bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-016-3119-y

Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity
Cited by: 12
Author(s): Michael M. Kasumovic, Zhiliang Chen, Marc R. Wilkins
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-13-652

Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome
Cited by: 24
Author(s): Joanna L. Kelley, Courtney N. Passow, Martin Plath, Lenin Arias‐Rodríguez, Muh Ching Yee, Michael Tobler
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2164-13-396

RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
Cited by: 30
Author(s): Sanjiveeni Dhamgaye, Maria Bernard, Gaëlle Lelandais, Odile Sismeiro, Sophie Lemoine, Jean‐Yves Coppée, Stéphane Le Crom, Rajendra Prasad, Frédéric Devaux
Software Mentions: 2
Published: about 14 years ago

10.1186/s12864-021-07695-y

The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension
Cited by: 9
Author(s): Orçun Haçarız, Charles Viau, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-1492-6

Histone modifications induced by MDV infection at early cytolytic and latency phases
Cited by: 13
Author(s): Apratim Mitra, Juan Luo, Yanghua He, Yue Gu, Huanmin Zhang, Keji Zhao, Kairong Cui, Jiuzhou Song
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-020-06900-8

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken
Cited by: 28
Author(s): Donghua Li, Guirong Sun, Meng Zhang, Yanfang Cao, Chenxi Zhang, Yawei Fu, Fang Li, Guoxi Li, Ruirui Jiang, Ruili Han, Zhuanjian Li, Yanbin Wang, Yadong Tian, Xiaojun Liu, Wenting Li, Xin Kang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-016-3333-7

Latitudinal clines in gene expression and cis-regulatory element variation in Drosophila melanogaster
Cited by: 33
Author(s): Punita Juneja, Andrew Quinn, Francis M. Jiggins
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-2959-9

Sea lampreys elicit strong transcriptomic responses in the lake trout liver during parasitism
Cited by: 13
Author(s): Frederick W. Goetz, Sara E. Smith, Giles Goetz, Cheryl A. Murphy
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-15-929

Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents
Cited by: 2
Author(s): Nicholas J. Marra, J. Andrew DeWoody
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-12-514

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
Cited by: 180
Author(s): Diana V. Dugas, Marcela K. Monaco, Andrew Olson, Robert R. Klein, Sunita Kumari, Doreen Ware, Patricia E. Klein
Software Mentions: 2
Published: about 15 years ago

10.1186/s12864-015-1287-9

Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms
Cited by: 68
Author(s): Shou-Min Fang, HU Bi-li, Qi Zhou, Qiuhan Yu, Ze Zhang
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-017-3697-3

Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack
Cited by: 32
Author(s): Laura Salazar-Jaramillo, Kirsten M. Jalvingh, Ammerins de Haan, Ken Kraaijeveld, Henk P.J. Buermans, Bregje Wertheim
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-016-2400-4

Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq
Cited by: 21
Author(s): Minseok Seo, Kelsey Caetano-Anollés, Sandra L. Rodriguez-Zas, Sojeong Ka, Jin Young Jeong, Sungkwon Park, Min Ji Kim, Whan Gook Nho, Seoae Cho, Heebal Kim, Hyun Jeong Lee
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-14-846

Complex gene expression in the dragline silk producing glands of the Western black widow (Latrodectus hesperus)
Cited by: 27
Author(s): A. Kelly Lane, Cheryl Y. Hayashi, Gregg B. Whitworth, Nadia A. Ayoub
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-020-6734-6

Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam
Cited by: 31
Author(s): Hongtao Nie, Huamin Wang, Kunyin Jiang, Xiwu Yan
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07456-x

Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season
Cited by: 3
Author(s): Hsin-Hsin Shen, Caiwu Li, Ming He, Yan Huang, Jing Wang, Minglei Wang, Bisong Yue, Xiuyue Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-3902-4

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls
Cited by: 34
Author(s): Colleen MacMillan, Hannah Birke, Aaron Chuah, Elizabeth Brill, Yukiko Tsuji, John Ralph, Elizabeth S. Dennis, Danny Llewellyn, Filomena Pettolino
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-020-6584-2

Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury
Cited by: 4
Author(s): Xin Zhao, Wei Du, Manchao Zhang, Zainab Atiq, Fang Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-305

A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines
Cited by: 12
Author(s): Zhilin Qu, Geoffrey E. Hill, Scott V. Edwards, Niclas Backström
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-400

Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata
Cited by: 69
Author(s): Eshita Sharma, Axel Künstner, Bonnie A. Fraser, Gideon Zipprich, Verena A. Kottler, Stefan R. Henz, Detlef Weigel, Christine Dreyer
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-020-07074-z

Differentially expressed genes in cotyledon of ewes fed mycotoxins
Cited by: 1
Author(s): Jessica Britt, Rooksana E. Noorai, S. K. Duckett
Software Mentions: 2
Published: about 6 years ago

10.1186/s12870-019-2069-3

Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas
Cited by: 10
Author(s): Maosheng Chen, Miaomiao Zhao, Guijuan Wang, Hua He, Xue Bai, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Mingyong Tang, Jorge Martínez‐Herrera, Zeng-Fu Xu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-015-0596-0

Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants
Cited by: 59
Author(s): Jillian M. Hagel, Jeremy S. Morris, Eun-Jeong Lee, Isabel Desgagné‐Penix, Crystal D. Bross, Lihong Chang, Xue Chen, Scott C. Farrow, Ye Zhang, Jung Soh, Christoph Wilhelm Sensen, Peter J. Facchini
Software Mentions: 2
Published: about 11 years ago

10.1186/s12870-015-0598-y

A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance
Cited by: 39
Author(s): Chen Liang, Jibiao Fan, Longxing Hu, Zhengrong Hu, Yan Xie, Yingzi Zhang, Yanhong Lou, Eviatar Nevo, Jinmin Fu
Software Mentions: 2
Published: about 11 years ago

10.1186/s12870-016-0831-3

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways
Cited by: 54
Author(s): Stephen Pearce, Néstor Kippes, Andrew Chen, Juan M. Debernardi, Jorge Dubcovsky
Software Mentions: 2
Published: over 10 years ago

10.1186/s13104-018-3154-7

Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout
Cited by: 3
Author(s): Hao Ma, Guangtu Gao, Gregory M. Weber
Software Mentions: 2
Published: almost 9 years ago

10.1186/1756-0500-6-503

Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
Cited by: 18
Author(s): Emmanuel González, Simon Joly
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13104-021-05624-6

Effects of FUdR on gene expression in the C. elegans bacterial diet OP50
Cited by: 3
Author(s): Grace McIntyre, Justin Wright, Hoi Tong Wong, Regina Lamendella, Jason P. Chan
Software Mentions: 2
Published: over 5 years ago

10.1186/s12918-019-0699-6

A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data
Cited by: 15
Author(s): Shuang Sun, Yabo Chen, Liu Yang, Xuequn Shang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12918-017-0466-5

Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma
Cited by: 8
Author(s): Xinan Yang, Fangming Tang, Jisu Shin, John M. Cunningham
Software Mentions: 2
Published: about 9 years ago

10.1186/s12917-018-1583-0

Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Rodrigo A. Gallardo, Susan J. Lamont, Jack Dekkers, T. Ross Kelly, Huaijun Zhou
Software Mentions: 2
Published: about 8 years ago

10.1007/s00395-021-00846-y

AMPKα1 deletion in myofibroblasts exacerbates post-myocardial infarction fibrosis by a connexin 43 mechanism
Cited by: 19
Author(s): Cécile Dufeys, Evangelos-Panagiotis Daskalopoulos, Diego Castanares-Zapatero, Simon J. Conway, Audrey Ginion, Caroline Bouzin, Jérôme Ambroise, Bertrand Bearzatto, Jean‐Luc Gala, Stéphane Heymans, Anna-Pia Papageorgiou, Stefan Vinckier, Julien Cumps, Jean‐Luc Balligand, Maarten Vanhaverbeke, Peter Sinnaeve, Stefan Janssens, Luc Bertrand, Christophe Beauloye, Sandrine Horman
Software Mentions: 2
Published: over 5 years ago

