bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-84080-5

Persistent COUP-TFII expression underlies the myopathy and impaired muscle regeneration observed in resistance to thyroid hormone-alpha
Cited by: 1
Author(s): Paola Aguiari, Yanyun Liu, Astgik Petrosyan, Sheue-yann Cheng, Gregory A. Brent, Laura Perin, Anna Milanesi
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00321

Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach
Cited by: 4
Author(s): Yangyang Pang, Long He, Yameng Song, Xiaozhe Song, Jiahuan Lv, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01628-20

Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway
Cited by: 11
Author(s): Siqi Hong, Yan Li, Paul J. Kaminski, Jorge Andrade, Laimonis A. Laimins
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2015.00174

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations
Cited by: 44
Author(s): Ovidiu D. Iancu, Alexandre M. Colville, Denesa Oberbeck, Priscila Darakjian, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 3
Published: over 11 years ago

10.1098/rsos.170910

Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis
Cited by: 32
Author(s): Evan A. Eskew, Barbara C. Shock, Elise E B LaDouceur, Kevin Keel, Michael R. Miller, Janet E. Foley, Brian D. Todd
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2021.583568

Aberrantly DNA Methylated-Differentially Expressed Genes in Pancreatic Cancer Through an Integrated Bioinformatics Approach
Cited by: 4
Author(s): Haifeng Sun, Rui Xin, Changjun Zheng, Ge Huang
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms17101749

Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle
Cited by: 14
Author(s): Changlin Liu, Fazhen Zhao, Jing Yan, Chunsheng Liu, Siwei Liu, Siqing Chen
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2021.642227

Selecting Classification Methods for Small Samples of Next-Generation Sequencing Data
Cited by: 2
Author(s): Jiadi Zhu, Ziyang Yuan, Lianjie Shu, Wenhui Liao, Mingtao Zhao, Yan Zhou
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-76688-w

Identification of immune-related genes as prognostic factors in bladder cancer
Cited by: 12
Author(s): Jie Zhu, Han Wang, Ting Ma, Yan He, Meng‐Ru Shen, Wei Song, Jingjing Wang, Jianping Shi, Mengyao Wu, Chao Liu, Wenjie Wang, Yongzhen Huang
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.01215

Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome
Cited by: 8
Author(s): Gabriella Farries, Kenneth Bryan, C. L. McGivney, Paul A. McGettigan, K. F. Gough, John A. Browne, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 3
Published: almost 7 years ago

10.3390/medicines6030071

Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth
Cited by: 5
Author(s): Tung-Chin Chiang, Brian Koss, L. Joseph Su, Charity L. Washam, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1009650

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence
Cited by: 7
Author(s): Amanda L. Fry, Amy K. Webster, Julia Burnett, Rojin Chitrakar, L. Ryan Baugh, E. Jane Albert Hubbard
Software Mentions: 3
Published: over 5 years ago

10.1186/s12958-021-00801-5

Trophoblast derived extracellular vesicles specifically alter the transcriptome of endometrial cells and may constitute a critical component of embryo-maternal communication
Cited by: 19
Author(s): Kasun Godakumara, James Ord, Freddy Lättekivi, Keerthie Dissanayake, Janeli Viil, Nageswara Rao Boggavarapu, Omid R. Faridani, Kersti Jääger, Agne Velthut-Meikas, Ülle Jaakma, Andres Salumets, Alireza Fazeli
Software Mentions: 3
Published: over 5 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of Paeonia lactiflora Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: almost 10 years ago

10.3390/cells8090986

RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications
Cited by: 19
Author(s): Kai Sen Tan, Anand Kumar Andiappan, Bernett Lee, Yan Yan, Jing Liu, See Aik Tang, Josephine Lum, Ting He, Yew Kwang Ong, Mark Thong, Hui Fang Lim, Hyung-Jin Choi, Olaf Rötzschke, Vincent Chow, De Yun Wang
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2018.00291

