bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-52903-1

Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness
Cited by: 46
Author(s): S. Luján Marco, Ettore Caroppo, Craig S. Niederberger, Joan‐Carles Arce, Ingrid Sadler‐Riggleman, Daniel Beck, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.1093/biostatistics/kxu038

Joint analysis of differential gene expression in multiple studies using correlation motifs
Cited by: 29
Author(s): Yingying Wei, Toyoaki Tenzen, Hongkai Ji
Software Mentions: 4
Published: about 12 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-50271-4

Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle
Cited by: 9
Author(s): Thazin Nwe Aung, Saeed Nourmohammadi, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Hao Shen, Andrea J. Yool, Tara L. Pukala, Hongling Du, R. Daniel Kortschak, Wenxin Wei, David L. Adelson
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-92725-8

Lung adenocarcinoma and lung squamous cell carcinoma cancer classification, biomarker identification, and gene expression analysis using overlapping feature selection methods
Cited by: 43
Author(s): Joe W. Chen, Joseph M. Dhahbi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-49829-z

Adenovirus infection is associated with altered gut microbial communities in a non-human primate
Cited by: 27
Author(s): . Wasimuddin, Victor M. Corman, Jörg U. Ganzhorn, Jacques Rakotondranary, Yedidya R. Ratovonamana, Christian Drosten, Simone Sommer
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20123101

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Cited by: 29
Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller‐Roeber, Tsanko Gechev
Software Mentions: 4
Published: over 7 years ago

10.1186/s13068-018-1060-9

Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses
Cited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 11 years ago

10.1038/s41598-019-47363-6

Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma
Cited by: 20
Author(s): Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Luíza Ferreira de Araújo, Isabela Ichihara de Barros, Kamila Chagas Peronni, Greice Andreotti de Molfetta, Carlos Alberto Oliveira de Biagi, Enilza Maria Espreáfico, Josane F. Sousa, Wilson A. Silva
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-87547-7

Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm
Cited by: 5
Author(s): Christina Markouli, Edouard Couvreu De Deckersberg, Dominika Dziedzicka, Marius Regin, Silvie Franck, Alexander Keller, Alexander Gheldof, Mieke Geens, Karen Sermon, Claudia Spits
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-020-02757-x

Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains
Cited by: 5
Author(s): Bárbara Simões Santos Leal, Marcelo Mendes Brandão, Clarisse Palma‐Silva, Fábio Pinheiro
Software Mentions: 4
Published: almost 6 years ago

10.3389/fnbeh.2017.00069

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
Cited by: 26
Author(s): Tove Porseryd, Kristina Volkova, Nasim Reyhanian Caspillo, Thomas Källman, Patrik Dinnétz, Inger Porsch Hällström
Software Mentions: 4
Published: over 9 years ago

10.3389/fonc.2020.609601

Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma
Cited by: 4
Author(s): Dingdong He, Xiaokang Zhang, Xinyu Zhu, Narayani Maharjan, Yingchao Wang, Ping Luo, Chunzi Liang, Jiancheng Tu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-87805-8

Integrin αvβ5 heterodimer is a specific marker of human pancreatic beta cells
Cited by: 4
Author(s): Jacqueline V. Schiesser, Thomas Loudovaris, Helen E. Thomas, Andrew G. Elefanty
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2021.650828

Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma
Cited by: 6
Author(s): Teng Deng, Yizhen Gong, Xiwen Liao, Xiangkun Wang, Xin Zhou, Guangzhi Zhu, Ligen Mo
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-88743-1

Identification of candidate PAX2-regulated genes implicated in human kidney development
Cited by: 6
Author(s): Yuta Yamamura, Kengo Furuichi, Yuji Murakawa, Shigeki Hirabayashi, Masahito Yoshihara, Keisuke Sako, Shinji Kitajima, Tadashi Toyama, Yasunori Iwata, Norihiko Sakai, Kazuyoshi Hosomichi, Philip M. Murphy, Atsushi Tajima, Keisuke Okita, Kenji Osafune, Shuichi Kaneko, Takashi Wada
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 9 years ago

10.3390/biomedicines9060646

Identification of MicroRNAs as Viable Aggressiveness Biomarkers for Prostate Cancer
Cited by: 11
Author(s): Luis Javier Martínez-González, Victor Sánchez-Conde, Jose María González-Cabezuelo, Alba Antúnez-Rodríguez, Eduardo Andrés-León, Inmaculada Robles-Fernández, José A. Lorente, Fernando Vázquez-Alonso, María Jesús Álvarez-Cubero
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-017-17996-6

Identification of long non-coding RNAs in the immature and mature rat anterior pituitary
Cited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-021-90540-9

Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)
Cited by: 3
Author(s): Candace J. Grimes, Lene H. Petersen, Anja Schulze
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-021-92385-8