10.1186/s13040-019-0204-1

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
Cited by: 83
Author(s): Aurélien Brionne, Amélie Juanchich, Christelle Hennequet-Antier
Software Mentions: 2
Published: about 7 years ago

10.1186/s13040-015-0050-8

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study
Cited by: 2
Author(s): Jiang Gui, Casey S. Greene, Claire Sullivan, W. Rowland Taylor, Jason H. Moore, Carol H. Kim
Software Mentions: 2
Published: over 11 years ago

10.1093/bioinformatics/btu333

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Cited by: 254
Author(s): María José Nueda, Sonia Tarazona, Ana Conesa
Software Mentions: 2
Published: over 12 years ago

10.1093/bioinformatics/btx049

FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions
Cited by: 7
Author(s): Koji Iwayama, Yuri Aisaka, Natsumaro Kutsuna, Atsushi J. Nagano
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/btaa735

FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
Cited by: 1
Author(s): Rajinder K. Gupta, Yannick Schrooders, Marcha Verheijen, Adrian Roth, Jos Kleinjans, Florian Caiment
Software Mentions: 2
Published: about 6 years ago

10.1186/s13062-018-0205-x

Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures
Cited by: 2
Author(s): Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska‐Berȩsewicz, Michał Okoniewski
Software Mentions: 2
Published: over 8 years ago

10.1242/bio.043372

Unanchored ubiquitin chains do not lead to marked alterations in gene expression inDrosophila melanogaster
Cited by: 6
Author(s): Jessica R. Blount, Danielle Meyer, Camille Akemann, Sean L. Johnson, Katherine Gurdziel, Tracie R. Baker, Sokol V. Todi
Software Mentions: 2
Published: almost 8 years ago

10.1242/bio.020891

Early molecular events during retinoic acid induced differentiation of neuromesodermal progenitors
Cited by: 38
Author(s): Thomas J. Cunningham, Alexandre R. Colas, Gregg Duester
Software Mentions: 2
Published: about 10 years ago

10.1242/bio.050260

RNA-seq analysis and compound screening highlight multiple signalling pathways regulating secondary cell death after acute CNS injury in vivo
Cited by: 2
Author(s): Chiara Herzog, David Greenald, Juan Larraz, Marcus Keatinge, Leah Herrgen
Software Mentions: 2
Published: over 6 years ago

10.1242/bio.023473

Reprogramming towards totipotency is greatly facilitated by synergistic effects of small molecules
Cited by: 27
Author(s): Kazuaki Miyamoto, Yosuke Tajima, Koki Yoshida, Mami Oikawa, Rika Azuma, George E. Allen, Tomomi Tsujikawa, Tomomasa Tsukaguchi, Charles R. Bradshaw, Jérôme Jullien, Kazuya Yamagata, Kazuya Matsumoto, Masayuki Anzai, Hiroshi Imai, J. B. Gurdon, Masao Yamada
Software Mentions: 2
Published: over 9 years ago

10.1242/bio.037937

Physiological profile of undifferentiated bovine blastocyst-derived trophoblasts
Cited by: 13
Author(s): Viju Vijayan Pillai, L. G. B. Siqueira, Moubani Das, Tiffany G. Kei, Lan N. Tu, Anthony W. Herren, Brett S. Phinney, Soon Hon Cheong, Peter J. Hansen, Vimal Selvaraj
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40659-016-0095-2

Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence
Cited by: 29
Author(s): Shiva Marthandan, Uwe Menzel, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Christoph Kaether, Stephan Diekmann
Software Mentions: 2
Published: over 10 years ago

10.3390/biology10090830

Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis
Cited by: 6
Author(s): Jing Li, Shaowen Bao, Chongnv Wang, Changwei Shao, Xuezhou Liu, Daiqiang Zhang
Software Mentions: 2
Published: about 5 years ago

