bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fonc.2021.714267

M6A Classification Combined With Tumor Microenvironment Immune Characteristics Analysis of Bladder Cancer
Cited by: 12
Author(s): Huili Zhu, Xiaocan Jia, Yuping Wang, Zhijuan Song, Nana Wang, Yongli Yang, Xiaoguang Shi
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2619-6

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics
Cited by: 16
Author(s): Philip Berg, Evan W. McConnell, Leslie M. Hicks, S. Popescu, George V. Popescu
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2020.00627

High Levels of HIST1H2BK in Low-Grade Glioma Predicts Poor Prognosis: A Study Using CGGA and TCGA Data
Cited by: 20
Author(s): Weidong Liu, Zhentao Xu, Jie Zhou, Shuang Xing, Zhiqiang Li, Xu Gao, Shiyu Feng, Yi Xiao
Software Mentions: 4
Published: over 6 years ago

10.1186/s13024-018-0254-8

Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimer’s disease
Cited by: 227
Author(s): Srikant Rangaraju, Eric B. Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M. Duong, Michael W. Pennington, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-014-0534-8

Prioritizing causal disease genes using unbiased genomic features
Cited by: 39
Author(s): Rahul C. Deo, Gabriel Musso, Murat Taşan, Paul Ling-Fung Tang, Annie Poon, Christiana Yuan, Janine F. Felix, Ramachandran S. Vasan, Rameen Beroukhim, Teresa De Marco, Pui‐Yan Kwok, Calum A. MacRae, Frederick P. Roth
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: almost 20 years ago

10.1039/c8mo00042e

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data
Cited by: 78
Author(s): Benjamin Alexander-Dann, Lavinia Lorena Pruteanu, Erin Oerton, Naomi L. Sharma, Ioana Berindan‐Neagoe, Dezső Módos
Software Mentions: 4
Published: over 8 years ago

10.1002/1878-0261.12811

High‐grade serous peritoneal cancer follows a high stromal response signature and shows worse outcome than ovarian cancer
Cited by: 1
Author(s): Francis Jacob, Rosa Lina Marchetti, André B. Kind, Kenneth J. Russell, Andreas Schoetzau, Viola Heinzelmann‐Schwarz
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2018.02902

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens
Cited by: 35
Author(s): Joannah R. Fergusson, Michael D. Morgan, Mélanie Bruchard, Leonie F. A. Huitema, Balthasar A. Heesters, Vincent van Unen, Jan Piet van Hamburg, Nicole N. van der Wel, Daisy I. Picavet, Frits Koning, Sander W. Tas, Mark S. Anderson, John C. Marioni, Georg A. Holländer, Hergen Spits
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0052021

Prospective Transcriptomic Pathway Analysis of Human Lymphatic Vascular Insufficiency: Identification and Validation of a Circulating Biomarker Panel
Cited by: 46
Author(s): Shin Lin, Jeanna Kim, Mi-Joung Lee, Leslie Roche, Nancy L. Yang, Philip S. Tsao, Stanley G. Rockson
Software Mentions: 4
Published: almost 14 years ago

10.1002/1878-0261.12438

Molecular evidence of field cancerization initiated by diabetes in colon cancer patients
Cited by: 10
Author(s): Laura del Puerto‐Nevado, Pablo Mínguez, Marta Cortón, Sonia Solanes-Casado, I. Prieto, Sebastián Mas, Ana B. Sanz, Paula Gónzález-Alonso, Cristina Villaverde, Sergio Portal‐Núñez, Óscar Aguilera, Carmen Gómez-Guerrero, Pedro Esbrit, Fernando Vivanco, Nieves González, Carmen Ayuso, Alberto Ortíz, Federico Rojo, Jesús Egido, Gloria Alvarez-Llamas, Jesús Garcı́a-Foncillas
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12312

<i>N</i> ‐glycan signatures identified in tumor interstitial fluid and serum of breast cancer patients: association with tumor biology and clinical outcome
Cited by: 21
Author(s): Thilde Terkelsen, Vilde Drageset Haakensen, Radka Saldova, Pavel Gromov, Morten Hansen, Henning Stöckmann, Ole Christian Lingjærde, Anne‐Lise Børresen‐Dale, Elena Papaleo, Åslaug Helland, Pauline M. Rudd, Irina Gromova
Software Mentions: 4
Published: over 8 years ago

10.1186/gb-2014-15-3-r52

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis
Cited by: 120
Author(s): Hai Wu, Troy W. Whitfield, Jonathan A. R. Gordon, Jason R. Dobson, Phillip W. L. Tai, André J. van Wijnen, Janet L. Stein, Jane B. Lian
Software Mentions: 4
Published: over 12 years ago

10.1186/gb-2013-14-5-r42

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance
Cited by: 174
Author(s): David Martino, Yuk Jing Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M. Craig
Software Mentions: 4
Published: over 13 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0031505

Uniform Approximation Is More Appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis
Cited by: 10
Author(s): Zhide Fang, Ruofei Du, Xiangqin Cui
Software Mentions: 4
Published: over 14 years ago