Transcriptome Analyses Reveal Adult Metabolic Syndrome With Intrauterine Growth Restriction in Pig Models
Cited by: 21
Author(s): Linyuan Shen, Mailin Gan, Shunhua Zhang, Jideng Ma, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Jinyong Wang, Xuewei Li, Lianqiang Che, Li Zhu
Software Mentions: 3
Published: about 8 years ago

10.3389/fimmu.2019.00708

Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii
Cited by: 15
Author(s): Shervi Lie, E Rochet, Erik Segerdell, Yuefang Ma, Liam M. Ashander, Audra Shadforth, Timothy A. Blenkinsop, Michael Michael, Binoy Appukuttan, Beth Wilmot, Justine R. Smith
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01083

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: over 10 years ago

10.1128/mBio.03533-20

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses
Cited by: 23
Author(s): Carl J. Yeoman, Christopher J. Fields, Pascale Lepercq, Philippe Ruiz, Evelyne Forano, Bryan A. White, Pascale Mosoni
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2018.00603

Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment
Cited by: 20
Author(s): Cory H. White, Nadejda Beliakova-Bethell, Steven M. Lada, Michael S. Breen, Tara Hurst, Celsa A. Spina, Douglas D. Richman, John Frater, Gkikas Magiorkinis, Christopher H. Woelk
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00294

Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline
Cited by: 23
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Lei Yu, Yanling Wang, Philip L. De Jager, David A. Bennett
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-77105-y

Deep phenotyping of myalgic encephalomyelitis/chronic fatigue syndrome in Japanese population
Cited by: 16
Author(s): Toshimori Kitami, Sanae Fukuda, Tamotsu Kato, Kouzi Yamaguti, Yasuhito Nakatomi, Emi Yamano, Yosky Kataoka, Kei Mizuno, Yuuri Tsuboi, Yasushi Kogo, Harukazu Suzuki, Masayoshi Itoh, M. Morioka, Hideya Kawaji, Haruhiko Koseki, Jun Kikuchi, Yoshihide Hayashizaki, Hiroshi Ohno, Hirohiko Kuratsune, Yasuyoshi Watanabe
Software Mentions: 3
Published: almost 6 years ago

10.3390/cells10092376

Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli
Cited by: 4
Author(s): Kimberly Wellman, Rui Fu, Amber Baldwin, Juilee Rege, Elisabeth Murphy, William E. Rainey, Neelanjan Mukherjee
Software Mentions: 3
Published: about 5 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.01410

A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes
Cited by: 3
Author(s): Qifei Wang, Haojian Zhang, Yuqing Liang, Huichuan Jiang, Siqiao Tan, Feng Luo, Zheming Yuan, Yuan Chen
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2019.02736

Exacerbation of Chikungunya Virus Rheumatic Immunopathology by a High Fiber Diet and Butyrate
Cited by: 28
Author(s): Natalie A. Prow, Thiago Dominguez Crespo Hirata, Bing Tang, Thibaut Larcher, Pamela Mukhopadhyay, Tiago Lubiana Alves, Thuy T. Le, Joy Gardner, Yee Suan Poo, Eri Nakayama, Viviana P. Lutzky, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms9020452

Supernatants of Bifidobacterium longum and Lactobacillus plantarum Strains Exhibited Antioxidative Effects on A7R5 Cells
Cited by: 11
Author(s): Yusheng Wang, Zhifeng Fang, Qixiao Zhai, Shumao Cui, Jianxin Zhao, Hao Zhang, Wenwei Liu
Software Mentions: 3
Published: over 5 years ago

10.3390/cells10092289

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Cited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: about 5 years ago

10.1038/sdata.2014.21

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq
Cited by: 24
Author(s): Binsheng Gong, Charles Wang, Zhenqiang Su, Huasheng Hong, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Leming Shi, Scott S. Auerbach, Weida Tong, Joshua Xu
Software Mentions: 3
Published: about 12 years ago

