bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: over 14 years ago

High-throughput proteomic profiling of the fish liver following bacterial infection
Cited by: 58
Author(s): Dwight R. Causey, Moritz A N Pohl, David Stead, Samuel Martín, Christopher J. Secombes, Daniel J. Macqueen
Software Mentions: 9
Published: about 8 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: about 13 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: about 8 years ago

10.18632/aging.203290

Expression mode and prognostic value of FXYD family members in colon cancer
Cited by: 8
Author(s): Ming Jin, Hui Zhang, Jun Yang, Zheng Zhao, Kaitai Liu
Software Mentions: 9
Published: over 5 years ago

10.15252/msb.20198849

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
Cited by: 24
Author(s): Antje Dittmann, Norman J. Kennedy, Nina L Soltero, Nader Morshed, Miyeko Mana, Ömer H. Yılmaz, Roger J. Davis, Forest M. White
Software Mentions: 9
Published: about 7 years ago

10.7554/eLife.58178

16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development
Cited by: 24
Author(s): Julien G. Roth, Kristin Muench, Aditya Asokan, Victoria M Mallett, Hongwei Gai, Yogendra Verma, Stephen G. Weber, Carol Charlton, Jonas L. Fowler, Kyle M. Loh, Ricardo E. Dolmetsch, Theo Palmer
Software Mentions: 9
Published: almost 6 years ago

10.3389/fonc.2021.711020

Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model
Cited by: 37
Author(s): Leilei Liang, Jing Yu, Jian Li, Ning Li, Jing Liu, Lin Xiu, Jia Zeng, Tiantian Wang, Lingying Wu
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-019-55434-x

QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis
Cited by: 28
Author(s): Susan M. Corley, Niamh M. Troy, Anthony Bosco, Marc R. Wilkins
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12864-018-5166-z

RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data
Cited by: 17
Author(s): Amanda Ernlund, Robert J. Schneider, Kelly V. Ruggles
Software Mentions: 9
Published: almost 8 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 6 years ago

10.3389/fphar.2021.621359

Compound Dihuang Granule Inhibits Nigrostriatal Pathway Apoptosis in Parkinson’s Disease by Suppressing the JNK/AP-1 Pathway
Cited by: 8
Author(s): Li Wang, Yufang Yang, Long Chen, Zhu-qing He, Dian-yong Bi, Lei Zhang, Yuanfu Xu, Jiancheng He
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-020-1935-5

Opportunities and challenges in long-read sequencing data analysis
Cited by: 1,295
Author(s): Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data
Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Software Mentions: 9
Published: over 6 years ago

10.15252/msb.20199389

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Cited by: 63
Author(s): Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, T. P. Speed, David M. Lin, Pengyi Yang, Jean Yee Hwa Yang
Software Mentions: 9
Published: over 6 years ago

10.15252/msb.20177862

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
Cited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: about 8 years ago

10.1186/1471-2105-10-211

puma: a Bioconductor package for propagating uncertainty in microarray analysis
Cited by: 67
Author(s): Richard D. Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D. Lawrence, Magnus Rattray
Software Mentions: 9
Published: over 17 years ago

10.3389/fmolb.2020.604252

Prognostic Model of Colorectal Cancer Constructed by Eight Immune-Related Genes
Cited by: 14
Author(s): Shuting Wen, Lina He, Zhuotai Zhong, Hong Mi, Fengbin Liu
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12885-019-6235-7

lionessR: single sample network inference in R
Cited by: 22
Author(s): Marieke L. Kuijjer, Ping-Han Hsieh, John Quackenbush, Kimberly Glass
Software Mentions: 9
Published: about 7 years ago

10.3390/biomedicines9040368

Single-Cell RNA Sequencing in Parkinson’s Disease
Cited by: 13
Author(s): Shi-Xun Ma, Su Bin Lim
Software Mentions: 9
Published: over 5 years ago

10.1186/s12885-020-6638-5

Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis
Cited by: 33
Author(s): Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen, Haixing Jiang
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.ppat.1009278