Genome-enabled discovery of evolutionary divergence in brains and behavior
Cited by: 4
Author(s): Chinar Patil, J. B. Sylvester, Kawther Abdilleh, Michael Norsworthy, Karen Pottin, Milan Malinsky, Ryan F. Bloomquist, Zachary V. Johnson, Patrick T. McGrath, J. Todd Streelman
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-50573-7

Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness
Cited by: 14
Author(s): Gautami Das, Doreen Becker, Vidhya Jagannathan, Orly Goldstein, Evelyn Santana, Kendall Carlin, Raghavi Sudharsan, Tosso Leeb, Yuji Nishizawa, Mineo Kondo, Gustavo D. Aguirre, Keiko Miyadera
Software Mentions: 4
Published: about 7 years ago

10.1186/s12870-021-02997-5

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: over 5 years ago

10.1155/2017/7183516

PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage Tissue
Cited by: 6
Author(s): Patricia Klinger, Söeren Lukassen, Fulvia Ferrazzi, Arif B. Ekici, Thilo Hotfiel, B. Swoboda, Thomas Aigner, Kolja Gelse
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-01943-6

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1
Cited by: 16
Author(s): Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel, Dirk Eick
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-01032-8

Transcriptomic analysis reveals a previously unknown role for CD8+ T-cells in rVSV-EBOV mediated protection
Cited by: 28
Author(s): Andrea Menicucci, Suhas Sureshchandra, Andrea Marzi, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 4
Published: over 9 years ago

10.1038/srep45125

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Cited by: 42
Author(s): Matthew D. MacManes, Suzanne H. Austin, Andrew S. Lang, April M. Booth, Victoria S. Farrar, Rebecca M. Calisi
Software Mentions: 4
Published: over 9 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-93616-8

MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene
Cited by: 7
Author(s): Wipasiri Soonthornchai, Pattarin Tangtanatakul, Kornvalee Meesilpavikkai, Virgil A. S. H. Dalm, Patipark Kueanjinda, Jongkonnee Wongpiyabovorn
Software Mentions: 4
Published: over 5 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 5 years ago

10.1155/2015/621690

The Impact of Normalization Methods on RNA-Seq Data Analysis
Cited by: 81
Author(s): Joanna Zyprych-Walczak, Alicja Szabelska, Luiza Handschuh, Katarzyna Górczak, Kamila Klamecka, Marek Figlerowicz, Idzi Siatkowski
Software Mentions: 4
Published: almost 12 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: almost 6 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: over 5 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: about 6 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 9 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: over 9 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: almost 6 years ago

10.1155/2019/2601271

Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma
Cited by: 10
Author(s): Dongkai Zhou, Bo Gao, Qifan Yang, Yahui Kong, Weilin Wang
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.11820

Clinical and prognostic relevance of CXCL12 expression in acute myeloid leukemia
Cited by: 2
Author(s): Shi-sen Wang, Zi‐jun Xu, Yue Jin, Ji‐chun Ma, Pei‐hui Xia, Xiang‐mei Wen, Zhen-wei Mao, Lin Jiang, Jun Qian
Software Mentions: 4
Published: over 5 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 6 years ago

10.1155/2014/986048

Advanced Heat Map and Clustering Analysis Using Heatmap3
Cited by: 187
Author(s): Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Software Mentions: 4
Published: almost 13 years ago

10.1111/jcmm.15271

Systematic prediction of key genes for ovarian cancer by co‐expression network analysis
Cited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: over 7 years ago

10.1038/s41396-020-0729-9

Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Cited by: 35
Author(s): Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, M. Maurhofer
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.7107

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.14779

Four transcription profile–based models identify novel prognostic signatures in oesophageal cancer
Cited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-94927-6

Neurotranscriptomic changes associated with chick-directed parental care in adult non-reproductive Japanese quail
Cited by: 6
Author(s): Patrícia C. Lopes, Robert de Bruijn
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.57260

Construction of a ceRNA Network and a Prognostic lncRNA Signature associated with Vascular Invasion in Hepatocellular Carcinoma based on Weighted Gene Co-Expression Network Analysis
Cited by: 10
Author(s): Haisu Tao, Li Jiang, Junjie Liu, Tong Yuan, Erlei Zhang, Huifang Liang, Zhiyong Huang
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.4600

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Cited by: 146
Author(s): Li Chen, James Reeve, Lujun Zhang, Shengbing Huang, Xuefeng Wang, Jun Chen
Software Mentions: 4
Published: over 8 years ago

10.7150/jca.49557

Construction of novel mRNA-miRNA-lncRNA regulatory networks associated with prognosis of ovarian cancer
Cited by: 18
Author(s): Lingling Gao, Xiao Li, Xin Nie, Qin Guo, Qing Liu, Yue Qi, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-96149-2

Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes
Cited by: 2
Author(s): V. D. Yakushina, В. В. Стрельников, А. С. Танас, А. В. Лавров
Software Mentions: 4
Published: about 5 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: almost 7 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-97306-3

