10.18632/aging.102693

Immunological analyses reveal an immune subtype of uveal melanoma with a poor prognosis
Cited by: 15
Author(s): Hui Pan, Lu Liu, Junqi Cui, Yuan Yang, Zhaoyang Wang, Xianqun Fan
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2019.00932

Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis
Cited by: 25
Author(s): Aftab Alam, Nikhat Imam, Mohd Murshad Ahmed, Safiya Tazyeen, Naaial Tamkeen, Anam Farooqui, Md. Zubbair Malik, Romana Ishrat
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphys.2021.645212

Exploration of Crucial Mediators for Carotid Atherosclerosis Pathogenesis Through Integration of Microbiome, Metabolome, and Transcriptome
Cited by: 9
Author(s): Lei Ji, Siliang Chen, Guangchao Gu, Jiawei Zhou, Wei Wang, Jinrui Ren, Jianhuang Wu, Dan Yang, Yuehong Zheng
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-236

svapls: an R package to correct for hidden factors of variability in gene expression studies
Cited by: 3
Author(s): Sutirtha Chakraborty, Somnath Datta, Susmita Datta
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pgen.1003868

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
Cited by: 71
Author(s): Nicholas J. Croucher, Andrea M. Mitchell, Katherine A. Gould, Donald Inverarity, Lars Barquist, Theresa Feltwell, María Fookes, Simon R. Harris, Janina Dordel, Susannah J. Salter, Sarah Browall, Helena Žemličková, Julian Parkhill, Staffan Normark, Birgitta Henriques‐Normark, Jason Hinds, Tim Mitchell, Stephen D. Bentley
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pgen.1009446

Critical role of the BAF chromatin remodeling complex during murine neural crest development
Cited by: 13
Author(s): Kathleen Wung Bi-Lin, Pratap Veerabrahma Seshachalam, Tran Tuoc, Anastassia Stoykova, Sujoy Ghosh, Manvendra K. Singh
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.566024

Novel Gene Signature Reveals Prognostic Model in Acute Myeloid Leukemia
Cited by: 8
Author(s): Ying Qu, Shuying Zhang, Yanzhang Qu, Heng Guo, Suling Wang, Xuemei Wang, Tianjiao Huang, Hong Zhou
Software Mentions: 3
Published: almost 6 years ago

10.1186/1868-7083-6-1

The effects of olanzapine on genome-wide DNA methylation in the hippocampus and cerebellum
Cited by: 55
Author(s): Melkaye G Melka, Benjamin I. Laufer, Patrick P. McDonald, Christina A Castellani, Nagalingam Rajakumar, Richard O’Reilly, Shiva M. Singh
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0232146

Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel
Cited by: 3
Author(s): Sònia Segura, Alejandra Gadea, Lara Nonell, Evelyn Andrades, Sílvia Sánchez, Ramón M. Pujol, Inmaculada Hernández-Muñoz, Agustí Toll
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.709666

Establishment of an Endocytosis-Related Prognostic Signature for Patients With Low-Grade Glioma
Cited by: 4
Author(s): Dawei Wang, Shiguang Liu, Guangxin Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-019-0618-0

A randomized controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57
Cited by: 32
Author(s): Rachelle E Irwin, Sara-Jayne Thursby, Miroslava Ondičová, Kristina Pentieva, Helene McNulty, Rebecca C Richmond, Aoife Caffrey, Diane J. Lees-Murdock, Marian McLaughlin, Tony Cassidy, Matthew Suderman, Caroline L Relton, Colum P. Walsh
Software Mentions: 3
Published: over 7 years ago

10.1186/s13148-020-00858-w

Histone deacetylase 9 promoter hypomethylation associated with adipocyte dysfunction is a statin-related metabolic effect
Cited by: 10
Author(s): Amna Khamis, Raphaël Boutry, Mickaël Canouil, Sunil Mathew, Stéphane Lobbens, Hutokshi Crouch, Toby Andrew, Amar Abderrahmani, Filippo Tamanini, Philippe Froguel
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-021-08356-9

Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology
Cited by: 9
Author(s): Yutao Wang, Kexin Yan, Linhui Wang, Jianbin Bi
Software Mentions: 3
Published: about 5 years ago

