bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.595757

Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis
Cited by: 4
Author(s): Jinlong Wu, Qisheng Lin, Shu Li, Xinghua Shao, Xuying Zhu, Minfang Zhang, Wenyan Zhou, Zhaohui Ni
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12885-021-08462-8

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for lung adenocarcinoma
Cited by: 12
Author(s): Lei Gao, Ling Zhang
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12894-021-00795-7

Comprehensive analysis of tumour mutational burden and its clinical significance in prostate cancer
Cited by: 14
Author(s): Limin Wang, Shucheng Pan, Binbin Zhu, Zhenliang Yu, Wei Wang
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-019-1912-z

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel
Cited by: 14
Author(s): Michael Frochaux, Maroun Bou Sleiman, Vincent Gardeux, Riccardo Dainese, Brian Hollis, Maria Litovchenko, Virginie Braman, Tommaso Andreani, Dani Osman, Bart Deplancke
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmolb.2021.656204

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse
Cited by: 12
Author(s): Núria Mach, Marco Moroldo, Andrea Rau, Jérôme Lecardonnel, Laurence Le Moyec, Céline Robert, Éric Barrey
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2020.00895

Identification of Hub Genes Associated With Hepatocellular Carcinoma Using Robust Rank Aggregation Combined With Weighted Gene Co-expression Network Analysis
Cited by: 10
Author(s): Hongjiang Song, Na Ding, Shang Li, Jianlong Liao, Aimin Xie, Youtao Yu, Chunlong Zhang, Caifang Ni
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-019-55453-8

MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Cited by: 2
Author(s): Andigoni Malousi, Sofia Kouidou, Maria Tsagiopoulou, Nikos Papakonstantinou, Emmanouil Bouras, Elisavet Georgiou, Georgios Tzimagiorgis, Kostas Stamatopoulos
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0183933

Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing
Cited by: 24
Author(s): Y-h. Taguchi
Software Mentions: 7
Published: over 7 years ago

10.1186/s12885-020-06777-6

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Cited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
Published: over 4 years ago

10.3389/fmolb.2021.656145

Identification and Exploration of Novel Macrophage M2-Related Biomarkers and Potential Therapeutic Agents in Endometriosis
Cited by: 10
Author(s): Zhongqi Cui, Ramesh Singh Bhandari, Lei Qin, Mingzhi Lu, Lei Zhang, Mengmei Zhang, Fenyong Sun, Lijin Feng, Shasha Zhao
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2020.00311

Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 57
Author(s): Yi Liao, Yulei Wang, Mengqing Cheng, Chengliang Huang, Xiaoxuan Fan
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0175657

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
Cited by: 28
Author(s): Wolfgang Kaisers, Petra Boukamp, Hans Jürgen Stark, Holger Schwender, Julia Tigges, Jean Krutmann, Heiner Schaal
Software Mentions: 6
Published: over 7 years ago

10.1038/leu.2015.172

Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia
Cited by: 15
Author(s): Jonathan Sive, Silvia Basilico, Rebecca Hannah, Sarah Kinston, Fernando J. Calero-Nieto, Berthold Göttgens
Software Mentions: 6
Published: over 9 years ago

10.3389/fcell.2021.561086

Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes
Cited by: 6
Author(s): Elisabeth Findeiss, Sigrid C. Schwarz, Valentin Evsyukov, Thomas W. Rösler, Matthias Höllerhage, Tasnim Chakroun, Niko-Petteri Nykänen, Yimin Shen, Wolfgang Wurst, Michael Köhl, Jörg Tost, Günter U. Höglinger
Software Mentions: 6
Published: over 3 years ago

10.1186/s13073-016-0282-3

Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis
Cited by: 45
Author(s): Deepa Rajamani, Manoj Bhasin
Software Mentions: 6
Published: over 8 years ago

10.3390/life11020115

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giz107

A field guide for the compositional analysis of any-omics data
Cited by: 162
Author(s): Thomas P. Quinn, Ionas Erb, Gregory B. Gloor, Cédric Notredame, Mark F. Richardson, Tamsyn M. Crowley
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2021.618277