10.3389/fpls.2015.01246

A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins “Switch-Off” in Olive (Olea europaea L.) Drupes at Different Stages of Maturation
Cited by: 30
Author(s): Domenico Iaria, Adriana Chiappetta, Innocenzo Muzzalupo
Software Mentions: 3
Published: almost 11 years ago

10.3389/fonc.2018.00374

Prognostic Genes of Breast Cancer Identified by Gene Co-expression Network Analysis
Cited by: 178
Author(s): Jianing Tang, Deguang Kong, Qiuxia Cui, Kun Wang, Dan Zhang, Yan Gong
Software Mentions: 3
Published: about 8 years ago

10.3389/fonc.2020.00780

Identification and Validation of a Prognostic lncRNA Signature for Hepatocellular Carcinoma
Cited by: 36
Author(s): Wang Li, Qifeng Chen, Tao Huang, Peihong Wu, Lujun Shen, Zijing Huang
Software Mentions: 3
Published: over 6 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms20236090

Disclosure of the Molecular Mechanism of Wheat Leaf Spot Disease Caused by Bipolaris sorokiniana through Comparative Transcriptome and Metabolomics Analysis
Cited by: 21
Author(s): Wei Ye, Taomei Liu, Weiyang Zhang, Saini Li, Muzi Zhu, Haohua Li, Yali Kong, Luoshan Xu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-25430-8

Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
Cited by: 22
Author(s): Prabin Bajgain, Blake Russell, Mohsen Mohammadi
Software Mentions: 3
Published: over 8 years ago

10.1186/s13020-020-00339-5

Identification of drug targets and potential molecular mechanisms for Wantong Jingu Tablet extract in treatment of rheumatoid arthritis: bioinformatics analysis of fibroblast-like synoviocytes
Cited by: 6
Author(s): Zhaodong Li, Fanghua Qi, Fan Li
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008934

A mega-analysis of expression quantitative trait loci in retinal tissue
Cited by: 20
Author(s): Tobias Strunz, Christina Kiel, Felix Graßmann, Rinki Ratnapriya, Madeline Kwicklis, Marcus Karlstetter, Sascha Fauser, Nicole Arend, Anand Swaroop, Thomas Langmann, Armin Wolf, Bernhard H. F. Weber
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1005652

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals
Cited by: 69
Author(s): Gung Wei Chirn, Reazur Rahman, Yuliya A. Sytnikova, Jessica Matts, Mei Zeng, Daniel Gerlach, Michael Yu, Bonnie Berger, Mayumi Naramura, Benjamin T. Kile, Nelson C. Lau
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1006405

Signaling through Lrg1, Rho1 and Pkc1 Governs Candida albicans Morphogenesis in Response to Diverse Cues
Cited by: 30
Author(s): Jinglin Lucy Xie, Nora Grahl, Trevor J.L. Sless, Michelle Leach, Sang Hu Kim, Deborah A. Hogan, Nicole Robbins, Leah E. Cowen
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2019.00916

An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure
Cited by: 3
Author(s): Guodong Yang, Aiqun Ma, Zhaohui S. Qin
Software Mentions: 3
Published: about 7 years ago

10.1186/s13148-020-00980-9

Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction
Cited by: 8
Author(s): Fieke Terstappen, Jorg J.A. Calis, Nina D. Paauw, Jaap A. Joles, Bas B. van Rijn, Michal Mokrý, Torsten Plösch, A. Titia Lely
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13148-018-0451-x

Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma
Cited by: 20
Author(s): Thomas Sanford, Maxwell V. Meng, Reema Railkar, Piyush K. Agarwal, Sima P. Porten
Software Mentions: 3
Published: over 8 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-26170-5

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Cited by: 6
Author(s): David Talavera, Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Graham D. Pavitt, Simon J. Hubbard
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-020-00916-3

