey Looft, Brian W. Brunelle, Judith A. Stasko
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.9661

Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica
Cited by: 4
Author(s): Yahui Wang, Xiaohong Liu, Rongrong Zhang, Zhiming Yan, Ai‐Sheng Xiong, Xiaojun Su
Software Mentions: 1
Published: about 6 years ago

10.1186/s12866-019-1497-4

Exploring the tissue tropism of pseudorabies virus based on miRNA level analysis
Cited by: 1
Author(s): Fan Yu, Ling Zhu, Xiangang Sun, Wenting Lyu, Lei Xu, Yin Yuan, Jun Zhao, Jianbo Huang, Yichao Den, Zhiyi Jiang, Shiyao Xu, Mao Xiyu, Zhinan Xu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-019-1462-2

Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model
Cited by: 10
Author(s): Barbara U. Metzler‐Zebeli, Monica A. Newman, Dietmar Grüll, Qendrim Zebeli
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-021-02214-1

Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study
Cited by: 19
Author(s): Lucas Moitinho‐Silva, Michelle Wegener, Sandra May, Florian Schrinner, Awais Akhtar, Teide Jens Boysen, Eva Schaeffer, Clint Hansen, Timo Schmidt, Malte Rühlemann, Matthias Hübenthal, Philipp Rausch, Mustafa T. Kondakci, Walter Maetzler, Stephan Weidinger, Matthias Laudes, Philip Süß, Dominik M. Schulte, Ralf Junker, Felix Sommer, Burkhard Weisser, Corinna Bang, André Franke
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.8768

Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi
Cited by: 7
Author(s): Kunyuan Guo, Yiming Yao, Meng Yang, Yanni Li, Bin Wu, Xianming Lin
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8895

Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains
Cited by: 4
Author(s): Bao-Wei Lu, Fengxia An, Liangjing Cao, Qian Gao, Xuan Wang, Yongjian Yang, Pengming Liu, Baoliang Yang, Tong Chen, Xin-Chang Li, Qinghua Chen, Jun Li
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.2819

Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection
Cited by: 5
Author(s): Stephanie M. Rosales, Rebecca L. Vega Thurber
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.10593

Transcriptome analysis reveals liver metabolism programming in kids from nutritional restricted goats during mid-gestation
Cited by: 5
Author(s): Chao Yang, Xiaoling Zhou, Hong Yang, Kefyalew Gebeyew, Qiongxian Yan, Chunfang Zhou, Zhixiong He, Zhiliang Tan
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.5011

Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs
Cited by: 48
Author(s): Duo Yu, Yunfeng Li, Zhi‐Hui Ming, Hongyong Wang, Zuo-Ren Dong, Ling Qiu, Zhihui Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/s41388-020-1259-7

Loss of the nuclear Wnt pathway effector TCF7L2 promotes migration and invasion of human colorectal cancer cells
Cited by: 40
Author(s): Janna Wenzel, Katja Rose, Elham Bavafaye Haghighi, Constanze Lamprecht, Gilles Rauen, Vivien Freihen, Rebecca Kesselring, Melanie Boerries, Andreas Hecht
Software Mentions: 1
Published: over 6 years ago

10.1186/s12866-019-1578-4

Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds
Cited by: 6
Author(s): Thorsten Bufe, André Hennig, Jochen Klumpp, Agnes Weiß, Kay Nieselt, Herbert Schmidt
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.6845

Exploring the transcriptome ofluxI−andΔainSmutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy-decanoyl-L-homoserine lactones on biofilm formation inAliivibrio salmonicida
Cited by: 7
Author(s): Miriam Khider, Hilde Hansen, Erik Hjerde, Jostein Johansen, Nils Peder Willassen
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.11081

RNA-seq analysis of antibacterial mechanism of Cinnamomum camphora essential oil against Escherichia coli
Cited by: 5
Author(s): Yutian Yu, Jing Dong, Yanlu Wang, Xiaohua Gong
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-020-01873-w

