bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/pathogens8040195

An Acute Stress Model in New Zealand White Rabbits Exhibits Altered Immune Response to Infection with West Nile Virus
Cited by: 5
Author(s): Willy W. Suen, Mitchell Imoda, Albert W Thomas, Nur N B M Nasir, Nawaporn Tearnsing, Wenqi Wang, Helle Bielefeldt‐Ohmann
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.652211

Comprehensive Pan-Cancer Analysis Confirmed That ATG5 Promoted the Maintenance of Tumor Metabolism and the Occurrence of Tumor Immune Escape
Cited by: 18
Author(s): Chunxiao Xu, Yusheng Zang, Yuxiang Zhao, Weiqiang Cui, Hong Zhang, Yingcui Zhu, Man Xu
Software Mentions: 6
Published: over 3 years ago

10.15252/embj.2018100882

Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: about 5 years ago

10.12688/wellcomeopenres.15115.1

Single-cell transcriptome analysis of CD8+ T-cell memory inflation
Cited by: 7
Author(s): Andrew J. Highton, Madeleine E Zinser, Lian Ni Lee, Claire Hutchings, Catherine de Lara, Chansavath Phetsouphanh, Christian Willberg, Claire L. Gordon, Paul Klenerman, Emanuele Marchi
Software Mentions: 6
Published: over 5 years ago

10.1017/S0031182021000111

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella
Cited by: 5
Author(s): Arnar K. S. Sandholt, Feifei Xu, Robert Söderlund, Anna Lundén, Karin Troell, Staffan G. Svärd, Eva Wattrang
Software Mentions: 6
Published: almost 4 years ago

10.12688/f1000research.13049.2

RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
Cited by: 6
Author(s): Travis L. Jensen, Michael Frasketi, Kevin P. Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes Goll
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2021.571231

Identification and Analysis of Potential Key Genes Associated With Hepatocellular Carcinoma Based on Integrated Bioinformatics Methods
Cited by: 21
Author(s): Zhuolin Li, Yao Lin, Bizhen Cheng, Qiaoxin Zhang, Yingmu Cai
Software Mentions: 6
Published: almost 4 years ago

10.18632/aging.203448

Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts
Cited by: 1
Author(s): Anastasiya V. Lipatova, George S. Krasnov, Pavel Vorobyov, Pavel Melnikov, Olga N. Alekseeva, Yulia S. Vershinina, Alexander G. Brzhozovskiy, Daria Goliusova, Faniya Maganova, Natalia F. Zakirova, Anna V. Kudryavtseva, Alexey Moskalev
Software Mentions: 6
Published: over 3 years ago

10.1038/srep35671

RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways
Cited by: 22
Author(s): Lulu Jiang, Charles Hindmarch, Mark F. Rogers, Colin Campbell, Christy Waterfall, Jane A. Coghill, Peter W. Mathieson, Gavin I. Welsh
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pgen.1009162

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation
Cited by: 18
Author(s): Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Víctor Latorre, Frank Ladam, Marta Losa, Syed Murtuza Baker, Charles G. Sagerström, Kimberly A. Mace, Magnus Rattray, Nicoletta Bobola
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-019-5686-1

aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data
Cited by: 4
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-019-46932-z

DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Cited by: 73
Author(s): Christian T. Wohnhaas, Germán Leparc, Francesc Fernández-Albert, David Kind, Florian Gantner, Coralie Viollet, Tobias Hildebrandt, Patrick Baum
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2019.00209

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data
Cited by: 23
Author(s): Shenhe Liu, Tingzhu Ye, Zipeng Li, Jun Li, Muhammad Jamil Ahmad, Yang Zhou, Guohua Hua, Aixin Liang, Tingxian Deng, Liguo Yang
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2021.654517

Identification of Key Genes Associated With the Process of Hepatitis B Inflammation and Cancer Transformation by Integrated Bioinformatics Analysis
Cited by: 7
Author(s): Jingyuan Zhang, Xinkui Liu, Wei Zhou, Shan Lu, Chao Wu, Zhishan Wu, Runping Liu, Xiaojiaoyang Li, Jiarui Wu, Yingying Liu, Siyu Guo, Shanshan Jia, Xiaomeng Zhang, Miaomiao Wang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-45714-x

