bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3390/jcm8050639

The Role of MicroRNAs in the Regulation of Gastric Cancer Stem Cells: A Meta-Analysis of the Current Status
Cited by: 22
Author(s): Vitalba Ruggieri, Sabino Russi, Pietro Zoppoli, Francesco La Rocca, Tiziana Angrisano, Geppino Falco, Giovanni Calice, Simona Laurino
Software Mentions: 4
Published: over 7 years ago

10.1002/mgg3.1346

Dysregulated expression of androgen metabolism genes and genetic analysis in hypospadias
Cited by: 7
Author(s): Zhongzhong Chen, Xiaoling Lin, Yaping Wang, Hua Xie, Fang Chen
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-021-00393-9

H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum
Cited by: 10
Author(s): Jessica Connacher, Gabrielle A. Josling, Lindsey M. Orchard, Janette Reader, Manuel Llinás, Lyn‐Marié Birkholtz
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13061421

Efficacy of Targeted Radionuclide Therapy Using [131I]ICF01012 in 3D Pigmented BRAF- and NRAS-Mutant Melanoma Models and In Vivo NRAS-Mutant Melanoma
Cited by: 5
Author(s): Hussein Akil, Mercédès Quintana, J. Raymond, Tommy Billoux, Valentin Benboubker, Sophie Besse, Philippe Auzeloux, Véronique Delmas, Valérie Petit, Lionel Larue, M. D’Incan, Françoise Degoul, Jacques Rouanet
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20092177

Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity
Cited by: 9
Author(s): Fernanda C. S. Lupinacci, Hellen Kuasne, Martín Roffé, Julia Avian Vassalakis, Fernanda Ferreira da Silva, Tiago G. Santos, Victor Piana de Andrade, Paulo Sanematsu, Vilma R. Martins, Sílvia Regina Rogatto, Glaucia Noeli Maroso Hajj
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers12020470

Transcriptome Analysis Identifies ALCAM Overexpression as a Prognosis Biomarker in Laryngeal Squamous Cell Carcinoma
Cited by: 10
Author(s): Pedro Nicolau-Neto, Paulo Thiago de Souza-Santos, Mariana Severo Ramundo, Priscila Valverde, Ivanir Martins, Izabella Costa Santos, Fernando Luiz Dias, Tatiana de Almeida Simão, Luís Felipe Ribeiro Pinto
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: about 7 years ago

10.1155/2020/8604340

MCM2andNUSAP1Are Potential Biomarkers for the Diagnosis and Prognosis of Pancreatic Cancer
Cited by: 16
Author(s): Yajun Deng, Hanyun Ma, Jinyong Hao, Qiqi Xie, Rui Zhao
Software Mentions: 4
Published: over 6 years ago

10.1186/1756-8935-7-26

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2
Cited by: 23
Author(s): Heba Saadeh, Reiner Schulz
Software Mentions: 4
Published: almost 12 years ago

10.3389/fgene.2019.01119

Tumor Characterization in Breast Cancer Identifies Immune-Relevant Gene Signatures Associated With Prognosis
Cited by: 46
Author(s): Jie Li, Cun Liu, Yi Chen, Chundi Gao, Miyuan Wang, Xiaoran Ma, Wenfeng Zhang, Jing Zhuang, Yan Yao
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2021.652601

Construction and Comprehensive Prognostic Analysis of a lncRNA–miRNA–mRNA Regulatory Network and Tumor Immune Cell Infiltration in Colorectal Cancer
Cited by: 8
Author(s): Xiong Guo, Xiaolong Liang, Yujun Wang, Anqi Cheng, Chuan Qin, Han Zhang, Ziwei Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12967-020-02463-0

Identifying the pattern of immune related cells and genes in the peripheral blood of ischemic stroke
Cited by: 24
Author(s): Zijian Li, Yueran Cui, Juan Feng, Yanxia Guo
Software Mentions: 4
Published: about 6 years ago

10.3390/nu11112804

DNA Methylation Signatures of Breastfeeding in Buccal Cells Collected in Mid-Childhood
Cited by: 16
Author(s): Veronika V. Odintsova, Fiona A. Hagenbeek, Matthew Suderman, Doretta Caramaschi, Catharina E. M. van Beijsterveldt, Noah A. Kallsen, Erik A. Ehli, Gareth E. Davies, Г. Т. Сухих, Vassilios Fanos, Caroline L Relton, Meike Bartels, Dorret I. Boomsma, Jenny van Dongen
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-67743-7