10.3389/fphys.2020.00653

Rehabilitative Impact of Exercise Training on Human Skeletal Muscle Transcriptional Programs in Parkinson’s Disease
Cited by: 13
Author(s): Kaleen M. Lavin, Yongchao Ge, Stuart C. Sealfon, Venugopalan D. Nair, Katarzyna Wilk, Jeremy McAdam, Samuel T. Windham, Preeti Lakshman Kumar, Merry-Lynn McDonald, Marcas M. Bamman
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0148450

Molecular and Cellular Profiling of Scalp Psoriasis Reveals Differences and Similarities Compared to Skin Psoriasis
Cited by: 31
Author(s): Juan Ruano, Mayte Suárez‐Fariñas, Avner Shemer, Margeaux Oliva, Emma Guttman‐Yassky, James G. Krueger
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1006620

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease
Cited by: 47
Author(s): Thomas M. Connor, Simon Hoer, Andrew Mallett, Daniel P. Gale, Aurora Gómez-Durán, Viktor Posse, Robin Antrobus, Pablo Moreno, Marco Sciacovelli, Christian Frezza, Jennifer Duff, Neil Sheerin, John A. Sayer, Margaret Ashcroft, Michael S. Wiesener, Gavin Hudson, Claes M. Gustafsson, Patrick F. Chinnery, Patrick H. Maxwell
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0183928

Triple DMARD treatment in early rheumatoid arthritis modulates synovial T cell activation and plasmablast/plasma cell differentiation pathways
Cited by: 27
Author(s): Alice M. Walsh, Mihir D. Wechalekar, Yanxia Guo, Xiaoli Yin, Helen Weedon, Susanna Proudman, Malcolm D. Smith, Sunil Nagpal
Software Mentions: 3
Published: about 9 years ago

10.3389/fgene.2020.503256

Construction and Analysis of a ceRNA Network in Cardiac Fibroblast During Fibrosis Based on in vivo and in vitro Data
Cited by: 7
Author(s): Qingyuan Gao, Haifeng Zhang, Zhi-Teng Chen, Yuewei Li, Shaohua Wang, Zheng Wen, Yong Xie, Jing-Ting Mai, Jingfeng Wang, Yangxin Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-017-0336-4

Interaction between prenatal pesticide exposure and a common polymorphism in the PON1 gene on DNA methylation in genes associated with cardio-metabolic disease risk—an exploratory study
Cited by: 28
Author(s): Ken Declerck, Sylvie Remy, Christine Wohlfahrt-Veje, Katharina M. Main, Guy Van Camp, Greet Schoeters, Wim Vanden Berghe, Helle Raun Andersen
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1005969

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators
Cited by: 49
Author(s): So Yeon Kwon, Valentina Grisan, Boyun Jang, John Herbert, Paul Badenhorst
Software Mentions: 3
Published: over 10 years ago

10.1186/s13148-017-0376-9

Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD
Cited by: 50
Author(s): Kristina Gervin, Hedvig Nordeng, Eivind Ystrøm, Ted Reichborn‐Kjennerud, Robert Lyle
Software Mentions: 3
Published: about 9 years ago

10.1155/2019/2841814

RNA-seq Reveals Dysregulation of Novel Melanocyte Genes upon Oxidative Stress: Implications in Vitiligo Pathogenesis
Cited by: 21
Author(s): Konduru S. Sastry, Haroon Naeem, Younes Mokrab, Aouatef Ismail Chouchane
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0010247

Evaluation of the Psoriasis Transcriptome across Different Studies by Gene Set Enrichment Analysis (GSEA)
Cited by: 153
Author(s): Mayte Suárez‐Fariñas, Michelle A. Lowes, Lisa C. Zaba, James G. Krueger
Software Mentions: 3
Published: over 16 years ago

10.1186/s13148-019-0619-z

Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors
Cited by: 16
Author(s): Songlin Li, Yuan Yuan, He Xiao, Jiajia Dai, Yunfei Ye, Qin Zhang, Zhimin Zhang, Yuhan Jiang, Jia Luo, Jing Hu, Chuan Chen, Ge Wang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0147151

Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs
Cited by: 32
Author(s): Han Rauwerda, Paul Wackers, J.F.B. Pagano, Mark de Jong, Wim A. Ensink, R.J. Dekker, Ulrike Nehrdich, Herman P. Spaink, Martijs J. Jonker, Timo M. Breit
Software Mentions: 3
Published: over 10 years ago

10.1186/s13148-019-0621-5

Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis
Cited by: 43
Author(s): Changliang Wang, Liang Chen, Yang Yang, Menglei Zhang, Garry Wong
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-11-63

Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing
Cited by: 14
Author(s): Corey Yanofsky, David R. Bickel
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: about 17 years ago

10.18632/aging.102161

Identification of 9 key genes and small molecule drugs in clear cell renal cell carcinoma
Cited by: 47
Author(s): Yongwen Luo, Dexin Shen, Liang Chen, Gang Wang, Xuefeng Li, Kaiyu Qian, Yu Xiao, Xinghuan Wang, Lingao Ju
Software Mentions: 3
Published: about 7 years ago

10.1186/s12885-021-08358-7

Identification of novel hub genes associated with gastric cancer using integrated bioinformatics analysis
Cited by: 17
Author(s): Xin Lu, Jiaqian Zhang, Sheng‐Xiao Zhang, Jun Qiao, Mengting Qiu, Xiangrong Liu, Xiaoxia Chen, Chong Gao, Huan-Hu Zhang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1006477

Gene Expression Differences in Prostate Cancers between Young and Old Men
Cited by: 26
Author(s): Yuan-Chun Ding, Huiqing Wu, Charles Warden, Linda Steele, Xueli Liu, Maarten van Iterson, Xiwei Wu, Rebecca A. Nelson, Zheng Liu, Yate-Ching Yuan, Susan L. Neuhausen
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0113660

Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus
Cited by: 9
Author(s): Ettore Mosca, Roberta Alfieri, Luciano Milanesi
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12885-021-08541-w

Molecular identification of an immunity- and Ferroptosis-related gene signature in non-small cell lung Cancer
Cited by: 10
Author(s): Taisheng Liu, Honglian Luo, Jinye Zhang, Xiaoshan Hu, Jian Zhang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.00970

Hub Genes Identification in a Murine Model of Allergic Rhinitis Based on Bioinformatics Analysis
Cited by: 5
Author(s): Chen Le, Le Shi, Yue Ma, Cheng Zheng
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0138210

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma
Cited by: 9
Author(s): Brian J. Capaldo, Devin G. Roller, Mark J. Axelrod, Alexander F. Koeppel, Emanuel F. Petricoin, Craig L. Slingluff, Michael J. Weber, Aaron J. Mackey, Daniel Gioeli, Stefan Bekiranov
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1008513

Drosophila RpS12 controls translation, growth, and cell competition through Xrp1
Cited by: 34
Author(s): Zhejun Ji, Marianthi Kiparaki, Virginia Folgado, Amit Kumar, Jorge Polo Blanco, Gerard Rimesso, Jacky Chuen, Yang Liu, Deyou Zheng, Nicholas E. Baker
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2019.01410

A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes
Cited by: 3
Author(s): Qifei Wang, Haojian Zhang, Yuqing Liang, Huichuan Jiang, Siqiao Tan, Feng Luo, Zheming Yuan, Yuan Chen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-30587-3

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Cited by: 2
Author(s): Brett W. Engelmann, Chiaowen Joyce Hsiao, John Blischak, Yannick Fourne, Zia Khan, Michael J. Ford, Yoav Gilad
Software Mentions: 3
Published: about 8 years ago

10.18632/aging.203451

Intravascular emboli relates to immunosuppressive tumor microenvironment and predicts prognosis in stage III colorectal cancer
Cited by: 1
Author(s): Xiangping Song, Di Xie, Fengbo Tan, Yuan Zhou, Yuqiang Li, Zhongyi Zhou, Qian Pei, Haiping Pei
Software Mentions: 3
Published: about 5 years ago

10.1093/ajcn/nqaa193

Effect of maternal preconceptional and pregnancy micronutrient interventions on children’s DNA methylation: Findings from the EMPHASIS study
Cited by: 17
Author(s): Ayden Saffari, Smeeta Shrestha, Prachand Issarapu, Sara Sajjadi, Modupeh Betts, Sirazul A. Sahariah, Ashutosh Singh Tomar, Philip James, Akshay Dedaniya, Dilip Kumar Yadav, Kalyanaraman Kumaran, Andrew M. Prentice, Karen A. Lillycrop, Caroline Fall, Giriraj Ratan Chandak, Matt J. Silver
Software Mentions: 3
Published: almost 6 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.1016/j.ajhg.2014.07.005

Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels
Cited by: 46
Author(s): Ronald J. Hause, Amy L. Stark, Nirav Antao, Lidija K. Gorsic, Suyoun Chung, Christopher D. Brown, Shan S. Wong, Daniel Gill, Jamie L. Myers, Lida Anita To, Kevin P. White, M. Eileen Dolan, Richard B. Jones
Software Mentions: 3
Published: about 12 years ago

10.1186/s13195-021-00810-x

Comorbidity between Alzheimer’s disease and major depression: a behavioural and transcriptomic characterization study in mice
Cited by: 15
Author(s): Ana Martín‐Sánchez, Janet Piñero, Lara Nonell, Magdalena Arnal, Elena M. Ribé, Alejo J. Nevado‐Holgado, Simon Lovestone, Ferrán Sanz, Laura I. Furlong, Olga Valverde
Software Mentions: 3
Published: over 5 years ago

10.1186/1868-7083-5-2

BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Cited by: 27
Author(s): Eddy Hj van Roon, Arnoud Boot, Ashwin A. Dihal, Robert F Ernst, Tom van Wezel, Hans Morreau, Judith M. Boer
Software Mentions: 3
Published: over 13 years ago

10.1186/s13148-015-0131-z

Epigenetic synergy between decitabine and platinum derivatives
Cited by: 32
Author(s): Taichun Qin, Jiali Si, Noël J.-M. Raynal, Xiaodan Wang, Vazganush Gharibyan, Saira Ahmed, Xin Hu, Chunlei Jin, Yue Lu, Jingmin Shu, Marcos R.H. Estécio, Jaroslav Jelı́nek, Jean–Pierre J. Issa
Software Mentions: 3
Published: about 11 years ago

10.18632/aging.202370

Identification of candidate genes encoding tumor-specific neoantigens in early- and late-stage colon adenocarcinoma
Cited by: 3
Author(s): Chong Wang, Wenhua Xue, Haohao Zhang, Yang Fu
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: over 12 years ago

10.1186/s12886-020-01365-5

Identification of lncRNA–miRNA–mRNA regulatory network associated with primary open angle glaucoma
Cited by: 24
Author(s): Minwen Zhou, Bing Lu, Wei Tan, Mingshui Fu
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms20194822

Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection
Cited by: 4
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphar.2016.00119

E2F4 Promotes Neuronal Regeneration and Functional Recovery after Spinal Cord Injury in Zebrafish
Cited by: 11
Author(s): Shota Sasagawa, Yuhei Nishimura, Yuka Hayakawa, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Reiko Kawase, Toshio Tanaka
Software Mentions: 3
Published: over 10 years ago

10.1016/j.ajhg.2021.01.013

Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation
Cited by: 27
Author(s): Victoria L. Wyckelsma, Tomas Venckūnas, Peter J. Houweling, Maja Schlittler, Volker M. Lauschke, Chrystal Tiong, H. M. Wood, Niklas Ivarsson, Henrikas Paulauskas, Nerijus Eimantas, Daniel Andersson, Klaus North, Marius Brazaitis, Håkan Westerblad
Software Mentions: 3
Published: over 5 years ago

10.1186/s12891-021-04662-2

Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method
Cited by: 3
Author(s): Arezou Lari, Hamid Gholami Pourbadie, Ali Sharifi‐Zarchi, Maryam Akhtari, Leila Nejatbakhsh Samimi, Ahmadreza Jamshidi, Mahdi Mahmoudi
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-26902-7

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

10.1186/s12891-021-03958-7

HEMGN and SLC2A1 might be potential diagnostic biomarkers of steroid-induced osteonecrosis of femoral head: study based on WGCNA and DEGs screening
Cited by: 10
Author(s): Zhixin Wu, Yinxian Wen, Guanlan Fan, Hangyuan He, Siqi Zhou, Liaobin Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2016.00137

Gene Coexpression Analyses Differentiate Networks Associated with Diverse Cancers Harboring TP53 Missense or Null Mutations
Cited by: 19
Author(s): Kathleen Klein, Karim Oualkacha, Marie-Hélène Lafond, Sahir Bhatnagar, Patricia N. Tonin, Celia M.T. Greenwood
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-29708-9

Loss of function of miR-342-3p results in MCT1 over-expression and contributes to oncogenic metabolic reprogramming in triple negative breast cancer
Cited by: 70
Author(s): Sandra Romero-Córdoba, Sergio Rodríguez‐Cuevas, Verónica Bautista-Piña, Antonio Maffuz‐Aziz, Elvira D’Ippolito, Giulia Cosentino, Sara Baroni, Marilena V. Iorio, Alfredo Hidalgo-Miranda
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30781-3

Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke
Cited by: 11
Author(s): Kimberly Glass, Derek Thibault, Feng Guo, Joseph F. Mitchel, Brandon Pham, Weiliang Qiu, Yan Li, Zhiqiang Jiang, Peter J. Castaldi, Edwin K. Silverman, Benjamin A. Raby, Jin‐Ah Park, Guo‐Cheng Yuan, Xiaobo Zhou
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-29496-2

Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains
Cited by: 47
Author(s): Carolien G.F. de Kovel, Steven Lisgo, Simon E. Fisher, Clyde Francks
Software Mentions: 3
Published: about 8 years ago

10.1186/s13148-018-0606-9

Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci
Cited by: 33
Author(s): Richa Gupta, Jenny van Dongen, Yu Fu, Abdel Abdellaoui, Rachel F. Tyndale, Vidya Velagapudi, Dorret I. Boomsma, Tellervo Korhonen, Jaakko Kaprio, Anu Loukola, Miina Ollikainen
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-020-2260-6

Transcriptomic study of pedicels from GA3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis
Cited by: 6
Author(s): Marco Meneses, Miguel García-Rojas, Claudia Muñoz-Espinoza, Tomás Carrasco-Valenzuela, Bruno G. Defilippi, Mauricio González-Agüero, Claudio Meneses, Rodrigo Infante, Patricio Hinrichsen
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-019-2169-0

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya
Cited by: 11
Author(s): Dessireé Zerpa‐Catanho, Jennifer Wai, Ming Li Wang, Liang Yu, Julie Nguyen, Ray Ming
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2180-10-159

Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation
Cited by: 32
Author(s): Marko Petek, Špela Baebler, Drago Kuzman, Ana Rotter, Zdravko Podlesek, Kristina Gruden, Maja Ravnikar, U. Urleb
Software Mentions: 3
Published: over 16 years ago

10.1155/2021/6697407

Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients
Cited by: 3
Author(s): He Huang, Shilei Xu, Aidong Chen, Fen Li, Jiezhong Wu, Xusheng Tu, Kunpeng Hu
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.698570

Comprehensive Bioinformatics Analysis Identifies POLR2I as a Key Gene in the Pathogenesis of Hypertensive Nephropathy
Cited by: 4
Author(s): Shilong You, Jiaqi Xu, Boquan Wu, Shaojun Wu, Ying Zhang, Yingxian Sun, Naijin Zhang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-23901-6

A comparative analysis of rod bipolar cell transcriptomes identifies novel genes implicated in night vision
Cited by: 11
Author(s): Sasha M Woods, Edward Mountjoy, Duncan Muir, Sarah E. Ross, Denize Atan
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2229-13-147

Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine
Cited by: 79
Author(s): Sarah Jane Cookson, Nathalie Ollat
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2180-8-109

Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains
Cited by: 40
Author(s): Sergio Carilla-Latorre, Javier Calvo‐Garrido, Gareth Bloomfield, Jason Skelton, Robert R. Kay, Alasdair Ivens, José Luis Martínez, Ricardo Escalante
Software Mentions: 3
Published: about 18 years ago

10.1038/s41598-018-31132-y

RNA-Seq Analysis of Spinal Cord Tissues from hPFN1G118V Transgenic Mouse Model of ALS at Pre-symptomatic and End-Stages of Disease
Cited by: 11
Author(s): Caroline Barham, Daniel Fil, Stephanie D. Byrum, Yasir Rahmatallah, Galina Glazko, Mahmoud Kiaei
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1004226

The Functional Consequences of Variation in Transcription Factor Binding
Cited by: 187
Author(s): Darren A. Cusanovich, Bryan J. Pavlovic, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 3
Published: over 12 years ago

10.18632/aging.203432

A comprehensive transcriptomic analysis of alternate interferon signaling pathways in peripheral blood mononuclear cells in rheumatoid arthritis
Cited by: 4
Author(s): Han Liang, Shenghao Tu, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Tingting Li, Wei Chen Lin, Huihui Li, Kun Yu, Jing Guo, Ying Huang, Kai Qin, Yu Wang, Zhe Chen
Software Mentions: 3
Published: about 5 years ago

