bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-019-5530-7

Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus
Cited by: 17
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Seung Hwan Lee, Cedric Gondro
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.631472

An Inflammatory Loop Between Spleen-Derived Myeloid Cells and CD4+ T Cells Leads to Accumulation of Long-Lived Plasma Cells That Exacerbates Lupus Autoimmunity
Cited by: 4
Author(s): Eunkyeong Jang, Somi Cho, Sung-Jin Pyo, Jin Wu Nam, Jeehee Youn
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12918-019-0693-z

Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms
Cited by: 22
Author(s): Yangyang Hao, Quan‐Yang Duh, Richard T. Kloos, Joshua E. Babiarz, R. Mack Harrell, S. Thomas Traweek, Su Yeon Kim, Grazyna Fedorowicz, P. Sean Walsh, Peter M. Sadow, Jing Huang, Giulia C. Kennedy
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-2114-z

Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: about 9 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.53127

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity
Cited by: 23
Author(s): Nairita Maitra, Chi He, Heidi M. Blank, Mitsuhiro Tsuchiya, Birgit Schilling, Matt Kaeberlein, Rodolfo Aramayo, Brian K. Kennedy, Michael Polymenis
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2019.00479

Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC
Cited by: 50
Author(s): Hirotsugu Oda, David B. Beck, Hye Sun Kuehn, Natalia Sampaio Moura, Patrycja Hoffmann, Maria Ibarra, Jennifer Stoddard, Wanxia Li Tsai, Gustavo Gutierrez-Cruz, Massimo Gadina, Sergio D. Rosenzweig, Daniel L. Kastner, Luigi D. Notarangelo, Ivona Aksentijevich
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep24375

RNA-seq analysis for detecting quantitative trait-associated genes
Cited by: 33
Author(s): Minseok Seo, Kwondo Kim, Joon Yoon, Jin Young Jeong, Hyun-Jeong Lee, Seoae Cho, Heebal Kim
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-016-2403-1

RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: almost 9 years ago

10.1084/jem.20200137

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification
Cited by: 6
Author(s): Verónica Delgado-Benito, Maria Berruezo-Llacuna, Robert Altwasser, Wiebke Winkler, Devakumar Sundaravinayagam, Sandhya Balasubramanian, Marieta Caganova, Robin Graf, Ali Rahjouei, Marie-Thérèse Henke, Madlen Driesner, Lisa Keller, Alessandro Prigione, Martin Janz, Altuna Akalin, Michela Di Virgilio
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
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 4 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.102820

Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: about 8 years ago

10.1111/acel.13195

Growth differentiation factor 15 protects against the aging‐mediated systemic inflammatory response in humans and mice
Cited by: 59
Author(s): Ji Sun Moon, Ludger Goeminne, Jung Tae Kim, Jing Tian, Seok Hwan Kim, Ha Thi Nga, Sun Hyung Kang, Baeki E. Kang, Jin Seok Byun, Young‐Sun Lee, Jae‐Han Jeon, Minho Shong, Johan Auwerx, Dongryeol Ryu, Hyon‐Seung Yi
Software Mentions: 4
Published: over 4 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: almost 7 years ago

10.1186/s12864-017-3809-0

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: over 7 years ago

10.3390/genes10020089

A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment
Cited by: 12
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Neda Barghi, François Mallard, Kerstin Otte, Christian Schlötterer
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 9 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1006760

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Cited by: 6
Author(s): Vikash Pandey, Vassily Hatzimanikatis
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.6946

Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: over 8 years ago

10.1111/acel.12352

Eicosapentaenoic acid but not docosahexaenoic acid restores skeletal muscle mitochondrial oxidative capacity in old mice
Cited by: 50
Author(s): Matthew L. Johnson, Antigoni Z. Lalia, Surendra Dasari, Maximilian Pallauf, Mark Fitch, Marc K. Hellerstein, Ian R. Lanza
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: over 5 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 8 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: about 4 years ago

10.18632/aging.101751

miRNA-mRNA crosstalk in myocardial ischemia induced by calcified aortic valve stenosis
Cited by: 12
Author(s): Chenyang Duan, Zhijun Cao, Fuqin Tang, Jian Zhao, Chunshui Liang, Hong Liu, Xiao Ye, Liangming Liu, Rong Ma
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: almost 11 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0137782

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization
Cited by: 23
Author(s): Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R. Barnes, Zhigang Luo
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: about 6 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 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 7 years ago

10.1007/s00395-021-00862-y

Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis
Cited by: 29
Author(s): Gesine M. Dittrich, Natali Froese, Xue Wang, Hannah Kröger, Honghui Wang, Malgorzata Szaroszyk, Mona Malek Mohammadi, Julio Cordero, Merve Keles, Mortimer Korf‐Klingebiel, Kai C. Wollert, Robert Geffers, Manuel Mayr, Simon J. Conway, Gergana Dobreva, Johann Bauersachs, Joerg Heineke
Software Mentions: 4
Published: over 3 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.67615