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity
Cited by: 30
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, Liubov Koval, Eugenia V. Schegoleva, Zulfiya G. Guvatova, George S. Krasnov, Ilya Solovev, Maksim A. Sheptyakov, Alex Zhavoronkov, Anna V. Kudryavtseva
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-019-44902-z

Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome
Cited by: 12
Author(s): Jingya Wang, Sadiye Amcaoglu Rieder, Jincheng Wu, Susana Hayes, Rebecca Halpin, Melissa de los Reyes, Yashaswi Shrestha, Roland Kolbeck, Rajiv Raja
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2021.665153

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species
Cited by: 9
Author(s): Annie Robic, Chloé Cerutti, Christa Kühn, Thomas Faraut
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-44302-3

Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.46464

Molecular and anatomical organization of the dorsal raphe nucleus
Cited by: 120
Author(s): Kee Wui Huang, Nicole Ochandarena, Adrienne C. Philson, Minsuk Hyun, Jaclyn E Birnbaum, Marcelo Cicconet, Bernardo L. Sabatini
Software Mentions: 6
Published: over 5 years ago

10.1590/1678-4685-GMB-2018-0259

Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean
Cited by: 16
Author(s): Wendell Jacinto Pereira, Arthur Tavares de Oliveira Melo, Alexandre Siqueira Guedes Coelho, Fabiana Aparecida Rodrigues, Sujan Mamidi, Sérgio Amorim de Alencar, Anna Cristina Lanna, P. A. M. R. Valdisser, C. Brondani, Ivanildo Ramalho do Nascimento-Júnior, T. C. de O. Borba, R. P. Vianello
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12711-019-0453-y

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs
Cited by: 24
Author(s): M. Piles, Carlos Fernández-Lozano, María Velasco-Galilea, Olga González‐Rodríguez, Juan Pablo Sánchez, D. Torrallardona, María Ballester, Raquel Quintanilla
Software Mentions: 6
Published: almost 6 years ago

10.1186/gb-2011-12-8-r83

Cistrome: an integrative platform for transcriptional regulation studies
Cited by: 583
Author(s): Tao Liu, Jorge Ortíz, Len Taing, Clifford A. Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Suei Nee Wong, Jian Ma, Ying Lei, Utz Johann Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Software Mentions: 6
Published: almost 14 years ago

10.1002/cam4.4115

Development and validation of a PBRM1‐associated immune prognostic model for clear cell renal cell carcinoma
Cited by: 5
Author(s): Jiayi Chen, Chunlin Yao, Nan Qiao, Yangyang Ge, Jianhua Li, Yun Lin, Shanglong Yao
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1009280

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-015-0815-x

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1
Cited by: 48
Author(s): Florian Duclot, Mohamed Kabbaj
Software Mentions: 6
Published: about 9 years ago

10.1007/s00439-020-02228-1

A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies
Cited by: 5
Author(s): Liliya Nazlamova, N. Simon Thomas, Man‐Kim Cheung, Jelmer Legebeke, Jenny Lord, Reuben J. Pengelly, William Tapper, Gabrielle Wheway
Software Mentions: 6
Published: about 4 years ago

10.1186/s13059-017-1359-z

Experimental design and quantitative analysis of microbial community multiomics
Cited by: 125
Author(s): Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan, Curtis Huttenhower
Software Mentions: 6
Published: about 7 years ago

10.1002/cam4.4161

Integrated pan‐cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance
Cited by: 12
Author(s): Noushin Miralaei, Ahmad Majd, Kamran Ghaedi, Maryam Peymani, Masoomeh Safaei
Software Mentions: 6
Published: over 3 years ago

10.1186/s40170-020-00217-6

Therapy-induced lipid uptake and remodeling underpin ferroptosis hypersensitivity in prostate cancer
Cited by: 56
Author(s): Kaylyn D. Tousignant, Anja Rockstroh, Berwyck L. J. Poad, Ali Talebi, Reuben S. E. Young, Atefeh Taherian Fard, Rajesh Gupta, Tuo Zang, Chenwei Wang, Melanie Lehman, Johan Swinnen, Stephen J. Blanksby, Colleen C. Nelson, Martin C. Sadowski
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.ppat.1009567

ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection
Cited by: 7
Author(s): Joseph M Cabral, Camille H. Cushman, Catherine Sodroski, David M. Knipe
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1874-1

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Cited by: 2,100
Author(s): Christoph Hafemeister, Rahul Satija
Software Mentions: 6
Published: about 5 years ago