Genome sequence and spore germination-associated transcriptome analysis of Corynespora cassiicola from cucumber
Cited by: 10
Author(s): Shigang Gao, Rong Zeng, Lihui Xu, Zhiwei Song, Ping Gao, Fangyin Dai
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.8797

Pan-cancer systematic identification of lncRNAs associated with cancer prognosis
Cited by: 3
Author(s): Matthew Ung, Evelien Schaafsma, Daniel Mattox, George L. Wang, Chao Cheng
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.3408

Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C
Cited by: 13
Author(s): Chuan Li, Zhigang Zhao, Yongming Liu, Bing Liu, Shuxian Guan, Hai Long, Jing Wang, Yanli Lu, Mengji Cao
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-020-01894-5

Evaluation of fecal DNA extraction protocols for human gut microbiome studies
Cited by: 18
Author(s): Mi Young Lim, Yong Soo Park, Jung-Ha Kim, Young-Do Nam
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.3315

Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled byHalobacteriovoraxpredators
Cited by: 59
Author(s): Rory M. Welsh, Stephanie M. Rosales, Jesse Zaneveld, Jérôme P. Payet, Ryan McMinds, Steven L Hubbs, Rebecca L. Vega Thurber
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-018-1352-z

The spent culture supernatant of Pseudomonas syringae contains azelaic acid
Cited by: 11
Author(s): Sree Gowrinadh Javvadi, Paola Cescutti, Roberto Rizzo, Valentina Lonzarich, Luciano Navarini, Danilo Licastro, Corrado Guarnaccia, Vittorio Venturi
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.11586

Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis
Cited by: 1
Author(s): Jiming Gao, Tong Chen, Chao Jiang, Tielin Wang, Ou Huang, Xiang Zhang, Juan Liu
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.8024

Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma
Cited by: 16
Author(s): Xiwen Wang, Rui Su, Qiqiang Guo, Jia Liu, Banlai Ruan, Guiling Wang
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.6832

Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
Cited by: 21
Author(s): Jie Li, Xinhao Liu
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.9357

Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach
Cited by: 42
Author(s): Tamizhini Loganathan, Srimathy Ramachandran, Prakash Shankaran, Devipriya Nagarajan, Suma Mohan
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.2486

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Cited by: 62
Author(s): Christian Rinke, Serene Low, Ben J. Woodcroft, Jean-Baptiste Raina, Adam Skarshewski, Xuyen H. Le, Margaret K. Butler, Roman Stocker, Justin R. Seymour, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 1
Published: almost 10 years ago

10.7717/peerj.8509

Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma
Cited by: 25
Author(s): Wei Li, Na Li, Lina Gao, Chongge You
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.6388

Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach
Cited by: 12
Author(s): Saleembhasha Asanigari, Seema Mishra
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.5782

Sex-biased expression between guppies varying in the presence of ornamental coloration
Cited by: 3
Author(s): Cynthia Dick, David N. Reznick, Cheryl Y. Hayashi
Software Mentions: 1
Published: almost 8 years ago

10.7717/peerj.6629

Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer
Cited by: 10
Author(s): Yuting Yang, Xiaoping Tang, Xueqin Song, Li Tang, Yong Cao, Xu Liu, Xiaoyan Wang, Yan Li, Minglan Yu, Haisu Wan, Feng Chen
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.8054

Ciglitazone—a human PPARγ agonist—disrupts dorsoventral patterning in zebrafish
Cited by: 7
Author(s): Vanessa Cheng, Subham Dasgupta, Aalekhya Reddam, David C. Volz
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.9994

Potential role of cellular miRNAs in coronavirus-host interplay
Cited by: 64
Author(s): Stepan Nersisyan, Narek Engibaryan, Aleksandra Gorbonos, Ksenia Kirdey, Alexey Makhonin, Alexander G. Tonevitsky
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.11506

Transcriptome analysis of Sonneratia caseolaris seedlings under chilling stress
Cited by: 6
Author(s): Yong Yang, Chunfang Zheng, Cairong Zhong, Tianxi Lu, Juma Gul, Xiang Jin, Ying Zhang, Qiang Liu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.12133