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease
Cited by: 11
Author(s): Dingailu Ma, Irfete S. Fetahu, Mei Wang, Rui Fang, Jia-hui Li, Huan Liu, Tobin Gramyk, Isabella Iwanicki, Sophie Zhaotao Gu, Winnie Xu, Li Tan, Feizhen Wu, Yujiang Geno Shi
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2021.691790

Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis
Cited by: 7
Author(s): Anna‐Lisa Paul, Natasha J. Haveman, Brandon Califar, Robert J. Ferl
Software Mentions: 3
Published: about 5 years ago

10.1186/s13045-021-01155-6

Combine and conquer: manganese synergizing anti-TGF-β/PD-L1 bispecific antibody YM101 to overcome immunotherapy resistance in non-inflamed cancers
Cited by: 46
Author(s): Ming Yi, Mengke Niu, Jing Zhang, Shiyu Li, Shuangli Zhu, Yongxiang Yan, Ning Li, Pengfei Zhou, Qian Chu, Kongming Wu
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-26841-3

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)
Cited by: 19
Author(s): Jun Zhang, Peng Yu, Qinyan Zhou, Xilei Li, Shuquan Ding, Shiping Su, Xiaohua Zhang, Xiaoli Yang, Weicheng Zhou, Qing Wan, Jian‐Fang Gui
Software Mentions: 3
Published: over 8 years ago

10.7150/thno.50051

Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis
Cited by: 17
Author(s): Stephanie Taha‐Mehlitz, Gaia Bianco, Mairene Coto‐Llerena, Venkatesh Kancherla, Glenn R. Bantug, John Gallon, Caner Ercan, Federica Panebianco, Serenella Eppenberger‐Castori, M. Strauß, Sebastian M. Staubli, Martin Bolli, Ralph Peterli, Matthias S. Matter, Luigi Terracciano, Markus von Flüe, Charlotte K.Y. Ng, Savas D. Soysal, Otto Kollmar, Salvatore Piscuoglio
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-27293-5

Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
Cited by: 283
Author(s): Andrew McKenzie, Minghui Wang, Mads E. Hauberg, John F. Fullard, Alexey Kozlenkov, Alexandra B. Keenan, Yasmin L. Hurd, Stella Dracheva, Patrizia Casaccia, Panos Roussos, Bin Zhang
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26902-7

Airway brushing as a new experimental methodology to detect airway gene expression signatures in mouse lung squamous cell carcinoma
Cited by: 5
Author(s): Jing Pan, Donghai Xiong, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Yian Wang, Ming You
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2019.00350

An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis
Cited by: 10
Author(s): Kalins Banerjee, Ni Zhao, A. Srinivasan, Lingzhou Xue, Steven D. Hicks, Frank A. Middleton, Rongling Wu, Xiang Zhan
Software Mentions: 3
Published: over 7 years ago

10.1186/s13148-020-00955-w

Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs
Cited by: 4
Author(s): Iraia Muñoa-Hoyos, John Halsall, Manu Araolaza, Carl Ward, Idoia García, Itziar Urizar-Arenaza, Marta Gianzo Citores, Paloma García, Bryan M. Turner, Nerea Subirán
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.53737

Intratumor heterogeneity of breast cancer detected by epialleles shows association with hypoxic microenvironment
Cited by: 5
Author(s): Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Software Mentions: 3
Published: almost 6 years ago

10.1128/JVI.00969-19

Differentiation into an Effector Memory Phenotype Potentiates HIV-1 Latency Reversal in CD4+T Cells
Cited by: 67
Author(s): Deanna A. Kulpa, Aarthi Talla, Jessica H. Brehm, Susan Pereira Ribeiro, Sally Yuan, Anne-Gaelle Bebin-Blackwell, Michael D. Miller, Richard Barnard, Steven G. Deeks, Daria J. Hazuda, Nicolas Chomont, Rafick‐Pierre Sékaly
Software Mentions: 3
Published: almost 7 years ago