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
Cited by: 11
Author(s): Fredrik Barrenäs, Scott G. Hansen, G. Lynn Law, Connor B. Driscoll, Richard Green, Eric E. Smith, Jean Chang, Inah Golez, Taryn Urion, Xinxia Peng, Leanne S. Whitmore, Daniel J. Newhouse, Colette M. Hughes, David W. Morrow, Kurt T. Randall, Andrea N. Selseth, Julia C. Ford, Roxanne M. Gilbride, Bryan E. Randall, Emily Ainslie, Kelli Oswald, Rebecca Shoemaker, Randy Fast, William J. Bosche, Michael K. Axthelm, Yoshinori Fukazawa, George N. Pavlakis, Barbara K. Felber, Slim Fourati, Rafick Pierre Sékaly, Jeffrey D. Lifson, Jan Komorowski, Ewelina Kosmider, Danica Shao, Wenjun Song, Paul T. Edlefsen, Louis J. Picker, Michael Gale
Software Mentions: 9
Published: over 5 years ago

10.1155/2021/7408893

Identification of a Four-lncRNA Prognostic Signature for Colon Cancer Based on Genome Instability
Cited by: 2
Author(s): Duo Yun, Zhimin Yang
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: over 5 years ago

10.18632/aging.203390

Comprehensive analysis of new prognostic signature based on ferroptosis-related genes in clear cell renal cell carcinoma
Cited by: 8
Author(s): Bin Zheng, Zhihong Niu, Shubin Si, Guiting Zhao, Jianwei Wang, Zhongshun Yao, Fajuan Cheng
Software Mentions: 9
Published: about 5 years ago

10.18632/aging.203455

Construction of an immune-related lncRNA signature as a novel prognosis biomarker for LUAD
Cited by: 9
Author(s): Hang Chen, Wei Shen, Saiqi Ni, Menglu Sang, Shibo Wu, Yinyu Mu, Kaitai Liu, Ni Li, Linwen Zhu, Guodong Xu
Software Mentions: 9
Published: about 5 years ago

10.1002/1878-0261.12595

Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltration
Cited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: almost 7 years ago

10.1155/2021/8864436

Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer
Cited by: 10
Author(s): Xuening Zhang, Xiaoguang Shi, Hao Zhao, Xiaocan Jia, Yongli Yang
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 10 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-020-3463-4

ORdensity: user-friendly R package to identify differentially expressed genes
Cited by: 0
Author(s): José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 9
Published: over 6 years ago

10.1186/s13073-020-00786-7

A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Cited by: 11
Author(s): Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo, Teresa Manzo, Luigi Nezi, Ugo Cavallaro, Davide Cacchiarelli, Jörn Walter, Giuseppe Testa
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pone.0165545

omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data
Cited by: 11
Author(s): Nestoras Karathanasis, Ioannis Tsamardinos, Vincenzo Lagani
Software Mentions: 9
Published: almost 10 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: almost 7 years ago

10.12688/f1000research.27868.3

WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
Cited by: 5
Author(s): Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Software Mentions: 9
Published: over 5 years ago

10.12688/f1000research.7563.2

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Cited by: 795
Author(s): Charlotte Soneson, Michael I. Love, Mark D. Robinson
Software Mentions: 9
Published: over 10 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2020.576566

Systematic Profiling of Immune Risk Model to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 9
Author(s): Xingyu Liu, Jiarui Chen, Wei Lu, Zhao-Yi Zeng, Jiali Li, Xueping Jiang, Yanping Gao, Yan Gong, Qiuji Wu, Conghua Xie
Software Mentions: 9
Published: about 6 years ago

10.12688/f1000research.2-264.v1

illuminaio: An open source IDAT parsing tool for Illumina microarrays
Cited by: 59
Author(s): Mike L. Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Software Mentions: 9
Published: almost 13 years ago

10.1038/s41598-021-84909-z

Omics data integration identifies ELOVL7 and MMD gene regions as novel loci for adalimumab response in patients with Crohn’s disease
Cited by: 8
Author(s): Mario Gorenjak, Mateja Zupin, Gregor Jezernik, Pavel Skok, Uroš Potočnik
Software Mentions: 9
Published: over 5 years ago