Transcriptome and structure analysis in root of Casuarina equisetifolia under NaCl treatment
Cited by: 6
Author(s): Yujiao Wang, Jin Zhang, Qiu Zhenfei, Bingshan Zeng, Yong Zhang, Xiaoping Wang, Jun Chen, Zhong Chen, Renhua Deng, Chunjie Fan
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.6425

Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis
Cited by: 24
Author(s): Yang Fang, Pingping Wang, Lin Xia, Suwen Bai, Yonggang Shen, Qing Li, Yang Wang, Jiaquan Zhu, Juan Du, Bing Shen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1007241

Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture
Cited by: 23
Author(s): Colin D. Donohoe, Gábor Csordás, Andreia Correia, Marek Jindra, Corinna Klein, Bianca Habermann, Mirka Uhlířová
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1008139

Functional robustness of adult spermatogonial stem cells after induction of hyperactive Hras
Cited by: 5
Author(s): Mika Yamada, Cai Winson, L. A. Martin, Thierry N’Tumba-Byn, Marco Seandel
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1009243

Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function
Cited by: 6
Author(s): Natalie C. Deans, Brian Giacopelli, Jay B. Hollick
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1006570

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra
Cited by: 64
Author(s): Sonal Shewaramani, Thomas J. Finn, Sinead C. Leahy, Rees Kassen, Paul B. Rainey, Christina D. Moon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006024

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States
Cited by: 72
Author(s): Konrad L. M. Rudolph, Bianca M Schmitt, Diego Villar, Robert J. White, John C. Marioni, Claudia Kutter, Duncan T. Odom
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1007749

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors
Cited by: 145
Author(s): François Rousset, Lun Cui, Elise Siouve, Christophe Bécavin, Florence Depardieu, David Bikard
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1006808

Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis
Cited by: 17
Author(s): Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F. Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O’Donovan, Rebecca C. Fitzgerald
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07506-4

Immune-related genes of the larval Holotrichia parallela in response to entomopathogenic nematodes Heterorhabditis beicherriana LF
Cited by: 7
Author(s): Li ErTao, Jianhui Qin, Honglin Feng, Jinqiao Li, Xiaofeng Li, Innocent Nyamwasa, Yujin Cao, Weibin Ruan, Kebin Li, Jing Yin
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.203018

Translational control of gene expression by eIF2 modulates proteostasis and extends lifespan
Cited by: 5
Author(s): Tamara Jiménez-Saucedo, Juan José Berlanga, M. Gabriel
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006683

Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies
Cited by: 31
Author(s): Rocío Acuña-Hidalgo, Pelagia Derizioti, Marloes Steehouwer, Christian Gilissen, Sarah A. Graham, Sipko van Dam, Julie Hoover‐Fong, Aida Telegrafi, Anne Destrée, Robert Śmigiel, Lindsday A. Lambie, Hülya Kayserili, Umut Altunoğlu, Elisabetta Lapi, Maria Luisa Giovannucci Uzielli, Mariana Aracena, Banu Nur, Ercan Mıhçı, Lília Maria Azevedo Moreira, Viviane Borges Ferreira, Dafne Dain Gandelman Horovitz, Kátia Maria da Rocha, Aleksandra Jezela‐Stanek, Alice S. Brooks, Heiko Reutter, Julie S. Cohen, Ali Fatemi, Martin Smitka, Theresa A. Grebe, Nataliya Di Donato, Charu Deshpande, Anthony Vandersteen, Charles Marques Lourenço, Andreas Dufke, Eva Rossier, Gwenaëlle André, Alessandra Baumer, Careni Spencer, Julie McGaughran, Lude Franke, Joris A. Veltman, Bert B.A. de Vries, Albert Schinzel, Simon E. Fisher, Alexander Hoischen, Bregje W.M. van Bon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1009098

Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development
Cited by: 9
Author(s): Lin Cheng, Yu Zhang, Yi Zhang, Tao Chen, Yan Xu, Yikang S. Rong
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-018-4500-9

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity
Cited by: 20
Author(s): Fátima Carvajal, Raquel Rosales, Francisco Palma, Susana Manzano, Joaquı́n Cañizares, Manuel Jamilena, Dolores Garrido
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1009822

Mitochondrial dysfunction in adult midbrain dopamine neurons triggers an early immune response
Cited by: 7
Author(s): Roberta Filograna, Seungmin Lee, Katarína Tiklová, Mara Mennuni, Viktor Jönsson, Markus Ringnér, Linda Gillberg, Elena Sopova, Oleg Shupliakov, Camilla Koolmeister, Lar̀s Olson, Thomas Perlmann, Nils-Göran Larsson
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms221910181

Transcriptomic Analysis Reveals Differential Expression of Genes between Lung Capillary and Post Capillary Venules in Abdominal Sepsis
Cited by: 3
Author(s): Milladur Rahman, Zhiyi Ding, Carl-Fredrik Rönnow, Henrik Thorlacius
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-019-6391-9

Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance
Cited by: 20
Author(s): Roni Tadmor‐Levi, Adi Doron‐Faigenboim, Evgeniya Marcos‐Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, G.F. Wiegertjes, Lior David
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1006239

Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers
Cited by: 240
Author(s): Seong-Keun Yoo, Seungbok Lee, Su Jin Kim, Hyeon Gun Jee, Byoung Ae Kim, Hyesun Cho, Young Shin Song, Sun Wook Cho, Jae Kyung Won, Jong Yeon Shin, Do Joon Park, Jong‐Il Kim, Kyu Eun Lee, Young Joo Park, Jeong Sun Seo
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-020-6648-3

Sexual-biased gene expression of olfactory-related genes in the antennae of Conogethes pinicolalis (Lepidoptera: Crambidae)
Cited by: 7
Author(s): Dapeng Jing, Tiantao Zhang, Shuxiong Bai, Kanglai He, Sivaprasath Prabu, Jing Luan, Zhenying Wang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1007105

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay
Cited by: 78
Author(s): Jennifer L. Anderson, Timothy S. Mulligan, Meifen Shen, Hui Wang, Catherine Scahill, Frederick J. Tan, Shao Jun Du, Elisabeth M Busch-Nentwich, Steven A. Farber
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1009452

Structure-function analysis of fission yeast cleavage and polyadenylation factor (CPF) subunit Ppn1 and its interactions with Dis2 and Swd22
Cited by: 4
Author(s): Bradley Benjamin, Ana M. Sánchez, Angad Garg, Beate Schwer, Stewart Shuman
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.64678

Correction: Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 0
Author(s): Carlos Martinez Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1009491

Widespread imprinting of transposable elements and variable genes in the maize endosperm
Cited by: 5
Author(s): Sarah N. Anderson, Peng Zhou, Kaitlin Higgins, Yaniv Brandvain, Nathan M. Springer
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1007578

The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish
Cited by: 17
Author(s): Deyong Xiao, Huijun Wang, Lili Hao, Xiao Guo, Xiaojing Ma, Yanyan Qian, Hongbo Chen, Jing Ma, Jin Zhang, Wei Sheng, Weinian Shou, Guoying Huang, Ding Ma
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1009785

Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network
Cited by: 3
Author(s): Changming Tan, Siting Zhu, Zee Chen, Canzhao Liu, Yang E. Li, Mason Zhu, Zhiyuan Zhang, Zhiwei Zhang, Lunfeng Zhang, Yusu Gu, Zhengyu Liang, Thomas G. Boyer, Kunfu Ouyang, Sylvia M. Evans, Xi Fang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-5987-4

Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows
Cited by: 24
Author(s): Pierre-Alexis Billa, Yannick Faulconnier, T. Ye, Mathilde Chervet, Fabienne Le Provost, José Pires, Christine Leroux
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-021-07528-y

Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium
Cited by: 14
Author(s): B. Dnate’ Baxter, Eric D. Larson, Laëtitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N. Bubak, Christy S. Niemeyer, James E. Hassell, Doug P. Shepherd, Vijay R. Ramakrishnan, Maria A. Nagel, Diego Restrepo
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1009521

Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function
Cited by: 7
Author(s): Kendra Reynaud, Molly Brothers, Michael Ly, Nicholas T. Ingolia
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006341

Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression
Cited by: 37
Author(s): Martha J. Snyder, Alyssa C. Lau, Elizabeth A. Brouhard, Mary Ellen Davis, Jiali Jiang, Margarita Sifuentes, Györgyi Csankovszki
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1007802

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability
Cited by: 111
Author(s): Mahdieh Jadaliha, Omid Gholamalamdari, Wei Tang, Yang Zhang, Ana Petracovici, Qinyu Hao, Aamira Tariq, Tae Gyoon Kim, Sarah E. Holton, Deepak Kumar Singh, Xiao Ling Li, Susan M. Freier, Stefan Ambs, Rohit Bhargava, Ashish Lal, Supriya G. Prasanth, Jian Ma, Kannanganattu V. Prasanth
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1006134

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa
Cited by: 88
Author(s): Anne Chevallereau, Bob Blasdel, Jeroen De Smet, Marc Monot, Michael Zimmermann, Maria Kogadeeva, Uwe Sauer, Peter Jorth, Marvin Whiteley, Laurent Debarbieux, Rob Lavigne
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007124

An Arabidopsis Nucleoporin NUP85 modulates plant responses to ABA and salt stress
Cited by: 62
Author(s): Yingfang Zhu, Bangshing Wang, Kai Tang, Chuan‐Chih Hsu, Shaojun Xie, Hongwu Du, Yuting Yang, W. Andy Tao, Jian‐Kang Zhu
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1008425

NusG prevents transcriptional invasion of H-NS-silenced genes
Cited by: 14
Author(s): Lionello Bossi, Mathilde Ratel, Camille Laurent, Patricia Kerboriou, Andrew Camilli, É. Éveno, Marc Boudvillain, Nara Figueroa‐Bossi
Software Mentions: 1
Published: almost 7 years ago

10.1099/acmi.0.000121

Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation
Cited by: 2
Author(s): Richard J. Fredendall, Jenny L. Stone, Michael J. Pehl, Paul M. Orwin
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1005691

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression
Cited by: 24
Author(s): David B. West, Eric K. Engelhard, Michael Adkisson, Alessia Nava, Julia V. Kirov, Andreanna Cipollone, Brandon Willis, Jared Rapp, Pieter J. de Jong, Kevin C K Lloyd
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07888-5

Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage
Cited by: 14
Author(s): Ailing Zhang, Jicheng Yang, Min Sun, Chuang Lin, Puding Zhou, Juncai Ren, Dan Luo, Xiaoshan Wang, Congyu Ma, Xinquan Zhang, Guangyan Feng, Gang Nie, Linkai Huang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-3334-6

Transcriptome profiling in the damselfly Ischnura elegans identifies genes with sex-biased expression
Cited by: 24
Author(s): Pallavi Chauhan, Maren Wellenreuther, Bengt Hansson
Software Mentions: 1
Published: almost 10 years ago

10.7554/eLife.50226

An RNAi screen unravels the complexities of Rho GTPase networks in skin morphogenesis
Cited by: 8
Author(s): Mélanie Laurin, Nicholas C. Gomez, John Levorse, Ataman Sendoel, Megan Sribour
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0221288

Fanconi-BRCA pathway mutations in childhood T-cell acute lymphoblastic leukemia
Cited by: 14
Author(s): Gayle P. Pouliot, James Degar, Laura Hinze, Bose Kochupurakkal, Chau D. Vo, Melissa Burns, Lisa A. Moreau, Chirag Ganesa, Justine E. Roderick, Sofie Peirs, Björn Menten, Mignon L. Loh, Stephen P. Hunger, Lewis B. Silverman, Marian H. Harris, Kristen E. Stevenson, David M. Weinstock, Andrew P. Weng, Pieter Van Vlierberghe, Alan D. D’Andrea, Alejandro Gutiérrez
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0216862