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Cited by: 7
Author(s): Mateusz Garbulowski, Karolina Smolińska, Klev Diamanti, Gang Pan, Khurram Maqbool, Lars Feuk, Jan Komorowski
Software Mentions: 6
Published: almost 4 years ago

10.1186/s41065-020-00169-3

Identification of differentially expressed genes, signaling pathways and immune infiltration in rheumatoid arthritis by integrated bioinformatics analysis
Cited by: 8
Author(s): Yanzhi Ge, Li Zhou, Zuxiang Chen, Yingying Mao, Ting Li, Peijian Tong
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giaa117

Correcting for experiment-specific variability in expression compendia can remove underlying signals
Cited by: 16
Author(s): Alexandra Lee, YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Software Mentions: 6
Published: about 4 years ago

10.1111/mec.15743

The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: almost 4 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 6 years ago

10.3389/fmolb.2021.619110

Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer
Cited by: 7
Author(s): Na Sun, Peng Gao, Yanling Li, Zexuan Yan, Zaihui Peng, Yi Zhang, Fei Han, Xiaowei Qi
Software Mentions: 6
Published: almost 4 years ago

10.3389/fgene.2016.00183

Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
Cited by: 78
Author(s): Benjamin Mayne, Tina Bianco‐Miotto, Sam Buckberry, James Breen, Vicki L. Clifton, Cheryl Shoubridge, Claire T. Roberts
Software Mentions: 6
Published: about 8 years ago

10.1093/gigascience/giaa116

The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways
Cited by: 8
Author(s): Paria Pooyan, Razieh Karamzadeh, Mehdi Mirzaei, Anna Meyfour, Ardeshir Amirkhan, Yunqi Wu, Vivek Gupta, Hossein Baharvand, Mohammad Javan, Ghasem Hosseini Salekdeh
Software Mentions: 6
Published: about 4 years ago

10.3389/fcell.2021.723676

Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition
Cited by: 5
Author(s): Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Software Mentions: 6
Published: over 3 years ago

10.3389/fcvm.2021.696321

Bioinformatics and Immune Infiltration Analyses Reveal the Key Pathway and Immune Cells in the Pathogenesis of Hypertrophic Cardiomyopathy
Cited by: 11
Author(s): Xuzhe Zhang, Si Zhang, Tingting Tang, Xiang Cheng
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1850-9

A benchmark of batch-effect correction methods for single-cell RNA sequencing data
Cited by: 506
Author(s): Hoa Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13046-019-1372-z

Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer
Cited by: 61
Author(s): Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz de Lucas, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos, Georgios D. Ayiomamitis
Software Mentions: 6
Published: over 5 years ago

10.1186/s12876-021-01734-4

Identification of the angiogenesis related genes for predicting prognosis of patients with gastric cancer
Cited by: 9
Author(s): Shu Zheng, Zizhen Zhang, Ning Ding, Jiawei Sun, Yaowang Lin, Jingyu Chen, Jing Zhong, Liming Shao, Zhenghua Lin, Min Xue
Software Mentions: 6
Published: over 3 years ago

10.3389/fnagi.2021.602781

Exploring the Key Genes and Identification of Potential Diagnosis Biomarkers in Alzheimer’s Disease Using Bioinformatics Analysis
Cited by: 20
Author(s): Wuhan Yu, Weihua Yu, Yan Yang, Yang Lü
Software Mentions: 6
Published: over 3 years ago

10.3389/fphar.2020.593247

Identification of FPR3 as a Unique Biomarker for Targeted Therapy in the Immune Microenvironment of Breast Cancer
Cited by: 7
Author(s): Jian Qi, Yu Liu, Jiliang Hu, Li Lu, Zhen Dou, Haiming Dai, Hongzhi Wang, Wulin Yang
Software Mentions: 6
Published: almost 4 years ago