10.3390/biology9120470

Inhibition of FGF and TGF-β Pathways in hESCs Identify STOX2 as a Novel SMAD2/4 Cofactor
Cited by: 2
Author(s): Peter F. Renz, Daniel Spies, Panagiota Tsikrika, Anton Wutz, Tobias A. Beyer, Constance Ciaudo
Software Mentions: 2
Published: almost 6 years ago

10.3390/biology10060500

Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer
Cited by: 9
Author(s): Jeeyong Lee, Joshua Kwon, Dayeon Kim, Misun Park, Kwang‐Seok Kim, In-Hwa Bae, Hyunkyung Kim, Joonseog Kong, Younjoo Kim, Ui-Sup Shin, EunJu Kim
Software Mentions: 2
Published: over 5 years ago

10.3390/biology10060462

Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease
Cited by: 10
Author(s): Zeen Shen, Dhiraj Kumar, Xunmeng Liu, Bingyu Yan, Ping Fang, Yuchao Gu, Manyun Li, Meiping Xie, Rui Yuan, Yongjie Feng, Xiaolong Hu, Guangwen Cao, Renyu Xue, Hui Chen, Xiaohan Liu, Chengliang Gong
Software Mentions: 2
Published: over 5 years ago

10.1155/2014/969768

Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series
Cited by: 2
Author(s): Haoqiang Zhao, Fenglin Cao, Yuanfeng Gong, Huafeng Xu, Yiping Fei, Longyue Wu, Xiangmei Ye, Dongguang Yang, Xiuhua Li, Xia Li, Jin Zhang
Software Mentions: 2
Published: almost 13 years ago

10.1155/2020/7165893

Profiling and Bioinformatics Analysis of Differentially Expressed circRNAs in Spinal Ligament Tissues of Patients with Ankylosing Spondylitis
Cited by: 16
Author(s): Jianqiang Kou, Guoming Liu, Xiangyun Liu, LI Tian-mi, Ying Wei, Yuanliang Sun, Ting Wang, Yingzhen Wang, Xiujun Zheng
Software Mentions: 2
Published: over 6 years ago

10.1155/2019/9749751

P4HB, a Novel Hypoxia Target Gene Related to Gastric Cancer Invasion and Metastasis
Cited by: 31
Author(s): Jun Zhang, Shuai Guo, Yue Wu, Zhichao Zheng, Yue Wang, Yan Zhao
Software Mentions: 2
Published: over 7 years ago

10.1155/2015/831314

Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer
Cited by: 27
Author(s): Antonio Colaprico, Claudia Cava, Gloria Bertoli, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 2
Published: almost 12 years ago

10.1155/2020/9081852

Five-mRNA Signature for the Prognosis of Breast Cancer Based on the ceRNA Network
Cited by: 12
Author(s): Wenjie Shi, Duanmin Hu, Shan‐Yang Lin, Rui Zhuo
Software Mentions: 2
Published: about 6 years ago

10.1155/2021/6676107

Plasma-Derived Exosomal hsa-miR-4488 and hsa-miR-1228-5p: Novel Biomarkers for Dermatomyositis-Associated Interstitial Lung Disease with Anti-Melanoma Differentiation-Associated Protein 5 Antibody-Positive Subset
Cited by: 10
Author(s): Danli Zhong, Caimei Wu, Dong Xu, Jingjing Bai, Qian Wang, Xiaofeng Zeng
Software Mentions: 2
Published: over 5 years ago

10.1155/2017/9084507

The Bioinformatic Analysis of the Dysregulated Genes and MicroRNAs in Entorhinal Cortex, Hippocampus, and Blood for Alzheimer’s Disease
Cited by: 20
Author(s): Xu Pang, Ying Zhao, Jinhua Wang, Qimeng Zhou, Lvjie Xu, Dennis E. Kyle, Ailin Liu, Guanhua Du
Software Mentions: 2
Published: almost 10 years ago