Local adaptation and archaic introgression shape global diversity at human structural variant loci
Cited by: 27
Author(s): Shouqing Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N Bortvin, Michael C. Schatz, Rajiv C. McCoy
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-5160-5

Analysis and correction of compositional bias in sparse sequencing count data
Cited by: 62
Author(s): M. S. Binoj Kumar, Eric V. Slud, Kwame Okrah, Stephanie Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.65979

Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation
Cited by: 8
Author(s): Maria-Daniela Cirnaru, Sicheng Song, Kizito-Tshitoko Tshilenge, Chuhyon Corwin, Justyna Mleczko, Carlos Galicia Aguirre, Houda Benlhabib, Jaroslav Bendl, Pasha Apontes, John F. Fullard, Jordi Creus-Muncunill, Azadeh Reyahi, Ali Moussavi Nik, Peter Carlsson, Panos Roussos, Sean D. Mooney, Lisa M. Ellerby, Michelle E. Ehrlich
Software Mentions: 4
Published: about 3 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 5 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 years ago

10.1038/s42003-020-01469-0

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association
Cited by: 27
Author(s): Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann‐Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michèle Milella, David K. Chang, Peter J. Bailey, Nigel B. Jamieson, Fraser Duthie, Marie‐Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, Apgi, ARC-Net, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber Johns, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond, Nicola Waddell, Kátia Nones, Aldo Scarpa
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: over 8 years ago

10.1186/s13046-020-1541-0

FKBP9 promotes the malignant behavior of glioblastoma cells and confers resistance to endoplasmic reticulum stress inducers
Cited by: 16
Author(s): Huizhe Xu, Peng Liu, Yumei Yan, Kun Fang, Dapeng Liang, Yangcheng Liu, Xiaohong Zhang, Songyan Wu, Jin Ma, Ruoyu Wang, Tao Li, Haozhe Piao, Meng Shao
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2018.00204

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses
Cited by: 55
Author(s): Elide Formentin, Cristina Sudiro, Giorgio Perin, Samantha Riccadonna, Elisabetta Barizza, Elena Baldoni, Enrico Lavezzo, Piergiorgio Stevanato, Gian Attilio Sacchi, Paolo Fontana, Stefano Toppo, Tomas Morosinotto, Michela Zottini, Fiorella Lo Schiavo
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep18630

De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty
Cited by: 17
Author(s): Debasis Chakrabarty, Puneet Singh Chauhan, Abhishek Chauhan, Yuvraj Indoliya, U. C. Lavania, Puneet Singh Chauhan
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-016-3130-3

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera)
Cited by: 15
Author(s): Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans, Greg J. Hunt
Software Mentions: 4
Published: about 8 years ago

10.18632/oncotarget.11788

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-14-S8-S2

Evaluation of read count based RNAseq analysis methods
Cited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: almost 12 years ago

10.1038/srep17901

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: about 9 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-74128-3

Magnetic separation of peripheral nerve-resident cells underscores key molecular features of human Schwann cells and fibroblasts: an immunochemical and transcriptomics approach
Cited by: 18
Author(s): Kangqiang Peng, David W. Sant, Natalia Denise Andersen, Risset Silvera, Vladimir Camarena, Gonzalo Piñero, Regina M. Graham, Aisha Khan, Xiao Ming Xu, Gaofeng Wang, Paula V. Monje
Software Mentions: 4
Published: about 4 years ago

10.1038/srep16238

IDH mutation status is associated with a distinct hypoxia/angiogenesis transcriptome signature which is non-invasively predictable with rCBV imaging in human glioma
Cited by: 243
Author(s): Philipp Kickingereder, Felix Sahm, Alexander Radbruch, Wolfgang Wick, Sabine Heiland, Andreas von Deimling, Martin Bendszus, Benedikt Wiestler
Software Mentions: 4
Published: about 9 years ago

10.1038/s42003-019-0406-6

P38 inhibition reverses TGFβ1 and TNFα-induced contraction in a model of proliferative vitreoretinopathy
Cited by: 27
Author(s): Lauren Schiff, Nathan C. Boles, Marie Fernandes, Bar Nachmani, Ronald C. Gentile, Timothy A. Blenkinsop
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.47835

Epigenetic silencing of a multifunctional plant stress regulator
Cited by: 25
Author(s): Mark Zander, Björn C. Willige, Yiping He, Thu Anh Nguyen, Amber E. Langford, Ramlah Nehring, Elizabeth D. Howell, Robert B. McGrath, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna N. Stepanova, Robert J. Schmitz, Mathew G. Lewsey, Joanne Chory, Joseph R. Ecker
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: about 4 years ago

10.1038/srep06347

GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data
Cited by: 52
Author(s): Qing Xiong, Sayan Mukherjee, Terrence S. Furey
Software Mentions: 4
Published: over 10 years ago

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: almost 6 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes8030090

Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
Cited by: 17
Author(s): Joachim von Wulffen, Andreas Ulmer, Günter Jäger, Oliver Sawodny, Ronny Feuer
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: about 7 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 3 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-4505-4

Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential
Cited by: 28
Author(s): Sarah Dickinson, Brock A. Griffin, Michelle F Elmore, L. A. Kriese-Anderson, J. Bradford Elmore, Paul W. Dyce, Soren P. Rodning, Fernando H. Biase
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 3 years ago

10.1111/mec.15216

Sex‐specific changes in the aphid DNA methylation landscape
Cited by: 32
Author(s): Thomas C. Mathers, Sam T. Mugford, Lawrence Percival‐Alwyn, Yazhou Chen, Gemy Kaithakottil, David Swarbreck, Saskia A. Hogenhout, Cock van Oosterhout
Software Mentions: 4
Published: over 5 years ago

10.3390/ani11082241

Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
Cited by: 8
Author(s): Hana Kim, Hye‐Ran Kim, Pil‐Nam Seong, D. K. Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0207952

RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns
Cited by: 8
Author(s): Gary P. Brennan, Dimitrios Vitsios, Sophie Casey, Ann-Marie Looney, Boubou Hallberg, David C. Henshall, Geraldine B. Boylan, Deirdre M. Murray, Catherine Mooney
Software Mentions: 4
Published: about 6 years ago

10.1186/s12885-021-07911-8

Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma
Cited by: 6
Author(s): Yuanliang Zhai, Bin Zhao, Yuzhen Wang, Lina Li, Jingjin Li, Li Xu, Linhan Chang, Qian Chen, Zhijun Liao
Software Mentions: 4
Published: almost 4 years ago

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13030577

Optimizing the Procedure to Manufacture Clinical-Grade NK Cells for Adoptive Immunotherapy
Cited by: 16
Author(s): Adrián Fernández, Alfonso Navarro-Zapata, Adela Escudero, Nerea Matamala, Beatriz Ruz-Caracuel, Isabel Mirones, Alicia Pernas, Marta Cobo, Gema Casado, Diego Lanzarot, Carlos Rodríguez-Antolín, María Vela, Cristina Ferreras, Carmen Mestre, Aurora Viejo, Alejandra Leivas, Javier Martı́nez, Lucía Fernández, Antonio Pérez‐Martínez
Software Mentions: 4
Published: almost 4 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2020.00808

Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration
Cited by: 10
Author(s): Dhanach Dhirachaikulpanich, Xin Li, Louise F. Porter, Luminita Paraoan
Software Mentions: 4
Published: over 4 years ago

10.3389/fcell.2021.607121

Loss of Ciliary Gene Bbs8 Results in Physiological Defects in the Retinal Pigment Epithelium
Cited by: 7
Author(s): Sandra Schneider, Rossella De Cegli, Jayapriya Nagarajan, Viola Kretschmer, Peter Andreas Matthiessen, Daniela Intartaglia, Nathan Hotaling, Marius Ueffing, Karsten Boldt, Iván Conte, Helen May-Simera
Software Mentions: 4
Published: almost 4 years ago

10.3389/fcell.2020.00688

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Colon Adenocarcinoma Metastasis
Cited by: 30
Author(s): Zhengyan Chang, Runzhi Huang, Wanting Fu, Jiehan Li, Guo Ji, Jinglei Huang, Weijun Shi, Huabin Yin, Weifeng Wang, Tong Meng, Zongqiang Huang, Qing Wei, Huanlong Qin
Software Mentions: 4
Published: over 4 years ago

10.3389/fcell.2020.571501

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells
Cited by: 4
Author(s): Andrea Cirino, Ilaria Aurigemma, Monica Franzese, Gabriella Lania, Dario Righelli, Rosa Ferrentino, Elizabeth Illingworth, Claudia Angelini, Antonio Baldini
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.00588-21

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic <i>Escherichia coli</i> Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 4 years ago

10.1186/s12974-018-1170-0

Novel insights into neuroinflammation: bacterial lipopolysaccharide, tumor necrosis factor α, and Ureaplasma species differentially modulate atypical chemokine receptor 3 responses in human brain microvascular endothelial cells
Cited by: 15
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Mathias Buttmann, Kirsten Glaser
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2021.657917

PSMC5 Promotes Proliferation and Metastasis of Colorectal Cancer by Activating Epithelial–Mesenchymal Transition Signaling and Modulating Immune Infiltrating Cells
Cited by: 8
Author(s): Zengyou He, Xiao Yang, Ling Huang, Leqi Zhou, Sen Zhang, Jing Ping Sun, Min Zheng, Junjun Ma, Bo Feng, Lu Zang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 8 years ago

10.3389/fbioe.2020.00348

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy
Cited by: 4
Author(s): Ben Wang, Mengmeng Liu, Zhujie Ran, Xin Li, Jie Li, Yunsheng Ou
Software Mentions: 4
Published: over 4 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568