Multivariate analysis reveals differentially expressed genes among distinct subtypes of diffuse astrocytic gliomas: diagnostic implications
Cited by: 10
Author(s): Nerea González‐García, Ana Belén Nieto Librero, Ana Luísa Vital, Hermínio Tão, María González-Tablas, Álvaro Otero, Purificación Galindo-Villardón, Alberto Órfão, María Dolores Tabernero
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2020.614888

Integrated Analysis of Immunity- and Ferroptosis-Related Biomarker Signatures to Improve the Prognosis Prediction of Hepatocellular Carcinoma
Cited by: 41
Author(s): Xuanlong Du, Zhang Ye-wei
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-46930-1

Distinct epigenetic profiles in children with perinatally-acquired HIV on antiretroviral therapy
Cited by: 17
Author(s): Stephanie Shiau, Renate Strehlau, Shuang Wang, Avy Violari, Catherine Do, Faeezah Patel, Afaaf Liberty, Izabela Krupska, Stephen M. Arpadi, Marc Foca, Ashraf Coovadia, Elaine J. Abrams, Benjamin Tycko, Mary Beth Terry, Louise Kuhn
Software Mentions: 4
Published: about 7 years ago

10.1172/JCI96138

REVERBa couples the circadian clock to hepatic glucocorticoid action
Cited by: 69
Author(s): Giorgio Caratti, Mudassar Iqbal, Louise Hunter, Dong Hwan Kim, Ping Wang, Ryan Vonslow, Nicola Begley, Abigail J. Tetley, Joanna Woodburn, Marie Pariollaud, Robert Maidstone, Ian J. Donaldson, Zhenguang Zhang, Louise Ince, Gareth Kitchen, Matthew Baxter, Toryn Poolman, Dion A. Daniels, David R. Stirling, Chad Brocker, Frank J. Gonzalez, A. S. I. Loudon, David A. Bechtold, Magnus Rattray, Laura Matthews, David Ray
Software Mentions: 4
Published: about 8 years ago

10.1038/s41431-021-00854-5

Regional heritability mapping identifies several novel loci (STAT4, ULK4, and KCNH5) for primary biliary cholangitis in the Japanese population
Cited by: 6
Author(s): Olivier Gervais, Kazuko Ueno, Yosuke Kawai, Yuki Hitomi, Yoshihiro Aiba, Mayumi Ueta, Minoru Nakamura, Katsushi Tokunaga, Masao Nagasaki
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms17091426

Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs
Cited by: 26
Author(s): Julia Welzenbach, Christiane Neuhoff, Hanna Heidt, Mehmet Ulaş Çınar, Christian Looft, K. Schellander, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 4
Published: about 10 years ago

10.1155/2020/2123787

Identification of lncRNA and mRNA Biomarkers in Osteoarthritic Degenerative Meniscus by Weighted Gene Coexpression Network and Competing Endogenous RNA Network Analysis
Cited by: 4
Author(s): Jun Zhao, Yu Su, Jianfei Jiao, Zhengchun Wang, Xiangchun Fang, Xuefeng He, Xiaofeng Zhang, Zhao Liu, Xilin Xu
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers13112760

Follow-Up Study Confirms the Presence of Gastric Cancer DNA Methylation Hallmarks in High-Risk Precursor Lesions
Cited by: 3
Author(s): Antonio Gómez, Miguel L Pato, Luís Bujanda, Núria Sala, Osmel Companioni, Ángel Cosme, Martina Tufano, David Hanly, Nadia García, José Miguel Sanz‐Anquela, Javier P. Gisbert, Consuelo López, José Ignacio Elizalde, Míriam Cuatrecasas, Victòria Andreu, María José Paúles, María Dolores Martín-Arranz, Luís Ortega, Elvira Poves, Jesús Barrio, María Ángeles Torres, Guillermo Muñoz, Ángel Ferrández, María José Ramírez‐Lázaro, Sergio Lario, Carlos González, Manel Esteller, María Berdasco
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.517637

The Landscape of Immune Cells Infiltrating in Prostate Cancer
Cited by: 54
Author(s): Zhicong Wu, Hua Chen, Wenyang Luo, Hanyun Zhang, Guihuan Li, Fanning Zeng, Fan Deng
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/2137319