10.3390/genes12091374

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods
Cited by: 5
Author(s): Yibing Liu, Ying Yu, Ai Hong, Fengxia Zhang, Xitong Zhao, Huatao Liu, Yong Shi, Kai Xing, Chuduan Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2020.01033

Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells
Cited by: 3
Author(s): Michael Pelst, Clara Hôbart, Charlotte Wallaeys, H. de Rooster, Yannick Gansemans, Filip Van Nieuwerburgh, Bert Devriendt, Eric Cox
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 8 years ago

10.4049/jimmunol.1901072

CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential
Cited by: 30
Author(s): Gabriele De Simone, Emilia Maria Cristina Mazza, Antonino Cassotta, Alexey N. Davydov, Mirela Kuka, Veronica Zanon, Fédérica De Paoli, Eloise Scamardella, Maria Metsger, Alessandra Roberto, Karolina Pilipow, Federico Colombo, Elena Tenedini, Enrico Tagliafico, Luca Gattinoni, Domenico Mavilio, Clelia Peano, David A. Price, Satya P. Singh, Joshua M. Farber, Valentina Serra, Francesco Cucca, Francesco Ferrari, Valeria Orrù, Edoardo Fiorillo, Matteo Iannacone, Dmitriy M. Chudakov, Federica Sallusto, Enrico Lugli
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-76762-3

Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203
Cited by: 7
Author(s): Juansheng Ren, Fan Zhang, Fangyuan Gao, Lihua Zeng, Xianjun Lu, Xiuqin Zhao, Jian Lv, Xiangwen Su, Liping Liu, Mingli Dai, Jianlong Xu, Guangjun Ren
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2021.619857

Identification of Predictor Genes for Feed Efficiency in Beef Cattle by Applying Machine Learning Methods to Multi-Tissue Transcriptome Data
Cited by: 14
Author(s): Wei-Hao Chen, Pâmela Almeida Alexandre, Gabriela de Cássia Ribeiro, Heidge Fukumasu, Wei Sun, Antônio Reverter, Yutao Li
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-021-01043-3

Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations
Cited by: 14
Author(s): Jiayi Pei, Maike Schuldt, Emília Nagyová, Zhujie Gu, Said el Bouhaddani, Loukia Yiangou, Manon A. A. Jansen, Jorg J.A. Calis, Larissa M. Dorsch, Christian Snijders Blok, Noortje A.M. van den Dungen, Nico Lansu, Bastiaan J. Boukens, Igor R. Efimov, Michelle Michels, Marianne C. Verhaar, Roel de Weger, Aryan Vink, Frank G. van Steenbeek, Annette F. Baas, Richard P. Davis, Hae‐Won Uh, Diederik W.D. Kuster, Caroline Cheng, Michal Mokrý, Jolanda van der Velden, Folkert W. Asselbergs, Magdaléna Harakaľová
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1002962

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals
Cited by: 119
Author(s): Frank W. Albert, Mehmet Somel, Miguel Carneiro, Ayinuer Aximu‐Petri, Michael Halbwax, Olaf Thalmann, José Antonio Blanco‐Aguiar, I. Z. Plyusnina, Lyudmila N. Trut, Rafael Villafuerte, Nuno Ferrand, Sylvia Kaiser, Per Jensen, Svante Pääbo
Software Mentions: 3
Published: about 14 years ago

10.1186/s12967-020-02550-2

Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm
Cited by: 13
Author(s): Kerry E. Poppenberg, Vincent M. Tutino, Li Lü, Muhammad Waqas, Armond June, Lee Chaves, Kaiyu Jiang, James N. Jarvis, Yijun Sun, Kenneth V. Snyder, Elad I. Levy, Adnan H. Siddiqui, John Kolega, Hui Meng
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.27112

Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
Cited by: 2
Author(s): Piyush More, Ute Goedtel-Armbrust, Viral Shah, Marianne Mathaes, Thomas Kindler, Miguel A. Andrade‐Navarro, Leszek Wojnowski
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.25998