10.1155/2020/4078596

Construction and Analysis of Competing Endogenous RNA Networks for Breast Cancer Based on TCGA Dataset
Cited by: 5
Author(s): Xue Wang, Chundi Gao, Fubin Feng, Jing Zhuang, Lijuan Liu, Huayao Li, Cun Liu, Jibiao Wu, Zheng Xia, Xia Ding, Changgang Sun
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/2547902

miR-30a-5p Inhibits Proliferation and Migration of Lung Squamous Cell Carcinoma Cells by Targeting FOXD1
Cited by: 18
Author(s): Chunhua Chen, Junhua Tang, Shan Xu, Wenxia Zhang, Hanliang Jiang
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/4951251

Comprehensive Analysis of Differentially Expressed Circular RNAs in Patients with Senile Osteoporotic Vertebral Compression Fracture
Cited by: 3
Author(s): Xiaocong Yao, Minbo Liu, Fang Jin, Zhongxin Zhu
Software Mentions: 2
Published: about 6 years ago

10.1155/2019/9379864

Combined Analysis of the Aberrant Epigenetic Alteration of Pancreatic Ductal Adenocarcinoma
Cited by: 11
Author(s): Rui Xu, Qian Xu, Guangwen Huang, Xinhai Yin, Jianguo Zhu, Yunsong Peng, Jukun Song
Software Mentions: 2
Published: almost 7 years ago

10.1155/2020/5304578

RNA Sequencing for Gene Expression Profiles in Peripheral Blood Mononuclear Cells with Ankylosing Spondylitis RNA
Cited by: 3
Author(s): Dan Huang, Jian Liu, Yunxiang Cao, Lei Wan, Hui Jiang, Yue Sun, Jianting Wen
Software Mentions: 2
Published: over 6 years ago

10.1155/2016/3290260

iTRAQ-Based Proteomics Identification of Serum Biomarkers of Two Chronic Hepatitis B Subtypes Diagnosed by Traditional Chinese Medicine
Cited by: 12
Author(s): Jiankun Yang, Liyu Yang, Baixue Li, Weilong Zhou, Sen Zhong, Zhenhua Zhuang, Bin Yang, Maoshan Chen, Feng Qian
Software Mentions: 2
Published: almost 11 years ago

10.1155/2020/7434737

Nomogram Based on microRNA Signature Contributes to Improve Survival Prediction of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Enfa Zhao, Xiaofang Bai
Software Mentions: 2
Published: over 6 years ago

10.1155/2019/8732023

Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging
Cited by: 8
Author(s): Xiaoyu Xi, Qin Zou, Yingying Wei, Chen Yan, Xue Wang, Daojun Lv, Peilin Li, Anxiang Wen, Li Zhu, Guoqing Tang, Jideng Ma, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Software Mentions: 2
Published: about 7 years ago

10.1155/2018/8518563

Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions
Cited by: 7
Author(s): Li Guo, Liang Zheng, Yang Zhao, Qianyun Wang
Software Mentions: 2
Published: almost 9 years ago

10.1155/2020/1836542

Development and Validation of a Seven-Gene Signature for Predicting the Prognosis of Lung Adenocarcinoma
Cited by: 5
Author(s): Yingqing Zhang, Xiaoping Zhang, Xiaodong Liu, Ming Zhang, Xixi Gao, Jialiang Li, Yufen Xu, Zhixian Fang, Wenyu Chen
Software Mentions: 2
Published: about 6 years ago

10.1155/2015/731938

Similarities in Gene Expression Profiles duringIn VitroAging of Primary Human Embryonic Lung and Foreskin Fibroblasts
Cited by: 33
Author(s): Shiva Marthandan, Stefan Priebe, Mario Baumgart, Marco Groth, Alessandro Cellerino, Reinhard Guthke, Peter Hemmerich, Stephan Diekmann
Software Mentions: 2
Published: almost 12 years ago

10.1155/2020/2094320

The Identification and Verification of Key Long Noncoding RNAs in Ischemic Stroke
Cited by: 7
Author(s): Houxi Xu, Jinzhi Zhang, Yuzhu Ma, Jialin Gu, Xianwen Jing, Lu Shen, Chen Xia, Wenguo Yang, Yaoyao Bian, Shunjun Fu
Software Mentions: 2
Published: almost 6 years ago