10.1084/jem.20192275

NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation
Cited by: 44
Author(s): Carla Castro, Michelle Rosenzwajg, Raphaël Carapito, Mohammad Shahrooei, Martina Konantz, Amjad Khan, Zhichao Miao, Miriam Groß, Thibaud Tranchant, Mirjana Radosavljevic, Nicodème Paul, Tristan Stemmelen, Fabien Pitoiset, Aurélie Hirschler, Benoît Nespola, Anne Molitor, Véronique Rolli, Angélique Pichot, Laura Faletti, Bruno Rinaldi, Sylvie Friant, Mark Mednikov, Hatice Karaüzüm, M. Javad Aman, Christine Carapito, Claudia Lengerke, Vahid Ziaee, Wafaa Eyaid, Stephan Ehl, Fayhan Alroqi, Nima Parvaneh, Seiamak Bahram
Software Mentions: 6
Published: over 4 years ago

10.1002/cam4.4115

Development and validation of a PBRM1‐associated immune prognostic model for clear cell renal cell carcinoma
Cited by: 5
Author(s): Jiayi Chen, Chunlin Yao, Nan Qiao, Yangyang Ge, Jianhua Li, Yun Lin, Shanglong Yao
Software Mentions: 6
Published: about 3 years ago

10.1186/s12967-021-03078-9

Low CCL19 expression is associated with adverse clinical outcomes for follicular lymphoma patients treated with chemoimmunotherapy
Cited by: 1
Author(s): Yu Zhou, Shasha Wang, Yunxia Tao, Haizhu Chen, Yan Qin, Xiaohong He, Shengyu Zhou, Peng Liu, Jianliang Yang, Sheng Yang, Lin Gui, Ning Lou, Zhishang Zhang, Jiarui Yao, Xiaohong Han, Yuankai Shi
Software Mentions: 6
Published: about 3 years ago

10.1186/s12967-018-1751-9

Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Cited by: 37
Author(s): Raúl Fernández Pérez, Pablo Santamarina, Juan Ramón Tejedor, Rocío G. Urdinguio, Julio Álvarez, P. Redon, Agustín F. Fernández, Mario F. Fraga, Empar Lurbe
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13073-015-0237-0

Identification of global regulators of T-helper cell lineage specification
Cited by: 36
Author(s): Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 6
Published: about 9 years ago

10.3389/fonc.2020.578933

Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes
Cited by: 7
Author(s): Yuanyuan Zhang, Shuai Ma, Moran Wang, Wei Shi, Yu Hu
Software Mentions: 6
Published: about 4 years ago

10.1111/febs.15578

Genome‐wide postnatal changes in immunity following fetal inflammatory response
Cited by: 0
Author(s): DC Costa, Núria Bonet, Amanda Solé, José Manuel González de Aledo-Castillo, Eduard Sabidó, Ferrán Casals, Carlota Rovira, Alfons Nadal, J. L. Marı́n, Teresa Cobo, Robert Castelo
Software Mentions: 6
Published: about 4 years ago

10.3389/fonc.2021.630706

The Immune-Related Gene HCST as a Novel Biomarker for the Diagnosis and Prognosis of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yongying Zhou, Xiao Wang, Weibing Zhang, Huiyong Liu, Daoquan Liu, Ping Chen, Dongmei Xu, Jianmin Liu, Yan Li, Guang Zeng, Mingzhou Li, Zhonghua Wu, Yingao Zhang, Xinghuan Wang, Michael E. DiSanto, Xinhua Zhang
Software Mentions: 6
Published: over 3 years ago

10.12688/f1000research.25713.2

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach
Cited by: 1
Author(s): Priyansh Srivastava, Mehak Talwar, Aishwarya Yadav, Alakto Choudhary, Sabyasachi Mohanty, Samuel Bharti, Priyanka Narad, Abhishek Sengupta
Software Mentions: 6
Published: almost 4 years ago

10.3389/fnins.2019.00392

Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease
Cited by: 19
Author(s): Lavida R. K. Brooks, George I. Mias
Software Mentions: 6
Published: over 5 years ago