Bladder cancer detection by urinary extracellular vesicle mRNA analysis
Cited by: 21
Author(s): Taku Murakami, Cindy M. Yamamoto, Tomoshige Akino, Hiroshi Tanaka, Nobuyuki Fukuzawa, Hiroyoshi Suzuki, Takahiro Osawa, Takeshi Tsuji, Toshimori Seki, Hiroshi Harada
Software Mentions: 3
Published: about 8 years ago

10.3390/ijms21186817

Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress
Cited by: 12
Author(s): Shanshan Chu, Xiangqian Zhang, Kaiye Yu, Lingling Lv, Chongyuan Sun, Xiaoqian Liu, Jinyu Zhang, Yongqing Jiao, Dan Zhang
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2016.01943

Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions
Cited by: 30
Author(s): Inderjit Singh Yadav, Amandeep Sharma, Satinder Kaur, Natasha Nahar, Subhash Bhardwaj, Tilak Raj Sharma, Parveen Chhuneja
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-018-29759-y

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis
Cited by: 36
Author(s): Simon Ghaly, Nadeem O. Kaakoush, Frances Lloyd, Terence McGonigle, D. Mok, Angela Baird, Borut Klopcic, Lavinia Gordon, Shelley Gorman, Cynthia Forest, Roger Bouillon, Ian C. Lawrance, Prue H. Hart
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-018-0508-x

H3K27 acetylation and gene expression analysis reveals differences in placental chromatin activity in fetal growth restriction
Cited by: 39
Author(s): Nina D. Paauw, A. Titia Lely, Jaap A. Joles, Arie Franx, Floris Groenendaal, Michal Mokrý, Bas B. van Rijn
Software Mentions: 3
Published: over 8 years ago

10.1098/rsob.160330

Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress
Cited by: 10
Author(s): Erica Acton, Ahwon Lee, Pei Zhao, Stéphane Flibotte, Mauricio Neira, Sunita Sinha, Jennifer Chiang, Patrick Flaherty, Corey Nislow, Guri Giaever
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21113870

Time-course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air
Cited by: 5
Author(s): Habibu Aliyu, Teresa Mohr, Don A. Cowan, Pieter De Maayer, Anke Neumann
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-30640-1

PyMT-1099, a versatile murine cell model for EMT in breast cancer
Cited by: 14
Author(s): Mohit Saxena, Ravi Kiran Reddy Kalathur, Melanie Neutzner, Gerhard Christofori
Software Mentions: 3
Published: about 8 years ago

10.1098/rsob.190141

Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome
Cited by: 4
Author(s): Fangfang Dou, Beiling Wu, Sun Liang, Jiulin Chen, Te Liu, Zhihua Yu, Chuan Chen
Software Mentions: 3
Published: almost 7 years ago

10.7150/thno.54999

Progressive stretch enhances growth and maturation of 3D stem-cell-derived myocardium
Cited by: 28
Author(s): Kun Lü, Thomas Seidel, Xiaochun Cao-Ehlker, Tatjana Dorn, Aarif M.N. Batcha, Christine Schneider, María Eugenia Aubet Semmler, Tilmann Volk, Alessandra Moretti, Andreas Dendorfer, Roland Tomasi
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.57237

The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity
Cited by: 14
Author(s): Petra I. Lorenzo, Eugenia Martin Vázquez, Livia López-Noriega, Esther Fuente-Martín, José Manuel Mellado-Gil, Jaime M. Franco, Nadia Cobo-Vuilleumier, José A. Guerrero-Martínez, Silvana Y. Romero-Zerbo, Jesús A Perez-Cabello, Sabrina Rivero, Antonio Campos‐Caro, Christian Claude Lachaud, Alejandra Crespo Barreda, Manuel Aguilar‐Diosdado, Esther Fuentes, Aléjandro Martín-Montalvo, Manuel Álvarez‐Dolado, Franz Martı́n, Gemma Rojo‐Martínez, David Pozo, Francisco Javier Bermúdez‐Silva, Valentine Comaills, José Carlos Castañeda Reyes, Benoît Gauthier
Software Mentions: 3
Published: almost 6 years ago