10.1186/s13059-020-01953-0

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators
Cited by: 7
Author(s): Shengen Hu, Dawei Huo, Zhaowei Yu, Yujie Chen, Jing Liu, Lin Liu, Xudong Wu, Yong Zhang
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.ppat.1008754

JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: over 4 years ago

10.26508/lsa.202000976

Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: over 3 years ago

10.1128/mSystems.00145-20

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens
Cited by: 14
Author(s): Briallen Lobb, Rhiannon Hodgson, Michael D. J. Lynch, Michael J. Mansfield, Jiujun Cheng, Trevor C. Charles, Josh D. Neufeld, Paul M. Craig, Andrew C. Doxey
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-018-4738-2

Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells
Cited by: 43
Author(s): Fernando H. Biase, Katelyn M. Kimble
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1008037

Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
Cited by: 24
Author(s): Kevin S. Myers, Nicholas M. Riley, Matthew E. MacGilvray, Trey K. Sato, Mick McGee, Justin Heilberger, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: over 8 years ago

10.1128/mBio.01849-21

Hofbauer Cells Spread Listeria monocytogenes among Placental Cells and Undergo Pro-Inflammatory Reprogramming while Retaining Production of Tolerogenic Factors
Cited by: 7
Author(s): Siavash Azari, Lauren J. Johnson, Amy Webb, Sophia M Kozlowski, Xiaoli Zhang, Kara M. Rood, Amal O. Amer, Stéphanie Seveau
Software Mentions: 6
Published: over 3 years ago

10.1128/mBio.02683-20

The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4 / UL5 Transcripts
Cited by: 23
Author(s): Ana Cristina Gonzalez-Perez, Markus Stempel, Emanuel Wyler, Christian Urban, Antonio Piras, Thomas Hennig, Sabina Ganskih, Yuanjie Wei, Albert Heim, Markus Landthaler, Andreas Pichlmair, Lars Dölken, Mathias Munschauer, Florian Erhard, Melanie M. Brinkmann
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-6748-0

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Cited by: 19
Author(s): Vladislav V. Babenko, Oleg V. Podgorny, Valentin A. Manuvera, Artem S. Kasianov, Alexander I. Manolov, Ekaterina N. Grafskaia, Dmitriy A. Shirokov, Alexey S. Kurdyumov, D. V. Vinogradov, Anastasia S. Nikitina, Sergey I. Kovalchuk, Nikolay Anikanov, Ivan Butenko, Olga Pobeguts, Daria Matyushkina, Daria V. Rakitina, Elena S. Kostryukova, Victor G. Zgoda, I. P. Baskova, В. М. Трухан, Mikhail S. Gelfand, Vadim M. Govorun, Helgi B. Schiöth, В. Н. Лазарев
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-019-6073-7

GENAVi: a shiny web application for gene expression normalization, analysis and visualization
Cited by: 36
Author(s): Alberto Luiz P Reyes, Tiago C. Silva, Simon Coetzee, Jasmine T Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther, Michelle R. Jones
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pgen.1009432

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1007633

Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion
Cited by: 45
Author(s): Yasmine J. Liu, Georges E. Janssens, Rebecca L. McIntyre, Marte Molenaars, Rashmi Kamble, Arwen W. Gao, Aldo Jongejan, Michel van Weeghel, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: about 13 years ago

10.1186/s12864-016-2746-7

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome
Cited by: 34
Author(s): Peijie Lin, Laura Nicholls, Hassan Assareh, Zhiming Fang, Timothy G. Amos, Richard J. Edwards, Amelia A. Assareh, Irina Voineagu
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0258069

Does algae β-glucan affect the fecal bacteriome in dairy calves?
Cited by: 6
Author(s): G.F. Virgínio, Maria Eduarda Reis, Ana Paula da Silva, Ariany Faria de Toledo, Amanda Moelemberg Cezar, Lucas William Mendes, L.F. Greco, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0204317

Association of metformin administration with gut microbiome dysbiosis in healthy volunteers
Cited by: 85
Author(s): Ilze Elbere, Ineta Kalniņa, Ivars Silamiķelis, Ilze Konrāde, Linda Zaharenko, Kristine Sekace, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Dita Gudrā, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 6
Published: about 6 years ago