10.1186/s42523-021-00110-7

The link between broiler flock heterogeneity and cecal microbiome composition
Cited by: 13
Author(s): Randi Lundberg, Christian Scharch, Dorthe Sandvang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-017-1143-y

Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes
Cited by: 80
Author(s): Tan Ming, Dan Cheng, Yunhai Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-23609-7

Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma
Cited by: 13
Author(s): Jessica E. Sagers, Adam S. Brown, Saša Vasilijić, Rebecca Lewis, Mehmet İlhan Şahin, Lukas D. Landegger, Roy H. Perlis, Isaac S. Kohane, D. Bradley Welling, Chirag Patel, Konstantina M. Stanković
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2180-7-78

Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition
Cited by: 48
Author(s): Herbert Wiesinger-Mayr, Klemens Vierlinger, Rudolf Pichler, Albert Kriegner, Alexander M. Hirschl, Elisabeth Presterl, Levente Bodrossy, Christa Noehammer
Software Mentions: 3
Published: over 19 years ago

10.1038/s41598-018-21937-2

The immune contexture of hepatocellular carcinoma predicts clinical outcome
Cited by: 82
Author(s): Friedrich Foerster, Moritz Hess, Aslihan Gerhold‐Ay, Jens U. Marquardt, Diana Becker, Peter R. Galle, Detlef Schuppan, Harald Binder, Ernesto Bockamp
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-018-1304-7

Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data
Cited by: 5
Author(s): Weibo Ren, Jihong Xie, Xiangyang Hou, Xiliang Li, Guo H, Ningning Hu, Lingyin Kong, Jize Zhang, Chun Chang, Zinian Wu
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms22179595

Regulation of the Golgi Apparatus by p38 and JNK Kinases during Cellular Stress Responses
Cited by: 6
Author(s): Cathrine Nordgaard, Maxim A. X. Tollenaere, Ana Martinez Del Val, Dorte B. Bekker-Jensen, Melanie Blasius, Jesper V. Olsen, Simon Bekker‐Jensen
Software Mentions: 3
Published: about 5 years ago

10.3390/ani10111944

Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Cited by: 12
Author(s): Shijun Li, Sayed Haidar Abbas Raza, Chunping Zhao, Gong Chen, Zan Liu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.00734

Analysis of Differentially Expressed Genes and Molecular Pathways in Familial Hypercholesterolemia Involved in Atherosclerosis: A Systematic and Bioinformatics Approach
Cited by: 75
Author(s): Sanjit Kumar, Dhirendra Kumar, R. Bithia, Srivarshini Sankar, R. Magesh, Mariem Sidenna, George Priya Doss C, Hatem Zayed
Software Mentions: 3
Published: about 6 years ago

10.1186/s12866-021-02110-8

HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium
Cited by: 1
Author(s): Selwan Hamed, Riham M. Shawky, Mohamed Emara, James M. Slauch, Christopher V. Rao
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2021.596535

The Widely Used Antihelmintic Drug Albendazole is a Potent Inducer of Loss of Heterozygosity
Cited by: 3
Author(s): Luiza Sheyla Evenni Porfírio Will Castro, Wietske Pieters, Mir Farshid Alemdehy, Muhammad Aslam, Olimpia Alessandra Buoninfante, Jonne A. Raaijmakers, Bas Pilzecker, Paul C.M. van den Berk, Hein te Riele, René H. Medema, Rozangela Curi Pedrosa, Heinz Jacobs
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-19871-4

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion
Cited by: 29
Author(s): Heather Armstrong, Joanna L. Gillis, I. R. Johnson, Zeyad D. Nassar, Max Moldovan, Claire Levrier, Martin C. Sadowski, Mei Yieng Chin, Emma S. Tomlinson Guns, Gerard A. Tarulli, David J. Lynn, Doug A. Brooks, Luke A. Selth, Margaret M. Centenera, Lisa M. Butler
Software Mentions: 3
Published: over 8 years ago

10.1186/s12866-020-02020-1

Berberine alters gut microbial function through modulation of bile acids
Cited by: 10
Author(s): Patricia G. Wolf, Saravanan Devendran, Heidi L. Doden, Lindsey K. Ly, Tyler Moore, Hiroyuki Takei, Hiroshi Nittono, Tsuyoshi Murai, Takao Kurosawa, George E. Chlipala, Stefan J. Green, Genta Kakiyama, Purna C. Kashyap, Vance J. McCracken, H. Rex Gaskins, Patrick M. Gillevet, Jason M. Ridlon
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22158072

LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells
Cited by: 6
Author(s): Talita de Sousa Laurentino, Roseli da Silva Soares, Antônio M. Lerário, Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-32549-1

Integrative metabolic and transcriptomic profiling of prostate cancer tissue containing reactive stroma
Cited by: 45
Author(s): Maria Andersen, Kjersti Rise, Guro F. Giskeødegård, Elin Richardsen, Helena Bertilsson, Øystein Størkersen, Tone Frost Bathen, Morten Rye, May‐Britt Tessem
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-32579-9

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

10.18632/aging.103868

Construction of a new tumor immunity-related signature to assess and classify the prognostic risk of ovarian cancer
Cited by: 6
Author(s): Jiashan Ding, Qiaoling Zhang, Shichao Chen, Huikai Huang, Linsheng He
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0181926

Whole blood microRNA expression may not be useful for screening non-small cell lung cancer
Cited by: 20
Author(s): Santosh K. Patnaik, Eric Kannisto, Reema Mallick, Anil Vachani, Sai Yendamuri
Software Mentions: 3
Published: about 9 years ago

10.1186/s12920-021-00886-2

Identification of S1PR3 gene signature involved in survival of sepsis patients
Cited by: 3
Author(s): Feng Ai, Wei Ma, Reem Faraj, Gabriel T. Kelly, Stephen M. Black, Michael B. Fallon, Ting Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-018-0451-x

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

10.1186/s12859-018-2224-0

Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy
Cited by: 41
Author(s): Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie Kim Yeager, Robert E. Akins
Software Mentions: 3
Published: about 8 years ago

10.1186/s12920-021-00892-4

Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis
Cited by: 7
Author(s): Zeyi Zhang, Jingjing Wang, Ou Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s13104-021-05788-1

miRkit: R framework analyzing miRNA PCR array data
Cited by: 0
Author(s): Maria Tsagiopoulou, Anastasis Togkousidis, Nikolaos Pechlivanis, Μαρία Μανιού, Aristea Batsali, Angelos Matheakakis, Charalampos Pontikoglou, Fotis Psomopoulos
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms20215400

Quantitative Phosphoproteomics Reveals System-Wide Phosphorylation Network Altered by Spry in Mouse Mammary Stromal Fibroblasts
Cited by: 6
Author(s): Tiezhu Shi, Lishuang Yao, Ying Han, Piliang Hao, Pengfei Lu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-33272-7

Increased levels of circulating MMP3 correlate with severe rejection in face transplantation
Cited by: 18
Author(s): Branislav Kollar, Andrey V. Shubin, Thiago J. Borges, Sotirios Tasigiorgos, Thet Su Win, Christine G. Lian, Simon T. Dillon, Xuesong Gu, Iris Wyrobnik, Gëorge F. Murphy, Bohdan Pomahac, Towia A. Libermann, Leonardo V. Riella
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12920-020-0673-6

Bioinformatics analyses on the immune status of renal transplant patients, a systemic research of renal transplantation
Cited by: 7
Author(s): Meng Mao, Weitao Zhang, Qin Tang, Baixue Yu, Tingting Li, Ruiming Rong, Tongyu Zhu, Ming Xu, Yi Shi
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-14905-9

Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster
Cited by: 13
Author(s): Diane Maitre, Oliver Selmoni, Anshu Uppal, Lucas Marques da Cunha, Laetitia G. E. Wilkins, Julien Roux, Kenyon B. Mobley, Isabelle Castro, Susanne Knörr, Marc Robinson‐Rechavi, Claus Wedekind
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.ppat.1008155

The alternative cap-binding complex is required for antiviral defense in vivo
Cited by: 18
Author(s): Anna Gebhardt, Valter Bergant, Daniel Schnepf, Markus Moser, Arno Meiler, Dieudonnée Togbe, Claire Mackowiak, Line S. Reinert, Søren R. Paludan, Bernhard Ryffel, Alexey Stukalov, Peter Staeheli, Andreas Pichlmair
Software Mentions: 3
Published: over 6 years ago

10.1111/acel.12995

Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes
Cited by: 20
Author(s): Anna Maierhofer, Julia Flunkert, Junko Oshima, George M. Martin, Martin Poot, Indrajit Nanda, Marcus Dittrich, Tobias Müller, Thomas Haaf
Software Mentions: 3
Published: about 7 years ago