Inflammatory response of mesenchymal stromal cells after in vivo exposure with selected trauma-related factors and polytrauma serum
Cited by: 15
Author(s): Elisa Maria Amann, Alexander Groß, Markus Rojewski, Hans A. Kestler, Miriam Kalbitz, Rolf E. Brenner, Markus Huber‐Lang, Hubert Schrezenmeier
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0218220

Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq
Cited by: 10
Author(s): Cameron V. Sayer, Bidisha Barat, David L. Popham
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.58295

Crosstalk between nitric oxide and retinoic acid pathways is essential for amphioxus pharynx development
Cited by: 4
Author(s): Filomena Caccavale, Giovanni Annona, Lucie Subirana, Héctor Escrivà, Stéphanie Bertrand, Salvatore D’Aniello
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0252597

Wound healing with topical BRAF inhibitor therapy in a diabetic model suggests tissue regenerative effects
Cited by: 4
Author(s): Helena Escuin-Ordinas, Yining Liu, Lingyun Sun, Willy Hugo, Robert Dimatteo, Rong Huang, Paige Krystofinski, Ariel M. Azhdam, Jordan Lee, Begoña Comı́n-Anduix, Alistair J. Cochran, Roger S. Lo, Tatiana Segura, Philip O. Scumpia, Antoni Ribas
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0170999

Identification of MiR-21-5p as a Functional Regulator of Mesothelin Expression Using MicroRNA Capture Affinity Coupled with Next Generation Sequencing
Cited by: 20
Author(s): Chiara De Santi, Sebastian Vencken, Jonathon Blake, Bettina Haase, Vladimı́r Beneš, Federica Gemignani, Stefano Landi, Catherine M. Greene
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07951-1

Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide
Cited by: 6
Author(s): David A. Skerrett‐Byrne, Brett Nixon, Elizabeth G. Bromfield, James Breen, Natalie A. Trigg, Simone J. Stanger, Ilana R. Bernstein, Andy Anderson, Tessa Lord, Raymond Aitken, Shaun D. Roman, Sarah A. Robertson, John E. Schjenken
Software Mentions: 1
Published: almost 5 years ago

10.18632/aging.202733

Sex-specific differences of humoral immunity and transcriptome diversification in older adults vaccinated with inactivated quadrivalent influenza vaccines
Cited by: 0
Author(s): Jing Yang, Xiaoyuan Huang, Jiayou Zhang, Renfeng Fan, Wei Zhao, Han Tian, Kai Duan, Xinguo Li, Peiyu Zeng, Jinglong Deng, Jikai Zhang, Xiaoming Yang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-4451-1

Differential gene expression in the evolution of sex pheromone communication in New Zealand’s endemic leafroller moths of the genera Ctenopseustis and Planotortrix
Cited by: 9
Author(s): Alessandro Grapputo, Amali H. Thrimawithana, Bernd Steinwender, Richard D. Newcomb
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0235183

ZBTB38 is dispensable for antibody responses
Cited by: 4
Author(s): Rachel Wong, Deepta Bhattacharya
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0181084

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure
Cited by: 6
Author(s): Julia Morud, Arghavan Ashouri, Erik Larsson, Mia Ericson, Bo Söderpalm
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.66703

Loss of Mir146b with aging contributes to inflammation and mitochondrial dysfunction in thioglycollate-elicited peritoneal macrophages
Cited by: 2
Author(s): Andrea Santeford, Aaron Lee, Abdoulaye Sène, Lynn M. Hassman, Alexey Sergushichev, Ekaterina Loginicheva, Maxim N. Artyomov, Philip A. Ruzycki, Rajendra S. Apte
Software Mentions: 1
Published: about 5 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583