10.1155/2017/8032910

RNA Sequencing Analysis Reveals Interactions between Breast Cancer or Melanoma Cells and the Tissue Microenvironment during Brain Metastasis
Cited by: 25
Author(s): Ryo Sato, T. Nakano, Mari Hosonaga, Oltea Sampetrean, Ritsuko Harigai, Takashi Sasaki, Ikuko Koya, Hideyuki Okano, Jun Kudoh, Hideyuki Saya, Yoshimi Arima
Software Mentions: 2
Published: almost 10 years ago

10.1155/2020/4951692

Comprehensive Analysis of lncRNA-Mediated ceRNA Crosstalk and Identification of Prognostic Biomarkers in Wilms’ Tumor
Cited by: 15
Author(s): Hong Zheng, Bai-Hui Li, Chang Liu, Jia Li, Fengting Liu
Software Mentions: 2
Published: over 6 years ago

10.1155/2020/5976127

Novel miRNA Predicts Survival and Prognosis of Cholangiocarcinoma Based on RNA-seq Data and In Vitro Experiments
Cited by: 11
Author(s): Yuan Yao, Dechao Jiao, Zaoqu Liu, Jianjian Chen, Xueliang Zhou, Zhaonan Li, Jing Li, Xinwei Han
Software Mentions: 2
Published: almost 6 years ago

10.1155/2021/1978434

RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker
Cited by: 1
Author(s): Deyong Ge, Yuhan Shao, Mengjie Wang, Huihui Tao, Min Mu, Xinrong Tao
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/9568976

MicroRNA-148b Inhibits the Malignant Biological Behavior of Melanoma by Reducing Sirtuin 7 Expression Levels
Cited by: 2
Author(s): Rui Sun, Meiliang Guo, Xiaojing Fan, Qinqin Meng, Ding Yuan, Xin–Rong Yang, Kexiang Yan, Hui Deng
Software Mentions: 2
Published: almost 6 years ago

10.1155/2017/8682057

Identifying the Genes Responsible for Iron-Limited Condition in Riemerella anatipestifer CH-1 through RNA-Seq-Based Analysis
Cited by: 11
Author(s): Mafeng Liu, Huang Mi, Dekang Zhu, Mingshu Wang, Renyong Jia, Shun Chen, Kunfeng Sun, Qiao Yang, Ying Wu, Francis Biville, Anchun Cheng
Software Mentions: 2
Published: almost 10 years ago

10.1155/2016/1035945

Modeling Gene Regulation in Liver Hepatocellular Carcinoma with Random Forests
Cited by: 7
Author(s): Hilal Kazan
Software Mentions: 2
Published: almost 11 years ago

10.1155/2018/1235097

Upregulation of Immune Process-Associated Genes in RAW264.7 Macrophage Cells in Response toBurkholderia pseudomalleiInfection
Cited by: 3
Author(s): Dongmei Peng, Feng Pang, Ruiyong Cao, Shu Zhu, Xinggang Yang, Xin Nie, Zhenxing Zhang, Baobao Li, Haifeng Huang, Yaying Li, Guohua Li, Lijun Du, Yafei Wang
Software Mentions: 2
Published: over 8 years ago

10.1155/2019/6581576

Identification of Potential Biomarkers in Glioblastoma through Bioinformatic Analysis and Evaluating Their Prognostic Value
Cited by: 41
Author(s): Yabo Zhou, Yang Li, Xiaoxi Zhang, Rui Chen, Xiuqiong Chen, Wilkin Tang, Mengxian Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/biomedicines9091136

Small Extracellular Vesicle Enrichment of a Retrotransposon-Derived Double-Stranded RNA: A Means to Avoid Autoinflammation?
Cited by: 2
Author(s): Marilou H. Barrios, Alexandra L. Garnham, Andrew D Foers, Lesley Cheng, Seth L. Masters, Ken C Pang
Software Mentions: 2
Published: about 5 years ago