Identification of Four Pathological Stage-Relevant Genes in Association with Progression and Prognosis in Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Dengyong Xu, Yuzi Xu, Yiming Lv, Fei Wu, Yunlong Liu, Ming Zhu, Dake Chen, Bingjun Bai
Software Mentions: 4
Published: over 6 years ago

10.1111/eva.13142

Transcriptional frontloading contributes to cross‐tolerance between stressors
Cited by: 8
Author(s): Michael T. Collins, Melody S. Clark, John I. Spicer, Manuela Truebano
Software Mentions: 4
Published: almost 6 years ago

10.3389/fendo.2019.00735

Reduced Expression of PLCXD3 Associates With Disruption of Glucose Sensing and Insulin Signaling in Pancreatic β-Cells
Cited by: 18
Author(s): Hayat Aljaibeji, Debasmita Mukhopadhyay, Abdul Khader Mohammed, Sarah Dhaiban, Mahmood Yaseen Hachim, Noha Mousaad Elemam, Nabil Sulaiman, Albert Salehi, Jalal Taneera
Software Mentions: 4
Published: almost 7 years ago

10.3389/fsurg.2021.717084

Identification of a Novel Signature Predicting Overall Survival in Head and Neck Squamous Cell Carcinoma
Cited by: 4
Author(s): Haige Zheng, Huixian Liu, Yumin Lu, Li Hengguo
Software Mentions: 4
Published: almost 5 years ago

10.3389/fonc.2020.560229

A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related Genes
Cited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: almost 6 years ago

10.3389/fendo.2021.665666

Comprehensive Analysis of the Expression and Prognostic Value of SPINT1/2 in Breast Carcinoma
Cited by: 3
Author(s): Qi Wu, Guang Yin, Jing Luo, Yingzi Zhang, Tiantian Ai, Jiao Tian, Yudi Jin, Jinwei Lei, Shengchun Liu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12967-021-02870-x

High copy number variations, particular transcription factors, and low immunity contribute to the stemness of prostate cancer cells
Cited by: 9
Author(s): Zao Dai, Ping Liu
Software Mentions: 4
Published: over 5 years ago

10.1093/function/zqaa004

The Mechanism of High-Output Cardiac Hypertrophy Arising From Potassium Channel Gain-of-Function in Cantú Syndrome
Cited by: 17
Author(s): Conor McClenaghan, Yan Huang, Scot J. Matkovich, Attila Kovács, Carla J. Weinheimer, Ronald A. Perez, Thomas J. Broekelmann, Theresa Harter, Jin-Moo Lee, Marı́a S. Remedi, Colin G. Nichols
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.56325

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms
Cited by: 11
Author(s): Alessandro Scacchetti, Tamás Schauer, Alexander Reim, Zivkos Apostolou, Aline Campos Sparr, Silke Krause, Patrick Heun, Michael Wierer, Peter B. Becker
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.118.200726

Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute theDrosophilaMushroom Bodies
Cited by: 43
Author(s): Min-Yi Shih, Fred P. Davis, Gilbert L. Henry, Josh Dubnau
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-60025-2

Identification of putative biomarkers for Infantile Hemangiomas and Propranolol treatment via data integration
Cited by: 14
Author(s): Horacio Gómez-Acevedo, Yuemeng Dai, Graham M. Strub, Carrie J. Shawber, June K. Wu, Gresham T. Richter
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0046045

MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma
Cited by: 95
Author(s): Santosh K. Patnaik, Sai Yendamuri, Eric Kannisto, John C. Kucharczuk, Sunil Singhal, Anil Vachani
Software Mentions: 4
Published: almost 14 years ago

10.3389/fgene.2020.00989

Identification of the Prognostic Value of Immune-Related Genes in Esophageal Cancer
Cited by: 16
Author(s): Xiong Guo, Yujun Wang, Han Zhang, Chuan Qin, Anqi Cheng, Jianjun Li, Xinglong Dai, Ziwei Wang
Software Mentions: 4
Published: about 6 years ago

10.1155/2020/4612158

CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0001061

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Cited by: 52
Author(s): Caitlin B. Conboy, Christiana Spyrou, Natalie Thorne, Elizabeth J. Wade, Nuno L. Barbosa‐Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
Software Mentions: 4
Published: almost 19 years ago