10.1155/2021/5510780

A Five-Gene Prognostic Nomogram Predicting Disease-Free Survival of Differentiated Thyroid Cancer
Cited by: 5
Author(s): Pan Ruchong, Hai-ping Tang, Xiang Wang
Software Mentions: 9
Published: over 5 years ago

10.1155/2021/9911184

Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis
Cited by: 7
Author(s): Fei Sun, Jian Zhou, Peiyu Pu, Chen Qiu, Jia rui Cao, Hao Peng
Software Mentions: 9
Published: over 5 years ago

10.7717/peerj.11687

Construction and validation of a 15-gene ferroptosis signature in lung adenocarcinoma
Cited by: 5
Author(s): Guangxu Tu, Weilin Peng, Qidong Cai, Zhenyu Zhao, Ping Xiong, Boxue He, Pengfei Zhang, Shuai Shi, Yongguang Tao, Xiang Wang
Software Mentions: 9
Published: over 5 years ago

10.1186/s12967-021-02770-0

Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis
Cited by: 9
Author(s): Hui Zhang, Chang Xu, Shi Chen, Junying Zhang, Ting Qian, Zhuo Wang, Rong Ma, Jianzhong Wu, Feng Jiang, Jifeng Feng
Software Mentions: 9
Published: over 5 years ago

10.1038/s42003-021-01945-1

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression
Cited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: over 7 years ago

10.1186/s12935-020-01230-x

A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis
Cited by: 19
Author(s): Yongzhi Wang, Zhonghua Yang
Software Mentions: 9
Published: over 6 years ago

10.7554/eLife.54756

ATR expands embryonic stem cell fate potential in response to replication stress
Cited by: 34
Author(s): Sina Atashpaz, Sara Samadi Shams, Javier Martín‐González, Endre Sebestyén, Negar Arghavanifard, Andrea Gnocchi, Eliene Albers, Simone Minardi, Giovanni Fagà, Paolo Soffientini, E. Allievi, Valeria Cancila, Ángela Bachi, Óscar Fernández-Capetillo, Claudio Tripodo, Francesco Ferrari, Andrés J. López-Contreras, Vincenzo Costanzo
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 11 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 12 years ago

10.7554/eLife.65537

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Cited by: 32
Author(s): Matthew T Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel F. A. Tomé, Xuhong Yu, Pascal G.P. Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 9
Published: over 5 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 7 years ago

10.3389/fgene.2020.00441

Prognostic Value of a Stemness Index-Associated Signature in Primary Lower-Grade Glioma
Cited by: 28
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Feibao Guo, Jinsheng Hong
Software Mentions: 9
Published: over 6 years ago

10.1016/j.celrep.2019.01.041

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Cited by: 510
Author(s): Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger, Alfred Zippelius, João Pedro de Magalhães, Anis Larbi
Software Mentions: 9
Published: over 7 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: about 12 years ago

10.1016/j.celrep.2019.11.077

Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids
Cited by: 42
Author(s): Jitu W. George, Huihui Fan, Benjamin K. Johnson, Tyler J. Carpenter, Kelly K. Foy, Anindita Chatterjee, Amanda L. Patterson, Julie Koeman, Marie Adams, Zachary Madaj, David Chesla, Erica E. Marsh, Timothy J. Triche, Hui Shen, Jose Teixeira
Software Mentions: 9
Published: almost 7 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: about 7 years ago

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-020-77201-z

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae
Cited by: 3
Author(s): José Córdoba-Caballero, Pedro Seoane, Fernando M. Jabato, James R. Perkins, Manuel Manchado, M. Gonzalo Claros
Software Mentions: 9
Published: almost 6 years ago

10.1242/bio.052993

Site-1 protease ablation in the osterix-lineage in mice results in bone marrow neutrophilia and hematopoietic stem cell alterations
Cited by: 2
Author(s): Debabrata Patra, Joongho Kim, Qiang Zhang, Eric Tycksen, Linda J. Sandell
Software Mentions: 9
Published: over 6 years ago

10.3389/fgene.2019.00880

LINC00460 Hypomethylation Promotes Metastasis in Colorectal Carcinoma
Cited by: 15
Author(s): Hui Zhang, Ya Lu, Jianzhong Wu, Jifeng Feng
Software Mentions: 9
Published: about 7 years ago