10.12688/f1000research.28608.2

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2019.01509

Screening the Cancer Genome Atlas Database for Genes of Prognostic Value in Acute Myeloid Leukemia
Cited by: 16
Author(s): Jie Ni, Yang Wu, Feng Qi, Xiao Li, Shengwen Yu, Siwen Liu, Jifeng Feng, Yuxiao Zheng
Software Mentions: 6
Published: almost 5 years ago

10.7717/peerj.9975

Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
Cited by: 11
Author(s): Xiuming Zhai, Zhaowei Yang, Xiji Liu, Z P Dong, Dandan Zhou
Software Mentions: 6
Published: about 4 years ago

10.3390/jpm9020021

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-021-08083-1

Gene expression and immune infiltration in melanoma patients with different mutation burden
Cited by: 8
Author(s): Liwei Wang, Chuanxi Fu, Rui Li, Lei Shi, Guosheng Zhao, Yan Zhang
Software Mentions: 6
Published: over 3 years ago

10.1186/s13148-018-0463-6

Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia
Cited by: 60
Author(s): Katherine Leavey, Samantha L. Wilson, Shannon Bainbridge, Wendy P. Robinson, Brian Cox
Software Mentions: 6
Published: almost 7 years ago

10.3389/fonc.2021.634841

miRNA-Based Signature Associated With Tumor Mutational Burden in Colon Adenocarcinoma
Cited by: 7
Author(s): Weijie Xue, Yixiu Wang, Yuwei Xie, Caifeng Yang, Zhiqi Gong, Chunyang Guan, Chuanliang Wei, Chunhui Zhu, Zhaojian Niu
Software Mentions: 6
Published: over 3 years ago

10.18632/oncotarget.22636

3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimicin-vivoconditions
Cited by: 11
Author(s): Gabriele Gamerith, Johannes Michael Rainer, Julia Huber, Hubert Hackl, Zlatko Trajanoski, Stefan Koeck, Edith Lorenz, Johann Kern, Reinhard Kofler, Jens M. Kelm, Heinz Zwierzina, Arno Amann
Software Mentions: 6
Published: about 7 years ago

10.1186/s13148-019-0755-5

Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood
Cited by: 79
Author(s): Roy Lardenoije, Janou A. Y. Roubroeks, Ehsan Pishva, Markus Leber, Holger Wagner, Artemis Iatrou, Adam R. Smith, Rebecca G. Smith, Lars Eijssen, Luca Kleineidam, Amit Kawalia, Per Hoffmann, Tobias Luck, Steffi G. Riedel‐Heller, Frank Jessen, Wolfgang Maier, Michael Wagner, René Hurlemann, Günter Kenis, Muhammad Ali, Antonio del Sol, Diego Mastroeni, Elaine Delvaux, Paul D. Coleman, Jonathan Mill, Bart P. F. Rutten, Katie Lunnon, Alfredo Ramı́rez, Daniël L.A. van den Hove
Software Mentions: 6
Published: about 5 years ago

10.1186/s13148-019-0787-x

Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer’s disease-related dysregulation
Cited by: 12
Author(s): Larissa Haertle, Tobias Müller, Roy Lardenoije, Anna Maierhofer, Marcus Dittrich, Renzo J. M. Riemens, Samantha Stora, M Roche, Markus Leber, Steffi G. Riedel‐Heller, Michael Wagner, Martin Scherer, Aimé Ravel, Clotilde Mircher, Cécile Cieuta‐Walti, Sophie Durand, Daniel L. A. van de Hove, Per Hoffmann, Alfredo Ramı́rez, Thomas Haaf, Nady El Hajj, André Mégarbané
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.697198

A Pyroptosis-Related Gene Signature for Predicting Survival in Glioblastoma
Cited by: 40
Author(s): Xinyu Li, Luyu Zhang, Xueyuan Li, Xitao Yang, Lixin Su
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.597536

Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets
Cited by: 7
Author(s): Mehran Piran, Neda Sepahi, Afagh Moattari, A. M. Rahimi, Ali Ghanbariasad
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22105322

The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers
Cited by: 4
Author(s): Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David Powell, Traude H. Beilharz
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.9697

Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
Cited by: 2
Author(s): Karin Hirose, Yasuhiro Ishiga, Takashi Fujikawa
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2020.01001

Network-Based Approach to Identify the Antiproliferative Mechanisms of Bruceine D in Breast Cancer From the Cancer Genome Atlas
Cited by: 3
Author(s): Sai Tian, Rui Jiang, Weidong Zhang
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms22094598

Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.685065

Comprehensive Landscape of Ovarian Cancer Immune Microenvironment Based on Integrated Multi-Omics Analysis
Cited by: 4
Author(s): Jiacheng Shen, Tingwei Liu, Qiaoli Bei, Shaohua Xu
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2020.579868

Hypoxia-Associated Prognostic Markers and Competing Endogenous RNA Co-Expression Networks in Breast Cancer
Cited by: 20
Author(s): Peng Gong, You-Cheng Shao, Shu‐Chun Huang, Yifan Zeng, Xianglin Yuan, Jingjing Xu, Weinan Yin, Lei Wei, Jingwei Zhang
Software Mentions: 6
Published: about 4 years ago

10.1002/pld3.279

Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis
Cited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: about 4 years ago

10.3389/fgene.2021.698040

Identification of a Ferroptosis Gene Set That Mediates the Prognosis of Squamous Cell Carcinoma of the Head and Neck
Cited by: 1
Author(s): Chunyan Li, Xuemin Wang, Rujia Qin, Zhaoming Zhong, Chuanzheng Sun
Software Mentions: 6
Published: about 3 years ago

10.3389/fgene.2021.612011

TGFβ1: An Indicator for Tumor Immune Microenvironment of Colon Cancer From a Comprehensive Analysis of TCGA
Cited by: 3
Author(s): Jinyan Wang, Jinqiu Wang, Quan Gu, Yan Yang, Yajun Ma, Quan’an Zhang
Software Mentions: 6
Published: over 3 years ago

10.1155/2020/1686480

miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma
Cited by: 7
Author(s): Yu Xia, Qi Wang, Xiaolin Huang, Xinhai Yin, Jukun Song, Ke Zhao, Xiaofeng Duan
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2021.675545

Identification of a Ferroptosis-Related LncRNA Signature as a Novel Prognosis Model for Lung Adenocarcinoma
Cited by: 52
Author(s): Lu Lu, Leping Liu, Qiangqiang Zhao, Rong Gui, Qiancheng Zhao
Software Mentions: 6
Published: over 3 years ago

10.1186/s13007-020-00611-7

DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models
Cited by: 22
Author(s): Ilana Lambert, Christine Paysant‐Le Roux, Stefano Colella, Marie-Laure Martin
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms20164037

Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13148-020-00944-z

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: about 4 years ago

10.1080/20013078.2020.1785746

Influence of species and processing parameters on recovery and content of brain tissue‐derived extracellular vesicles
Cited by: 62
Author(s): Yiyao Huang, Lesley Cheng, Andrey Turchinovich, Vasiliki Mahairaki, Juan C. Troncoso, Olga Pletniková, Norman J. Haughey, Laura J. Vella, Andrew F. Hill, Lei Zheng, Kenneth W. Witwer
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms22179337

Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients
Cited by: 3
Author(s): Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, Michal R. Schweiger
Software Mentions: 6
Published: over 3 years ago

10.1186/s13046-021-02015-4

LncRNA CARMN overexpression promotes prognosis and chemosensitivity of triple negative breast cancer via acting as miR143-3p host gene and inhibiting DNA replication
Cited by: 15
Author(s): Xiaonan Sheng, Huijuan Dai, Yueyao Du, Jing Peng, Rui Sha, Fan Yang, Liheng Zhou, Yingsong Lin, Shuguang Xu, Yifan Wu, Weiqiang Yin, Jinsong Lu
Software Mentions: 6
Published: over 3 years ago

10.3390/jpm10040210

Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease
Cited by: 3
Author(s): Ying Chun Chen, Mei Yi Wu, Zhi Yu, Wan Hsuan Chou, Yi Ting Lai, Chih-Chin Kao, Imaniar Noor Faridah, Mai Szu Wu, Wei Chiao Chang
Software Mentions: 6
Published: about 4 years ago