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Cited by: 3
Author(s): Ludmila Mudri Hul, A. M. G. Ibelli, Igor Ricardo Savoldi, Débora Ester Petry Marcelino, Lana Teixeira Fernandes, J. O. Peixoto, Maurício Egídio Cantão, R. H. Higa, P. F. Giachetto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 4
Published: about 5 years ago

10.1186/2049-1891-3-8

Current status and future perspectives for sequencing livestock genomes
Cited by: 40
Author(s): Yongsheng Bai, Maureen A. Sartor, James D. Cavalcoli
Software Mentions: 4
Published: over 14 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: about 6 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-98907-8

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination
Cited by: 12
Author(s): Heqin Li, Haiwang Yue, Jiping Xie, Junzhou Bu, Li Li, Xueying Xin, Yanming Zhao, Haiyan Zhang, Li Yang, Jianhua Wang, Xuwen Jiang
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.11020

Differential gene expression in a tripartite interaction:Drosophila,Spiroplasmaand parasitic wasps
Cited by: 4
Author(s): Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cécilia Tamborindeguy, Esperanza Martínez‐Romero
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 7 years ago

10.1155/2020/6784138

Identification of FOS as a Candidate Risk Gene for Liver Cancer by Integrated Bioinformatic Analysis
Cited by: 10
Author(s): Jinwu Hu, Guangyu Ding, Pei-Yao Fu, Wei‐Guo Tang, Qiqing Sun, Xiao‐Dong Zhu, Ying‐Hao Shen, Ji Zhou, Jia Fan, Hui–Chuan Sun, Cheng Huang
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.7705

The clinical significance of collagen family gene expression in esophageal squamous cell carcinoma
Cited by: 30
Author(s): Jieling Li, Wang Xiao, Kai Zheng, Ying Liu, Junjun Li, Shaoqi Wang, Kaisheng Liu, Xianrang Song, Nan Li, Shouqi Xie, Shaoxiang Wang
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.11995

The modulatory properties of Astragalus membranaceus treatment on endometrial cancer: an integrated pharmacological method
Cited by: 4
Author(s): Qianqian Zhang, Xianghua Huang
Software Mentions: 4
Published: about 5 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.614497

Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer
Cited by: 6
Author(s): Qiang Liu, Yihang Qi, Xiangyi Kong, Xiangyu Wang, Wenxiang Zhang, Jie Zhai, Yazhe Yang, Yi Fang, Jing Wang
Software Mentions: 4
Published: over 5 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: almost 7 years ago

10.1097/MIB.0000000000001131

Azathioprine with Allopurinol
Cited by: 7
Author(s): Sally A. Coulthard, Phil Berry, Sarah McGarrity, Simon D. McLaughlin, Azhar Ansari, Christopher P.F. Redfern
Software Mentions: 4
Published: over 9 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: over 5 years ago

10.1155/2015/862130

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library
Cited by: 29
Author(s): Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian D. Lehmann, Jennifer A. Pietenpol, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: almost 12 years ago

10.3390/ijms21124470

Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13287-019-1218-9

Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics
Cited by: 25
Author(s): Ramil Hakim, Ruxandra Covacu, Vasilios Zachariadis, Arvid Frostell, Sreenivasa Raghavan Sankavaram, Lou Brundin, Mikael Svensson
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms21082800

Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00603

Genome-Wide Identification of Circular RNAs Revealed the Dominant Intergenic Region Circularization Model in Apostichopus japonicus
Cited by: 15
Author(s): Xuelin Zhao, Xuemei Duan, Jianping Fu, Yina Shao, Weiwei Zhang, Ming Guo, Chenghua Li
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2019.00210

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle
Cited by: 23
Author(s): Wellison J. S. Diniz, Gianluca Mazzoni, Luiz Lehmann Coutinho, Priyanka Banerjee, Ludwig Geistlinger, Francesca Bertolini, Juliana Afonso, P. S. N. Oliveira, P. C. Tizioto, Haja N. Kadarmideen, Luciana Correia de Almeida Regitano
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.658736

A Prognostic Model Based on the Immune-Related lncRNAs in Colorectal Cancer
Cited by: 16
Author(s): Fen Qin, Houxi Xu, Guoli Wei, Ji Yi, Jialin Yu, Canhong Hu, Chunyi Yuan, Yuzhu Ma, Jun Qian, Lingchang Li, Jiege Huo
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-018-1575-1

VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies
Cited by: 92
Author(s): Mengjie Chen, Xiang Zhou
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-018-1503-4

A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Cited by: 61
Author(s): François Mallard, Viola Nolte, Raymond Tobler, Martin Kapun, Christian Schlötterer
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2021.636419

Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer
Cited by: 6
Author(s): Lili Zhang, Wei Zhang, Hexin Li, Xiaokun Tang, Siyuan Xu, Meng Wu, Li Wan, Fei Su, Yaqun Zhang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2019.01018

Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer
Cited by: 12
Author(s): Yuanli Zuo, Liang Yu, Jiting Zhang, You-Zeng Hao, Menglong Li, Zhining Wen, Yun Zhao
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 9 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568