10.1590/1678-4685-GMB-2016-0101

A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits
Cited by: 32
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka‐Molik, M. Tyra, Artur Gurgul
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0254205

Lapatinib and poziotinib overcome ABCB1-mediated paclitaxel resistance in ovarian cancer
Cited by: 5
Author(s): Joseph R. McCorkle, J Górski, Jinpeng Liu, M.B. Riggs, Anthony McDowell, Nan Lin, Chi Wang, Frederick R. Ueland
Software Mentions: 3
Published: over 5 years ago

10.1128/mSphere.00378-19

Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats
Cited by: 15
Author(s): Julia M. McGonigle, Jeremiah A. Bernau, Brenda B. Bowen, William J. Brazelton
Software Mentions: 3
Published: about 7 years ago

10.1093/bioinformatics/btw585

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Cited by: 124
Author(s): Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: about 12 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: about 9 years ago

10.1155/2021/5589101

Weighted Gene Coexpression Network Analysis to Construct Competitive Endogenous RNA Network in Chromogenic Renal Cell Carcinoma
Cited by: 1
Author(s): Yon-Bo Chen, Liang Gao, Jindong Zhang, Jiang Guo, Ping-Hong You, Liang-you Tang, Ying-Wen Liu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-71210-8

Exploring the genetic basis of fatty liver development in geese
Cited by: 3
Author(s): Yu Yang, Huiying Wang, Guangquan Li, Yi Liu, Cui Wang, Daqian He
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-32310-8

The m6A-methylase complex recruits TREX and regulates mRNA export
Cited by: 82
Author(s): Simon Lesbirel, Nicolas Viphakone, Matthew T Parker, Jacob Parker, Catherine G. Heath, Ian Sudbery, Stuart A. Wilson
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-71527-4

A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Cited by: 17
Author(s): Mukesh Kumar, Elena Papaleo
Software Mentions: 3
Published: about 6 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-32579-9

ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse
Cited by: 32
Author(s): Valentin M. Sluch, Angela Banks, Hui Li, Maura Crowley, Vanessa Davis, Chuanxi Xiang, Junzheng Yang, John Demirs, Joanna Vrouvlianis, Barrett Leehy, Shawn Hanks, Alexandra M. Hyman, Jorge Aranda, Bo Chang, Chad E. Bigelow, Dennis S. Rice
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: about 7 years ago

10.1038/s41388-020-01435-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen
Cited by: 2
Author(s): Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2018.00445

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation
Cited by: 25
Author(s): Qinglong Wu, Nagendra P. Shah
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: about 8 years ago

10.1186/s40168-021-01117-7

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Cited by: 23
Author(s): Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg, Gabriele Berg
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-33943-5

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
Cited by: 33
Author(s): Erich Hofmann, Rhett M. Rautsaw, Jason L. Strickland, Matthew L. Holding, Michael Hogan, Andrew J. Mason, Darin R. Rokyta, Christopher L. Parkinson
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.5443

Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus albaL.)
Cited by: 20
Author(s): Dujun Wang, Li Zhao, Dan Wang, Jia Liu, Xin Yu, Yuan Wei, Zhen Ouyang
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.15829

Re-expression of miR-200c suppresses proliferation, colony formation andin vivotumor growth of murine claudin-low mammary tumor cells
Cited by: 18
Author(s): Robert A. Jones, Katrina L. Watson, Anthony Bruce, Sarah Nersesian, Jenna Kitz, Roger A. Moorehead
Software Mentions: 3
Published: over 9 years ago

10.3389/fonc.2020.533616

Expression Profile of Circular RNAs in Oral Squamous Cell Carcinoma
Cited by: 19
Author(s): Yanxiong Shao, Yuhan Song, Shuying Xu, Siyi Li, Huifang Zhou
Software Mentions: 3
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568