10.3389/fgene.2021.699385

Analysis of Immune–Stromal Score-Based Gene Signature and Molecular Subtypes in Osteosarcoma: Implications for Prognosis and Tumor Immune Microenvironment
Cited by: 3
Author(s): Dingzhao Zheng, Kai-Chun Yang, Xinjiang Chen, Yongwu Li, Yongchun Chen
Software Mentions: 4
Published: almost 5 years ago

10.1111/jcmm.16221

Expression and prognostic characteristics of m 5 C regulators in low‐grade glioma
Cited by: 11
Author(s): Xiaozhi Li, Yutong Meng
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0003916

A Snapshot of CNVs in the Pig Genome
Cited by: 110
Author(s): João Fadista, Marianne Nygaard, Lars‐Erik Holm, Bo Thomsen, Christian Berthou
Software Mentions: 4
Published: almost 18 years ago

10.1371/journal.pgen.1007473

RES complex is associated with intron definition and required for zebrafish early embryogenesis
Cited by: 23
Author(s): Juan Pablo Fernández, Miguel A. Moreno-Mateos, André Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giráldez
Software Mentions: 4
Published: about 8 years ago

10.1016/j.mcpro.2021.100065

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits
Cited by: 5
Author(s): F. Schober, Ilian Atanassov, David Moore, Javier Calvo‐Garrido, Marco F. Moedas, Anna Wedell, Christoph Freyer, Anna Wredenberg
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/6622437

CDCA3 Is a Novel Prognostic Biomarker Associated with Immune Infiltration in Hepatocellular Carcinoma
Cited by: 13
Author(s): Zhihuai Wang, Shuai Chen, Gaochao Wang, Li Sun, Xihu Qin
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2019.00235

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs
Cited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-44991-w

Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells
Cited by: 15
Author(s): Maryam Ghashghaei, Tamim Niazi, Adriana Aguilar‐Mahecha, Kathleen Klein, Celia M.T. Greenwood, Mark Basik, Thierry Muanza
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1002589

A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response
Cited by: 90
Author(s): Daniele Filiault, Julin N. Maloof
Software Mentions: 4
Published: over 14 years ago

10.1038/s41598-019-53471-0

Feature selection with the Fisher score followed by the Maximal Clique Centrality algorithm can accurately identify the hub genes of hepatocellular carcinoma
Cited by: 31
Author(s): Chengzhang Li, Jiucheng Xu
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1007891

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
Cited by: 47
Author(s): A. Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.55775

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers
Cited by: 13
Author(s): Özgür Genç, Joon Yong An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, Graeme W. Davis
Software Mentions: 4
Published: about 6 years ago

10.3390/cancers12030632

Model-Based Integration Analysis Revealed Presence of Novel Prognostic miRNA Targets and Important Cancer Driver Genes in Triple-Negative Breast Cancers
Cited by: 6
Author(s): Masood Zaka, Chris W. Sutton, Yonghong Peng, Savas Konur
Software Mentions: 4
Published: over 6 years ago

10.1186/1475-2859-8-37

Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli
Cited by: 7
Author(s): Theresa Scharl, Gerald Striedner, Florentina Pötschacher, Friedrich Leisch, Karl Bayer
Software Mentions: 4
Published: about 17 years ago

10.1371/journal.pone.0244556

Pathways of calcium regulation, electron transport, and mitochondrial protein translation are molecular signatures of susceptibility to recurrent exertional rhabdomyolysis in Thoroughbred racehorses
Cited by: 6
Author(s): Kennedy Aldrich, Deborah Velez‐Irizarry, Clara Fenger, Melissa Schott, Stephanie J. Valberg
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1004642

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cited by: 80
Author(s): Alessio Iannetti, Adeline Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam J. Moore, Holger Hummerich, Benjamin E. Gewurz, Simon Cockell, Parmjit Jat, Elaine Willmore, Neil D. Perkins
Software Mentions: 4
Published: almost 12 years ago

10.3389/fnins.2021.605654

Alteration of N6 -Methyladenosine mRNA Methylation in a Rat Model of Cerebral Ischemia–Reperfusion Injury
Cited by: 34
Author(s): Dazhuang Yi, Qunhui Wang, Yuhao Zhao, Shuhui Yu, Hong You, Jian Wang, Renjie Liu, Shi Zhong-qiang, Xuan Chen, Qi Luo
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006593

Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease
Cited by: 99
Author(s): Fiona Kerr, Oyinkan Sofola-Adesakin, Dobril Ivanov, Jemma Gatliff, Beatriz Gomez Perez‐Nievas, Hélène Bertrand, Pedro Martı́nez, Rebecca Callard, Inge Snoeren, Helena M. Cochemé, Jennifer Adcott, Mobina Khericha, Jorge Iván Castillo-Quan, Geoff Wells, Wendy Noble, Janet M. Thornton, Linda Partridge
Software Mentions: 4
Published: over 9 years ago

10.1155/2021/6648182

L Antigen Family Member 3 Serves as a Prognostic Biomarker for the Clinical Outcome and Immune Infiltration in Skin Cutaneous Melanoma
Cited by: 4
Author(s): Jingjing Song, Cong Jin, Endong Chen, Xubin Dong, Li Zhu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1002074

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex
Cited by: 53
Author(s): Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua Julie Zhu, Inmaculada M. Barrasa, Melissa M. Harrison, Robert Horvitz, Albertha J.M. Walhout, Kirsten Hagstrom
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 11 years ago

10.1186/1475-2859-10-18

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli
Cited by: 157
Author(s): Jeremy J. Minty, Ann A Lesnefsky, Fengming Lin, Yu Chen, Ted A. Zaroff, Artur Veloso, Bin Xie, Catie A McConnell, Rebecca J Ward, Donald R. Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gülari, Xiaoxia Lin
Software Mentions: 4
Published: over 15 years ago

10.7554/eLife.45310

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
Cited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-58779-w

A Group of Olfactory Receptor Alleles that Encode Full Length Proteins are Down-Regulated as Olfactory Sensory Neurons Mature
Cited by: 1
Author(s): Richard C. Krolewski, Brian M. Lin, Samuel D. Stampfer, Adam Packard, James E. Schwob
Software Mentions: 4
Published: over 6 years ago

10.1155/2020/1932948

The SLC Family Are Candidate Diagnostic and Prognostic Biomarkers in Clear Cell Renal Cell Carcinoma
Cited by: 20
Author(s): Weiting Kang, Meng Zhang, Qiang Wang, Dawei Gu, Zhilong Huang, Hanbo Wang, Yuzhu Xiang, Qinghua Xia, Zilian Cui, Xunbo Jin
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.29156

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria
Cited by: 33
Author(s): Jaclyn Quin, Ioana Bujila, Mariama Chérif, Guillaume S. Sanou, Ying Qu, Manijeh Vafa Homann, Anna Rolicka, Sodiomon B. Sirima, Mary A. O’Connell, Andreas Lennartsson, Marita Troye‐Blomberg, Issa Nébié, Ann‐Kristin Östlund Farrants
Software Mentions: 4
Published: almost 9 years ago

10.1155/2021/6680066

A Prognostic Model for Brain Glioma Patients Based on 9 Signature Glycolytic Genes
Cited by: 8
Author(s): Bing-xiang Xiao, Panxing Wu, Feng Lu, Yan Xiuyou, Chao Ding
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-020-02415-8

MicroRNA-181a as novel liquid biopsy marker of central nervous system involvement in pediatric acute lymphoblastic leukemia
Cited by: 16
Author(s): Bálint Egyed, Nóra Kutszegi, Judit C. Sági, András Gézsi, Andrea Rzepiel, Tamás Visnovitz, Péter Lőrincz, Judit Müller, Marianna Zombori, Csaba Szalai, Dániel Erdélyi, Gabòr Kovàcs, Ágnes F. Semsei
Software Mentions: 4
Published: about 6 years ago

10.1155/2019/7518374

Network Pharmacology and Bioinformatics Approach Reveals the Therapeutic Mechanism of Action of Baicalein in Hepatocellular Carcinoma
Cited by: 34
Author(s): Chongyang Ma, Tian Xu, Xiaoguang Sun, Shuang Zhang, Shu-Ling Liu, Shuning Fan, Chaofang Lei, Fei‐Fei Tang, Changming Zhai, Changxiang Li, Jian Luo, Qingguo Wang, Wei Wei, Xueqian Wang, Fang Cheng
Software Mentions: 4
Published: over 7 years ago