10.3389/fnmol.2021.637143

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data
Cited by: 7
Author(s): Jordan Sicherman, Dwight F. Newton, Paul Pavlidis, Etienne Sibille, Shreejoy J. Tripathy
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pbio.2006687

Quantitative assessment of cell population diversity in single-cell landscapes
Cited by: 40
Author(s): Qi Liu, Charles A. Herring, Quanhu Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, Ken S. Lau
Software Mentions: 6
Published: about 6 years ago

10.7150/ijbs.32899

A robust 6-mRNA signature for prognosis prediction of pancreatic ductal adenocarcinoma
Cited by: 14
Author(s): Chixing Zhou, Yue Zhao, Yuehui Yin, Zhiqiu Hu, Manar Atyah, Wanyong Chen, Zhi Qiang Meng, Huarong Mao, Qiang Zhou, Wei‐Guo Tang, Pengcheng Wang, Zhanming Li, Juyang Weng, Christiane Bruns, Marie Popp, Felix Popp, Qiongzhu Dong, Ning Ren
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: about 6 years ago

10.3389/fmolb.2021.628546

Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles
Cited by: 3
Author(s): Yujia Yang, Yuchen Cai, Yuan Zhang, Yuanfu Xu, Zhiqiang Xu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1006701

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Cited by: 271
Author(s): Mohamed Mounir, Marta Lucchetta, Tiago Henrique Da T.C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
Software Mentions: 6
Published: over 5 years ago

10.1186/s40246-021-00313-8

Identification of differentially expressed genes and signaling pathways in human conjunctiva and reproductive tract infected with Chlamydia trachomatis
Cited by: 3
Author(s): Guodong Zhu, Xun‐Jie Cao, Yaping Li, Jiaxin Li, Zi-Jian Leng, Lisha Xie, Xu‐Guang Guo
Software Mentions: 6
Published: over 3 years ago

10.1186/s12885-019-6101-7

A large cohort study identifying a novel prognosis prediction model for lung adenocarcinoma through machine learning strategies
Cited by: 43
Author(s): Yin Li, Di Ge, Jie Gu, Fan Xu, Qinqing Zhu
Software Mentions: 6
Published: about 5 years ago

10.3389/fmolb.2020.620765

Development and External Validation of a Novel Immune Checkpoint–Related Gene Signature for Prediction of Overall Survival in Hepatocellular Carcinoma
Cited by: 11
Author(s): Enfa Zhao, Shimin Chen, Yujie Dang
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2021.637023

CXCL5 Has Potential to Be a Marker for Hepatocellular Carcinoma Prognosis and Was Correlating With Immune Infiltrates
Cited by: 8
Author(s): Yuan Nie, Mei-chun Jiang, Cong Liu, Qi Liu, Xuan Zhu
Software Mentions: 6
Published: over 3 years ago

10.1128/mSphere.00167-17

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans
Cited by: 25
Author(s): Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R. Bezerra, Laura Carreto, Gabriela Moura, Mònica Bayés, Marta Gut, Attila Csikász‐Nagy, Duccio Cavalieri, Judith Berman, Manuel A. S. Santos
Software Mentions: 6
Published: over 7 years ago

10.12688/f1000research.11355.2

Arkas: Rapid reproducible RNAseq analysis
Cited by: 9
Author(s): Anthony Colombo, Timothy J. Triche, Giridharan Ramsingh
Software Mentions: 6
Published: over 7 years ago

10.1186/s12872-021-02166-4

Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis
Cited by: 4
Author(s): Zhiyuan Fan, Wei Peng, Zhiwen Wang, Ling Zhang, Kuo Li
Software Mentions: 6
Published: over 3 years ago

10.1155/2013/203681

Time Series Expression Analyses Using RNA-seq: A Statistical Approach
Cited by: 23
Author(s): Sangwon Oh, Seongho Song, Gregory A. Grabowski, Hongyu Zhao, James P. Noonan
Software Mentions: 6
Published: almost 12 years ago