10.1093/bioinformatics/btaa838

<i>MicrobiomeExplorer</i>: an R package for the analysis and visualization of microbial communities
Cited by: 16
Author(s): Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson
Software Mentions: 9
Published: almost 6 years ago

10.1080/21655979.2020.1822715

A novel prognostic models for identifying the risk of hepatocellular carcinoma based on epithelial-mesenchymal transition-associated genes
Cited by: 15
Author(s): Chen Xiong, Guifu Wang, Dou‐Sheng Bai
Software Mentions: 9
Published: almost 7 years ago

10.3389/fonc.2021.619242

The Identification and Validation of Two Heterogenous Subtypes and a Risk Signature Based on Ferroptosis in Hepatocellular Carcinoma
Cited by: 40
Author(s): Xinwei Han, Libo Wang, Long Liu, Taoyuan Lu, Dechao Jiao, Yuling Sun, Xinwei Han
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2020.626912

Molecular Subtypes and CD4+ Memory T Cell-Based Signature Associated With Clinical Outcomes in Gastric Cancer
Cited by: 15
Author(s): Zhikun Ning, Cegui Hu, Chao Huang, Jiang Liu, Taicheng Zhou, Zhen Zong
Software Mentions: 9
Published: over 5 years ago

10.1186/s13040-017-0125-9

Gene set analysis controlling for length bias in RNA-seq experiments
Cited by: 7
Author(s): Xing Ren, Qiang Hu, Song Liu, Jianmin Wang, Jeffrey C. Miecznikowski
Software Mentions: 9
Published: over 9 years ago

10.1186/s12943-020-01170-0

m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer
Cited by: 600
Author(s): Bo Zhang, Qiong Wu, Ben Li, Defeng Wang, Lei Wang, You Zhou
Software Mentions: 9
Published: over 6 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 7 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: about 6 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: over 10 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: over 15 years ago

10.1186/s12935-020-1113-6

Construction of a novel gene-based model for prognosis prediction of clear cell renal cell carcinoma
Cited by: 81
Author(s): Zedan Zhang, Enyu Lin, Hongkai Zhuang, Lu Xie, Xiaoqiang Feng, Jiumin Liu, Yuming Yu
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 9 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: over 7 years ago

10.1186/s12935-020-01560-w

Identification of an immune gene signature for predicting the prognosis of patients with uterine corpus endometrial carcinoma
Cited by: 19
Author(s): Cankun Zhou, Chaomei Li, Fangli Yan, Yuhua Zheng
Software Mentions: 8
Published: almost 6 years ago

10.3389/fonc.2021.642144

Complement C1q (C1qA, C1qB, and C1qC) May Be a Potential Prognostic Factor and an Index of Tumor Microenvironment Remodeling in Osteosarcoma
Cited by: 33
Author(s): Longhao Chen, Jinfu Liu, Yan Lu, Xinyu He, Chi Zhang, Huanyi Zhou
Software Mentions: 8
Published: over 5 years ago

10.1242/dmm.040444

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Cited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: almost 8 years ago

10.1371/journal.pone.0248889

Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Cited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 5 years ago

10.1186/s12935-020-01588-y

A four prognosis-associated lncRNAs (PALnc) based risk score system reflects immune cell infiltration and predicts patient survival in pancreatic cancer
Cited by: 14
Author(s): Hongkai Zhuang, Shanzhou Huang, Zixuan Zhou, Zuyi Ma, Zedan Zhang, Chuanzhao Zhang, Baohua Hou
Software Mentions: 8
Published: about 6 years ago

10.1016/j.devcel.2018.07.005

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development
Cited by: 184
Author(s): Sueli Marques, David van Bruggen, Darya Vanichkina, Elisa M. Floriddia, Hermany Munguba, Leif Väremo, Stefania Giacomello, Ana Mendanha Falcão, Mandy Meijer, Åsa K. Björklund, Jens Hjerling-Leffler, Ryan J. Taft, Gonçalo Castelo‐Branco
Software Mentions: 8
Published: about 8 years ago