10.1155/2020/3416807

Identification of Hub Genes as Biomarkers Correlated with the Proliferation and Prognosis in Lung Cancer: A Weighted Gene Co-Expression Network Analysis
Cited by: 2
Author(s): Xuting Xu, Limin Xu, Huilian Huang, Jing Li, Shunli Dong, Lili Jin, Zhiyong Ma, Liqin Li
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1001034

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
Cited by: 21
Author(s): Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor R. Lemischka, Olga G. Troyanskaya
Software Mentions: 4
Published: almost 16 years ago

10.1155/2019/1093815

Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis
Cited by: 9
Author(s): Yao Ma, Xiaofei Feng, Wan-Xia Yang, Chongge You
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.ppat.1007290

Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
Cited by: 33
Author(s): Brad R. Rosenberg, Marion Depla, Catherine A. Freije, Denis Gaucher, Sabrina Mazouz, Maude Boisvert, Nathalie Bédard, Julie Bruneau, Charles M. Rice, Naglaa H. Shoukry
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1009390

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition
Cited by: 11
Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Software Mentions: 4
Published: over 5 years ago

10.3389/fnins.2020.00774

Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.16764

Norrin/Frizzled4 signalling in the preneoplastic niche blocks medulloblastoma initiation
Cited by: 20
Author(s): Erin A. Bassett, Nicholas Tokarew, Ema A Allemano, Chantal Mazerolle, Katy Morin, Alan J. Mears, Brian McNeill, Randy Ringuette, Charles Macfie Campbell, Sheila Smiley, Nenad T. Pokrajac, Adrian M. Dubuc, Vijay Ramaswamy, Paul A. Northcott, Marc Remke, Philippe P. Monnier, David Potter, Kim Paes, Laura L. Kirkpatrick, Kenneth J. Coker, Dennis S. Rice, Carolina Perez‐Iratxeta, Michael D. Taylor, Valerie A. Wallace
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: over 7 years ago

10.3390/biomedicines9070829

Biphasic Effects of Blue Light Irradiation on Human Umbilical Vein Endothelial Cells
Cited by: 4
Author(s): Kejia Kan, Yi-Fei Mu, Marielle Bouschbacher, Carsten Sticht, Natalia Kuch, Martin Sigl, Nuh N. Rahbari, Norbert Gretz, Prama Pallavi, Michael Keese
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1003188

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene
Cited by: 29
Author(s): Dario Nicetto, Matthias Hahn, Julia Jeannine Jung, Tobias D. Schneider, Tobias Straub, Róbert Dávid, Gunnar Schotta, Ralph A.W. Rupp
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-019-50873-y

Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation
Cited by: 9
Author(s): Rachel L. Clifford, J. Patel, Julia L. MacIsaac, Lisa M. McEwen, Simon R. Johnson, Dominick Shaw, Alan J. Knox, Tillie-Louise Hackett, Michæl S. Kobor
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2019.01098

Identification of Candidate Adaxial–Abaxial-Related Genes Regulating Petal Expansion During Flower Opening in Rosa chinensis “Old Blush”
Cited by: 10
Author(s): Yu Han, Yong Xue, Jiayao Yu, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: about 7 years ago

10.1155/2021/6656622

Profiles of Innate Immune Cell Infiltration and Related Core Genes in Psoriasis
Cited by: 11
Author(s): Xiaoting Gong, Wei Wang
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/6644827

Multiomics Analysis of Genetics and Epigenetics Reveals Pathogenesis and Therapeutic Targets for Atrial Fibrillation
Cited by: 2
Author(s): Li Liu, Jianjun Huang, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Chengcai Chen, Yan Wang, Xian-Nan Huang, Fengzhen He, Lingling Qin, Hehua Huang, Xue Li, Xingshou Pan
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.16222

The pioneer and differentiation factor FOXA2 is a key driver of yolk‐sac tumour formation and a new biomarker for paediatric and adult yolk‐sac tumours
Cited by: 13
Author(s): Wasco Wruck, Felix Bremmer, Mara Kotthoff, Alexander Fichtner, Margaretha A. Skowron, Stefan Schönberger, Gabriele Calaminus, Christian Vokuhl, David Pfister, Axel Heidenreich, Peter Albers, James Adjaye, Daniel Nettersheim
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.664250