10.3390/biomedicines9081021

Utilizing Patient-Derived Epithelial Ovarian Cancer Tumor Organoids to Predict Carboplatin Resistance
Cited by: 11
Author(s): J Górski, Zhuwei Zhang, Joseph R. McCorkle, Jodi M. DeJohn, Chi Wang, Rachel W. Miller, Holly H. Gallion, Charles S. Dietrich, Frederick R. Ueland
Software Mentions: 2
Published: about 5 years ago

10.3390/biom10050698

Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations
Cited by: 3
Author(s): Carolina Cortes-Urrea, Fernando Bueno-Gutiérrez, Melissa Solarte, Miguel Guevara-Burbano, Fabián Tobar-Tosse, Patricia E. Vélez-Varela, Juan Carlos Leiva, Guillermo Barreto, Jaime Velasco-Medina, Pedro Moreno, Javier De Las Rivas
Software Mentions: 2
Published: over 6 years ago

10.3390/biom11081223

Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae
Cited by: 1
Author(s): Randi Yeager, G. Guy Bushkin, Emily Singer, Rui Fu, Benjamin Cooperman, Michael A. McMurray
Software Mentions: 2
Published: about 5 years ago

10.3390/biom10070974

Transcriptome Based Profiling of the Immune Cell Gene Signature in Rat Experimental Colitis and Human IBD Tissue Samples
Cited by: 3
Author(s): Éva Boros, Bence Prontvai, Zoltán Kellermayer, Péter Balogh, Silvia Patrícia, Áron Vincze, Csaba Varga, Zoltán Maróti, Balázs Balint, István Nagy
Software Mentions: 2
Published: over 6 years ago

10.3390/biom11020274

Low Expression of miR-375 and miR-190b Differentiates Grade 3 Patients with Endometrial Cancer
Cited by: 2
Author(s): Miłosz Pietrus, Michał Seweryn, Przemysław Kapusta, Paweł Wołkow, Kazimierz Pityński, Gracjan Wątor
Software Mentions: 2
Published: over 5 years ago

10.1042/BSR20200487

The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1
Cited by: 21
Author(s): Juntong Wang, Jingshun Gu, Aiwu You, Jun Li, Yuyan Zhang, Guomin Rao, Xuehua Ge, Kun Zhang, Jianfeng Li, Xiaohui Lu, Qianchao Wang, Tzu Chen Lin, Ling Cheng, Meiying Zhu, Xiaotang Wu, Dongchun Wang
Software Mentions: 2
Published: over 6 years ago

10.1042/BSR20190996

Integrated analysis of a competing endogenous RNA network in renal cell carcinoma using bioinformatics tools
Cited by: 14
Author(s): Weidong Jiang, Zhihua Ye
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20191554

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models
Cited by: 14
Author(s): Yan Yao, Tingting Zhang, Ling‐Yu Qi, Ruijuan Liu, Gongxi Liu, Wei Hua Jia, Qi Song, Changgang Sun
Software Mentions: 2
Published: almost 7 years ago

10.1042/BSR20181514

Differential expression and bioinformatics analysis of circRNA in osteosarcoma
Cited by: 36
Author(s): Yizhe Xi, Mitra Fowdur, Yun Liu, Hao Wu, Miao He, Jinmin Zhao
Software Mentions: 2
Published: over 7 years ago

10.1042/BSR20203200

Identifying breast cancer subtypes associated modules and biomarkers by integrated bioinformatics analysis
Cited by: 8
Author(s): Yanwei Wang, Li Yu, Baohong Liu, Ailin Song
Software Mentions: 2
Published: almost 6 years ago

10.1042/BSR20191251

The lncRNAs RP1-261G23.7, RP11-69E11.4 and SATB2-AS1 are a novel clinical signature for predicting recurrent osteosarcoma
Cited by: 9
Author(s): Ying Tang, Jia-Yi Dong, Cheng Yuan, Peng Li, Guo Qing-shan
Software Mentions: 2
Published: almost 7 years ago

10.1042/BSR20202203

Developing a risk scoring system based on immune-related lncRNAs for patients with gastric cancer
Cited by: 5
Author(s): Yuzhi Wang, Yu Zhong, Yi Zhang, Chengwen Li
Software Mentions: 2
Published: almost 6 years ago