10.7150/thno.55946

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome
Cited by: 28
Author(s): Xiaomin Hu, Hanyu Li, Xinyue Zhao, Ronggang Zhou, Honghong Liu, Yiting Sun, Yue Fan, Yanan Shi, Shushan Qiao, Shuang‐Jiang Liu, Hongwei Liu, Shuyang Zhang
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms20020263

Molecular Network-Based Drug Prediction in Thyroid Cancer
Cited by: 14
Author(s): Xingyu Xu, Hang Long, Baohang Xi, Binbin Ji, Zejun Li, Yunyue Dang, Cheng Jiang, Yao Yao, Jialiang Yang
Software Mentions: 6
Published: almost 6 years ago

10.7150/thno.56141

Distinct placental molecular processes associated with early-onset and late-onset preeclampsia
Cited by: 31
Author(s): Zhonglu Ren, Yunfei Gao, Yue Gao, Guanmei Liang, Qian Chen, Sijia Jiang, Xiaoxue Yang, Cui-Xia Fan, Haizhen Wang, Jing Wang, Yi‐Wu Shi, Chaoqun Xiao, Ming Zhong, Xinping Yang
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0071745

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol
Cited by: 20
Author(s): Zhifu Sun, Yan W. Asmann, Asha Nair, Yuji Zhang, Liguo Wang, Krishna R. Kalari, Aditya Bhagwate, Tiffany R. Baker, Jennifer M. Carr, Jean Pierre A. Kocher, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0183517

Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study
Cited by: 7
Author(s): Han Wang, Zhenyu Zhang, Bangshun He, Yu Xu, Jun Zhang, Weijun Cao
Software Mentions: 6
Published: over 7 years ago

10.3390/nu12041042

Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model
Cited by: 33
Author(s): Ping Xu, Feng Yan, Yuhai Zhao, Xiangbo Chen, Shili Sun, Yuefei Wang, Le Ying
Software Mentions: 6
Published: over 4 years ago

10.1016/j.celrep.2019.06.046

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
Cited by: 68
Author(s): Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Čápková, Hana Imrichová, Karolína Zoufalová, Vendula Páralová, Roman Hrstka, Yansheng Liu, H. Alexander Ebhardt, Eva Budínská, Rudolf Nenutil, Ruedi Aebersold
Software Mentions: 6
Published: over 5 years ago

10.1016/j.celrep.2021.108739

Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease
Cited by: 40
Author(s): Hongtian Yang, Kristen D. Onos, Kwangbom Choi, Kelly J. Keezer, Daniel A. Skelly, Gregory W. Carter, Gareth R. Howell
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.celrep.2019.12.019

Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii
Cited by: 81
Author(s): Madlaina Boillat, Pierre‐Mehdi Hammoudi, Sunil Kumar Dogga, Stéphane Pagès, Maged Goubran, Iván Rodríguez, Dominique Soldati‐Favre
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.celrep.2021.109362

Nutritional regulation of oligodendrocyte differentiation regulates perineuronal net remodeling in the median eminence
Cited by: 29
Author(s): Sara Kohnke, Sophie Buller, Danaé Nuzzaci, Katherine Ridley, Brian Lam, Helena Pivoňková, Marie A. Bentsen, Kimberly M. Alonge, Chao Zhao, John Tadross, Staffan Holmqvist, Takahiro Shimizu, Hannah A. Hathaway, Hui‐Liang Li, Wendy B. Macklin, Michael W. Schwartz, William D. Richardson, Giles S.H. Yeo, R. J. M. Franklin, Ragnhildur Thóra Káradóttir, David H. Rowitch, Clémence Blouet
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2020.108545

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
Cited by: 23
Author(s): Jonathan Martínez-Fábregas, Luopin Wang, Elizabeth Pöhler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 6
Published: about 4 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: about 5 years ago

10.1016/j.stem.2020.11.005

Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency
Cited by: 125
Author(s): Masaki Kinoshita, M. Barber, William Mansfield, Yingzhi Cui, Daniel Spindlow, Giuliano Giuseppe Stirparo, Sabine Dietmann, Jennifer Nichols, Austin Smith
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-019-55441-y

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Cited by: 50
Author(s): Konstantin Carlberg, Marina Korotkova, Ludvig Larsson, Anca I. Catrina, Patrik L. Ståhl, Vivianne Malmström
Software Mentions: 6
Published: about 5 years ago