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana
Cited by: 1
Author(s): Kim Hixson, Joaquim V. Marques, Jason P. Wendler, Jason McDermott, Karl K. Weitz, Therese RW Clauss, Matthew E. Monroe, Ronald J. Moore, Joseph N. Brown, Mary Lipton, Callum J. Bell, Ljiljana Paša‐Tolić, Laurence Davin, Norman Lewis
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.61798

Enhancing mitochondrial activity in neurons protects against neurodegeneration in a mouse model of multiple sclerosis
Cited by: 32
Author(s): Sina Cathérine Rosenkranz, Artem Shaposhnykov, Simone Träger, Jan Broder Engler, Maarten E. Witte, Vanessa Roth, Vanessa Vieira, Nanne J. Paauw, Simone Bauer, Celina Schwencke-Westphal, Charlotte Schubert, Lukas Can Bal, Benjamin Schattling, Ole Pleß, Jack van Horssen, Marc Freichel, Manuel A. Friese
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2015.00967

The effector repertoire of Fusarium oxysporum determines the tomato xylem proteome composition following infection
Cited by: 55
Author(s): Fleur Gawehns, Lisong Ma, Oskar Bruning, Petra M. Houterman, Sjef Boeren, Ben J. C. Cornelissen, Martijn Rep, Frank L. W. Takken
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0211854

The impact of the method of extracting metabolic signal from 1H-NMR data on the classification of samples: A case study of binning and BATMAN in lung cancer
Cited by: 7
Author(s): Trishanta Padayachee, Tatsiana Khamiakova, Evelyne Louis, Peter Adriaensens, Tomasz Burzykowski
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: about 10 years ago

10.1534/g3.118.200585

Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants
Cited by: 36
Author(s): Simon Snoeck, Nicky Wybouw, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2020.581789

Integrated Analysis of Key Genes and Pathways Involved in Fetal Growth Restriction and Their Associations With the Dysregulation of the Maternal Immune System
Cited by: 2
Author(s): Xue Wang, Hong Zhu, Lei Lei, Yang Zhang, Chao Tang, Jingyi Wu, Jing Zhou, Xirong Xiao
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.65760

Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
Cited by: 8
Author(s): Rachel A Johnston, Philippe Vullioud, Jack Thorley, Henry Kirveslahti, Leyao Shen, Sayan Mukherjee, Courtney M. Karner, Tim Clutton‐Brock, Jenny Tung
Software Mentions: 4
Published: over 5 years ago

10.1016/j.molcel.2021.06.016

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
Cited by: 31
Author(s): Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlösser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.690509

Identification and Validation of a Ferroptosis-Related Long Non-coding RNA Signature for Predicting the Outcome of Lung Adenocarcinoma
Cited by: 27
Author(s): Zhiyuan Zheng, Qian Zhang, Wei Wu, Yu Xue, Shuhan Liu, Qiaoqian Chen, Lin Dong
Software Mentions: 4
Published: about 5 years ago

10.1186/s12967-019-1851-1

Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia
Cited by: 17
Author(s): Zi‐jun Xu, Ji‐chun Ma, Jing‐Dong Zhou, Xiang‐mei Wen, Dong‐ming Yao, Wei Zhang, Runbi Ji, Dehong Wu, Li‐Juan Tang, Zhaoqun Deng, Jun Qian, Lin Jiang
Software Mentions: 4
Published: over 7 years ago

10.1186/s12934-016-0434-6

Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain
Cited by: 32
Author(s): Stéphanie Rollero, Jean-Roch Mouret, Isabelle Sanchez, Carole Camarasa, Anne Ortiz‐Julien, Jean‐Marie Sablayrolles, Sylvie Dequin
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.38014

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells
Cited by: 52
Author(s): Jacob W. Freimer, TJ Hu, Robert Blelloch
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1008076

Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures
Cited by: 57
Author(s): Dirk Schumacher, Geoffroy Andrieux, Karsten Boehnke, Marlen Keil, Alessandra Silvestri, Maxine Silvestrov, Ulrich Keilholz, Johannes Haybaeck, Gerrit Erdmann, Christoph Sachse, Markus F. Templin, Jens Hoffmann, Melanie Boerries, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0104504

Identification of Significant Features by the Global Mean Rank Test
Cited by: 17
Author(s): Martin Klammer, J. Nikolaj Dybowski, Daniel Hoffmann, Christoph Schaab
Software Mentions: 4
Published: about 12 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776