10.1042/BSR20210021

Construction and analysis of the abnormal lncRNA–miRNA–mRNA network in hypoxic pulmonary hypertension
Cited by: 5
Author(s): Jie Liu, Yuhua Deng, Zeqin Fan, Shuanglan Xu, Wei Li, Xiaoxian Huang, Xin Xing, Jiao Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-016-0471-8

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq
Cited by: 31
Author(s): Yuan Fu, Michele Poli, Gaurav Sablok, Bo Wang, Yanchun Liang, Nicola La Porta, Violeta Velikova, Francesco Loreto, Mingai Li, Claudio Varotto
Software Mentions: 2
Published: over 10 years ago

10.1186/s13068-015-0227-x

Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses
Cited by: 131
Author(s): Noppon Lertwattanasakul, Tomoyuki Kosaka, Akira Hosoyama, Yutaka Suzuki, Nadchanok Rodrussamee, Minenosuke Matsutani, Masayuki Murata, Naoko Fujimoto, Suprayogi Suprayogi, Keiko Tsuchikane, Savitree Limtong, Nobuyuki Fujita, Mamoru Yamada
Software Mentions: 2
Published: over 11 years ago

10.1186/s13068-020-01825-6

Evolutionary engineering of E. coli MG1655 for tolerance against isoprenol
Cited by: 12
Author(s): Heiko Babel, Jens O. Krömer
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13068-018-1331-5

Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment
Cited by: 9
Author(s): Pengfei Cheng, Chengxu Zhou, Yan Wu, Zhihui Xu, Jilin Xu, Dongqing Zhou, Yinghui Zhang, Haizhen Wu, Xuezhi Zhang, Tianzhong Liu, Ming Tang, Yang Qiyong, Xiaojun Yan, Jianhua Fan
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13068-015-0357-1

A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa
Cited by: 87
Author(s): Jyoti Dalal, Harry O. Lopez, Naresh Vasani, Zhaohui Hu, Jennifer Swift, Roopa Yalamanchili, Mia Dvora, Xiuli Lin, De‐Yu Xie, Rongda Qu, Heike Sederoff
Software Mentions: 2
Published: about 11 years ago

10.1186/s13068-019-1393-z

Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways
Cited by: 59
Author(s): Wenjuan Mo, Mengzhu Wang, Rongrong Zhan, Yao Yu, Yungang He, Hong Lü
Software Mentions: 2
Published: over 7 years ago

10.1038/s41408-019-0173-0

Identification of lenalidomide resistance pathways in myeloma and targeted resensitization using cereblon replacement, inhibition of STAT3 or targeting of IRF4
Cited by: 57
Author(s): Yuan Xiao Zhu, Chao Shi, Laura A. Bruins, Xuewei Wang, Daniel L. Riggs, Brooke Porter, Jonathan M. Ahmann, Cecília Bonolo de Campos, Esteban Braggio, P. Leif Bergsagel, A. Keith Stewart
Software Mentions: 2
Published: over 7 years ago

10.1038/s41408-020-00404-0

Gene expression profiling-based risk prediction and profiles of immune infiltration in diffuse large B-cell lymphoma
Cited by: 22
Author(s): Selin Merdan, Kritika Subramanian, Turgay Ayer, Johan Van Weyenbergh, Andrés Chang, Jean L. Koff, Christopher R. Flowers
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41413-020-00120-2

MEF2C regulates osteoclastogenesis and pathologic bone resorption via c-FOS
Cited by: 25
Author(s): Takayuki Fujii, Koichi Murata, Se-Hwan Mun, Seyeon Bae, Ye Ji Lee, Tannia Pannellini, Ki‐Woon Kang, David J. Oliver, Kyung‐Hyun Park‐Min, Lionel B. Ivashkiv
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40529-017-0185-7

Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata
Cited by: 20
Author(s): Zhiai Xu, Yuanyuan Li, Hong Ling, Sisi Liu, Mengmeng Liu, Juan Chen, Shun‐Xing Guo
Software Mentions: 2
Published: over 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568