10.1016/j.ccell.2017.03.007

TIAM1 Antagonizes TAZ/YAP Both in the Destruction Complex in the Cytoplasm and in the Nucleus to Inhibit Invasion of Intestinal Epithelial Cells
Cited by: 69
Author(s): Zoi Diamantopoulou, Gavin R M White, Muhammad Zaki Hidayatullah Fadlullah, Marcel Dreger, Karen Pickering, Joe Maltas, Garry Ashton, Ruth MacLeod, George S. Baillie, Valérie Kouskoff, Georges Lacaud, Graeme I. Murray, Owen J. Sansom, Adam Hurlstone, Angeliki Malliri
Software Mentions: 6
Published: over 7 years ago

10.1161/CIRCULATIONAHA.120.046464

Hyperglycemia Induces Trained Immunity in Macrophages and Their Precursors and Promotes Atherosclerosis
Cited by: 75
Author(s): Laurienne Edgar, Naveed Akbar, Adam Braithwaite, Thomas Krausgruber, Héctor Gallart-Ayala, Jade Bailey, Alastair Corbin, Tariq E. Khoyratty, Joshua T Chai, Mohammad Alkhalil, André F. Rendeiro, Klemen Žiberna, Ritu Arya, Thomas J. Cahill, Christoph Bock, Jurga Laurencikiene, Mark J. Crabtree, Madeleine E. Lemieux, Niels P. Riksen, Mihai G. Netea, Craig E. Wheelock, Keith M. Channon, Mikael Rydén, Irina A. Udalova, Ricardo Carnicer, Robin P. Choudhury
Software Mentions: 6
Published: about 3 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: over 9 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: about 6 years ago

10.1002/ctm2.234

Epigenetic consequences of hormonal interactions between opposite‐sex twin fetuses
Cited by: 4
Author(s): Siming Kong, Yong Peng, Wei Chen, Xinyi Ma, Wei Yuan, Yangyu Zhao, Rong Li, Jie Qiao, Liying Yan
Software Mentions: 6
Published: about 4 years ago

10.1038/s42003-020-01364-8

Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse
Cited by: 22
Author(s): Tingzhen Mu, Liqin Xu, Yu Zhong, Xinyu Liu, Zhikun Zhao, Changyuan Huang, Xiaofeng Lan, Chengchen Lufei, Yi Zhou, Yixun Su, Luang Xu, Miaomiao Jiang, Hong Zhou, Xinxin Lin, Liang Wu, Siqi Peng, Shiping Liu, Susanne Brix, Michael Dean, N. Ray Dunn, Kenneth S. Zaret, Xin-Yuan Fu, Yong Hou
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2021.745284

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats
Cited by: 2
Author(s): Laure Denoyelle, Pierre de Villemereuil, Frédéric Boyer, Meidhi Khelifi, Clément Gaffet, Florian J. Alberto, Badr Benjelloun, François Pompanon
Software Mentions: 6
Published: about 3 years ago

10.3389/fgene.2021.657658

Weighted Gene Co-expression Network Analysis Identified a Novel Thirteen-Gene Signature Associated With Progression, Prognosis, and Immune Microenvironment of Colon Adenocarcinoma Patients
Cited by: 2
Author(s): Cangang Zhang, Zhe Zhao, Haibo Li, Shukun Yao, Dongyan Zhao
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-47921-y

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
Cited by: 9
Author(s): Aline Daniela Lopes Júlio, Ubiana de Cássia Mourão Silva, Julliane Dutra Medeiros, Daniel Morais, Vera Lúcia dos Santos
Software Mentions: 6
Published: over 5 years ago

10.1186/s12935-020-01423-4

Identification of a three-long noncoding RNA prognostic model involved competitive endogenous RNA in kidney renal clear cell carcinoma
Cited by: 21
Author(s): Di Zhang, Song Zeng, Xiaopeng Hu
Software Mentions: 6
Published: over 4 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: over 4 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: over 5 years ago

10.1073/pnas.2005330117

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism
Cited by: 31
Author(s): Louise Hunter, Charlotte E Pelekanou, Antony Adamson, Polly Downton, Nichola J Barron, Thomas Cornfield, Toryn Poolman, Neil Humphreys, Peter Cunningham, Leanne Hodson, A. S. I. Loudon, Mudassar Iqbal, David A. Bechtold, David Ray
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: about 5 years ago