10.3389/fmolb.2020.582911

Comprehensive Analysis of the Relationships Between Tumor Mutation Burden With Immune Infiltrates in Cervical Cell Carcinoma
Cited by: 9
Author(s): Cankun Zhou, Chaomei Li, Shunqing Peng, Liangcheng Zhou, Huan Li
Software Mentions: 6
Published: about 4 years ago

10.3389/fmolb.2021.607090

Identification of an IRGP Signature to Predict Prognosis and Immunotherapeutic Efficiency in Bladder Cancer
Cited by: 12
Author(s): Lianghao Zhang, Long‐Qing Li, Yonghao Zhan, Zhaowei Zhu, Xuepei Zhang
Software Mentions: 6
Published: over 3 years ago

10.1155/2020/8537381

Autophagy Regulatory Genes MET and RIPK2 Play a Prognostic Role in Pancreatic Ductal Adenocarcinoma: A Bioinformatic Analysis Based on GEO and TCGA
Cited by: 10
Author(s): Xingyu Li, Zhiqiang Li, Hongwei Zhu, Xiao Yu
Software Mentions: 6
Published: about 4 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-69451-8

Intrinsic transcriptomic sex differences in human endothelial cells at birth and in adults are associated with coronary artery disease targets
Cited by: 31
Author(s): Robin Hartman, Daniek Kapteijn, Saskia Haitjema, Mireille N. Bekker, Michal Mokrý, Gérard Pasterkamp, Mete Civelek, Hester M. den Ruijter
Software Mentions: 6
Published: over 4 years ago

10.18632/oncotarget.28058

Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids
Cited by: 4
Author(s): Matthew Devall, Christopher H. Dampier, Stephen Eaton, Mourad W. Ali, Virginia Díez-Obrero, Ferrán Moratalla-Navarro, Jennifer Bryant, Lucas T. Jennelle, Vı́ctor Moreno, Steven M. Powell, Ulrike Peters, Graham Casey
Software Mentions: 6
Published: about 3 years ago

10.1016/j.cels.2018.08.001

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Cited by: 77
Author(s): Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, Markus Ralser
Software Mentions: 6
Published: over 6 years ago

10.3389/fmolb.2021.644620

Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers
Cited by: 24
Author(s): Rui Li, Yunhong Yin, Xiu-Li Ji, Xiao Liu, Jianping Li, Yi-Qing Qu
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-58493-7

VGLL3 is a prognostic biomarker and correlated with clinical pathologic features and immune infiltrates in stomach adenocarcinoma
Cited by: 13
Author(s): Lihua Zhang, Longhai Li, Yong Mao, Hua Dong
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmolb.2021.636991

Identifying Dendritic Cell–Related Genes Through a Co-Expression Network to Construct a 12-Gene Risk-Scoring Model for Predicting Hepatocellular Carcinoma Prognosis
Cited by: 7
Author(s): Chao-Yuan Huang, Xiaotao Jiang, Yuancheng Huang, Lina Zhao, Peiwu Li, Fengbin Liu
Software Mentions: 6
Published: over 3 years ago

10.1186/s12885-021-08431-1

Five metastasis-related mRNAs signature predicting the survival of patients with liver hepatocellular carcinoma
Cited by: 7
Author(s): Chao Chen, Yan Qun Liu, Shi Qiu, Ya Li, Ning Jun Yu, Kang Liu, Li Ming Zhong
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0102610

Potential Therapeutic Targets for Oral Cancer: ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF, CD70
Cited by: 28
Author(s): Saurabh Bundela, Anjana Sharma, Prakash S. Bisen
Software Mentions: 6
Published: over 10 years ago

10.3389/fgene.2021.571231

Identification and Analysis of Potential Key Genes Associated With Hepatocellular Carcinoma Based on Integrated Bioinformatics Methods
Cited by: 21
Author(s): Zhuolin Li, Yao Lin, Bizhen Cheng, Qiaoxin Zhang, Yingmu Cai
Software Mentions: 6
Published: over 3 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776