10.1038/s41419-021-03525-x

Loss of retinoic acid receptor-related receptor alpha (Rorα) promotes the progression of UV-induced cSCC
Cited by: 6
Author(s): Guolong Zhang, Guorong Yan, Fu Zhuo, Yuhao Wu, Fei Wu, Zhe Zheng, Shiji Fang, Ying Gao, Xiao Bao, Yeqiang Liu, Xiuli Wang, Sibo Zhu
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0240824

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data
Cited by: 0
Author(s): Dobril Ivanov, Gerrit Bostelmann, Benoît Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott‐Price, Janet M. Thornton
Software Mentions: 8
Published: about 6 years ago

10.3389/fonc.2020.01198

Immune Landscape of the Tumor Microenvironment Identifies Prognostic Gene Signature CD4/CD68/CSF1R in Osteosarcoma
Cited by: 25
Author(s): Yi-Jiang Song, Yanyang Xu, Xuejun Zhu, Jianchang Fu, Cong Deng, Hongmin Chen, Huaiyuan Xu, Guohui Song, Jinchang Lu, Qinglian Tang, Jin Wang
Software Mentions: 8
Published: over 6 years ago

10.1016/j.molcel.2019.01.009

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
Cited by: 195
Author(s): Alba Rodríguez-Meira, Gemma Buck, Sally-Ann Clark, Benjamin Povinelli, Verónica Alcolea, Eleni Louka, Simon J. McGowan, Angela Hamblin, Nikolaos Sousos, Nikolaos Barkas, Alice Giustacchini, Bethan Psaila, Sten Eirik W. Jacobsen, Supat Thongjuea, Adam J. Mead
Software Mentions: 8
Published: over 7 years ago

10.3389/fonc.2021.561763

Predict Colon Cancer by Pairing Plasma miRNAs: Establishment of a Normalizer-Free, Cross-Platform Model
Cited by: 3
Author(s): Dashan Qin, Qingdong Guo, Rui Wei, Si Liu, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 8
Published: over 5 years ago

10.1038/s41421-021-00279-w

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication
Cited by: 7
Author(s): Wen Juan Tu, Robert McCuaig, Michelle Melino, Daniel J. Rawle, Thuy T. Le, Kexin Yan, Andreas Suhrbier, Rebecca L. Johnston, Lambros T. Koufariotis, Nicola Waddell, E.M. Cross, S. Tsimbalyuk, Amanda L. Bain, Elizabeth Ahern, Natasha Collinson, Simon Phipps, Jade K. Forwood, Nabila Seddiki, Sudha Rao
Software Mentions: 8
Published: over 5 years ago

10.1186/gb-2013-14-9-r95

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: almost 14 years ago

10.1186/s12967-021-02981-5

N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosis
Cited by: 14
Author(s): Fei Ye, Tianzhu Wang, Xiaoxin Wu, Jie Liang, Jiaoxing Li, Wenli Sheng
Software Mentions: 8
Published: over 5 years ago

10.3389/fonc.2021.654388

MYD88 Is a Potential Prognostic Gene and Immune Signature of Tumor Microenvironment for Gliomas
Cited by: 13
Author(s): Qinglong Guo, Xing Xiao, Jinsen Zhang
Software Mentions: 8
Published: over 5 years ago

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: about 11 years ago

10.3390/jpm11020154

Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma
Cited by: 19
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 5 years ago

10.3389/fgene.2021.627508

Integrated Analysis of the Prognosis-Associated RNA-Binding Protein Genes and Candidate Drugs in Renal Papillary Cell Carcinoma
Cited by: 22
Author(s): Shuiping Jiang, Xiaohan Ren, Shouyong Liu, Zhongwen Lü, Aiming Xu, Chao Qin, Zengjun Wang
Software Mentions: 8
Published: over 5 years ago

10.1155/2021/8859996

Potential Prognostic Biomarkers of Lung Adenocarcinoma Based on Bioinformatic Analysis
Cited by: 17
Author(s): Jili Hou, Yong Cheng
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.celrep.2019.10.018

Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells
Cited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: almost 7 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776