10.1186/s12263-021-00688-2

An 8-week freeze-dried blueberry supplement impacts immune-related pathways: a randomized, double-blind placebo-controlled trial
Cited by: 7
Author(s): Michèle Rousseau, Justine Horne, Frédéric Guénard, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette
Software Mentions: 5
Published: over 3 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: over 4 years ago

10.3390/genes12081291

Regional Specific Differentiation of Integumentary Organs: Regulation of Gene Clusters within the Avian Epidermal Differentiation Complex and Impacts of SATB2 Overexpression
Cited by: 3
Author(s): Gee-Way Lin, Yung-Chih Lai, Ya-Chen Liang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-01960-1

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Cited by: 35
Author(s): Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving E. Vega, Viviane Labrie
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.ppat.1009346

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors
Cited by: 27
Author(s): Stuart R. Jefferys, Samuel D. Burgos, Jackson J Peterson, Sara R. Selitsky, Anne-Marie W. Turner, Lindsey I. James, Yi-Hsuan Tsai, Alisha R. Coffey, David M. Margolis, Joel S. Parker, Edward P. Browne
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.ppat.1008986

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: about 4 years ago

10.3390/life11060588

Impact TMPRSS2–ERG Molecular Subtype on Prostate Cancer Recurrence
Cited by: 7
Author(s): Anastasiya A. Kobelyatskaya, Elena A. Pudova, Anastasiya V. Snezhkina, Maria Fedorova, Vladislav Pavlov, Zulfiya G. Guvatova, М. В. Савватеева, Nataliya V. Melnikova, Alexey A. Dmitriev, Trofimov D.Yu. Trofimov, Г. Т. Сухих, K. M. Nyushko, B. Ya. Alekseev, Sergey V. Razin, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 5
Published: over 3 years ago

10.1093/jxb/eraa124

Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: almost 5 years ago

10.3390/genes12030385

Maternal Vitamin and Mineral Supplementation and Rate of Maternal Weight Gain Affects Placental Expression of Energy Metabolism and Transport-Related Genes
Cited by: 25
Author(s): Wellison J. S. Diniz, Lawrence P. Reynolds, P. P. Borowicz, Alison K Ward, Kevin K. Sedivec, Kacie L McCarthy, Cierrah J Kassetas, Friederike Baumgaertner, James D Kirsch, Sheri T. Dorsam, Tammi L Neville, J Chris Forcherio, Ronald Scott, J. S. Caton, Carl R Dahlen
Software Mentions: 5
Published: almost 4 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms21124302

Identification and Characterization of Circular Intronic RNAs Derived from Insulin Gene
Cited by: 11
Author(s): Debojyoti Das, Aniruddha Das, Mousumi Sahu, Smruti Sambhav Mishra, Shaheerah Khan, Pruthvi Raj Bejugam, Pranita K Rout, Arundhoti Das, Shehnaz Bano, Gyan P. Mishra, Sunil K. Raghav, Anshuman Dixit, Amaresh C. Panda
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1005385

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: over 9 years ago

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1009213

Gene regulatory effects of a large chromosomal inversion in highland maize
Cited by: 38
Author(s): Taylor M. Crow, James Ta, Saghi Nojoomi, M. Rocío Aguilar-Rangel, Jorge Vladimir Torres Rodríguez, David M. Gates, Rubén Rellán‐Álvarez, Ruairidh J. H. Sawers, Daniel E. Runcie
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-017-4380-4

Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome
Cited by: 36
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 5
Published: about 7 years ago

10.1186/s12864-020-07228-z

Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model
Cited by: 6
Author(s): Annette M. McCoy, Ann M. Kemper, M. Boyce, M. P. Brown, Troy N. Trumble
Software Mentions: 5
Published: about 4 years ago

10.1186/s12931-019-1085-z

Airway host-microbiome interactions in chronic obstructive pulmonary disease
Cited by: 82
Author(s): Zhang Wang, Barbara Maschera, Simon Lea, Umme Kolsum, David Michalovich, Stephanie Van Horn, Christopher Traini, James R. Brown, Edith M. Hessel, Dave Singh
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 11 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1007431

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
Cited by: 18
Author(s): Timothy M. Johanson, Hannah D. Coughlan, Aaron T. L. Lun, Naiara G. Bediaga, Gaetano Naselli, Alexandra L. Garnham, Leonard C. Harrison, Rhys S. Allan
Software Mentions: 5
Published: over 6 years ago

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: almost 4 years ago

Projects: bioconductor: edgeR

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