10.1002/1878-0261.12769

KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1‐driven and independent disease‐promoting gene expression in fusion‐positive Rhabdomyosarcoma
Cited by: 3
Author(s): Lays Martin Sobral, Hannah M. Hicks, Janet K. Parrish, Tyler McCann, Joseph Hsieh, Andrew Goodspeed, James C. Costello, Joshua C. Black, Paul Jedlicka
Software Mentions: 4
Published: about 6 years ago

10.1002/1878-0261.12620

A 10‐year prediagnostic follow‐up study shows that serum RNA signals are highly dynamic in lung carcinogenesis
Cited by: 14
Author(s): Sinan Uğur Umu, Hilde Langseth, Andreas Keller, Eckart Meese, Åslaug Helland, Robert Lyle, Trine B. Rounge
Software Mentions: 4
Published: over 6 years ago

10.1002/1878-0261.12796

CircFNDC3B sequestrates miR‐937‐5p to derepress TIMP3 and inhibit colorectal cancer progression
Cited by: 52
Author(s): Wei Zeng, Yi Liu, Wenting Li, Yang Li, Jin-Feng Zhu
Software Mentions: 4
Published: almost 6 years ago

10.1002/1878-0261.12478

Identification of tumor suppressor miRNAs by integrative miRNA and mRNA sequencing of matched tumor–normal samples in lung adenocarcinoma
Cited by: 38
Author(s): Namhee Yu, Seunghui Yong, Hong Kwan Kim, Yoon La Choi, Yeonjoo Jung, Doyeon Kim, Jihae Seo, Ye Eun Lee, Daehyun Baek, Jinseon Lee, Seungjae Lee, Jong Eun Lee, Jaesang Kim, Young Tae Kim, Sanghyuk Lee
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0211491

A five-gene signature predicts overall survival of patients with papillary renal cell carcinoma
Cited by: 29
Author(s): Zhe Gao, Dong Zhang, Yi Duan, Lei Yan, Yi‐Ming Fan, Zhiqing Fang, Zhaoxu Liu
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12503

HDAC7‐mediated control of tumour microenvironment maintains proliferative and stemness competence of human mammary epithelial cells
Cited by: 27
Author(s): Valentina Cutano, Eros Di Giorgio, Martina Minisini, Raffaella Picco, Emiliano Dalla, Claudio Brancolini
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0115964

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

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-10-189

Platform dependence of inference on gene-wise and gene-set involvement in human lung development
Cited by: 3
Author(s): Rose Du, Kelan G. Tantisira, Vincent J. Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T. Kho, Barbara J. Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J. Mariani, J. Steven Leeder, Scott T. Weiss
Software Mentions: 4
Published: over 17 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: almost 9 years ago

10.15252/msb.20209526

Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
Cited by: 6
Author(s): Alok Jaiswal, Prson Gautam, Elina Pietilä, Sanna Timonen, Nora Nordström, Yevhen Akimov, Nina Sipari, Ziaurrehman Tanoli, Thomas Fleischer, Kaisa Lehti, Krister Wennerberg, Tero Aittokallio
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.01579

A Novel Immune-Related Competing Endogenous RNA Network Predicts Prognosis of Acute Myeloid Leukemia
Cited by: 8
Author(s): Shujuan Wang, Lu Yang, Yajun Liu, Yan Xu, Danfeng Zhang, Zhongxing Jiang, Chong Wang, Yanfang Liu
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2020.00707

Construction and Validation of an Autophagy-Related Prognostic Risk Signature for Survival Predicting in Clear Cell Renal Cell Carcinoma Patients
Cited by: 12
Author(s): Huiying Yang, Mengjiao Han, Hua Li
Software Mentions: 4
Published: over 6 years ago

10.15252/msb.20145141

Intercellular network structure and regulatory motifs in the human hematopoietic system
Cited by: 56
Author(s): Wenlian Qiao, Weijia Wang, Elisa Laurenti, Andrei L. Turinsky, Shoshana J. Wodak, Gary D. Bader, John E. Dick, Peter W. Zandstra
Software Mentions: 4
Published: about 12 years ago

10.15252/msb.20209596

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
Cited by: 108
Author(s): Erika Kelmer Sacramento, Joanna Kirkpatrick, Mariateresa Mazzetto, Mario Baumgart, Aleksandar Bartolome, Simone Di Sanzo, Cinzia Caterino, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Sara Bagnoli, Eva Terzibasi Tozzini, Domenico Di Fraia, Natalie Romanov, Peter H. Sudmant, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, Alessandro Ori
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.614497

Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer
Cited by: 6
Author(s): Qiang Liu, Yihang Qi, Xiangyi Kong, Xiangyu Wang, Wenxiang Zhang, Jie Zhai, Yazhe Yang, Yi Fang, Jing Wang
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.01211

Exploration the Significance of a Novel Immune-Related Gene Signature in Prognosis and Immune Microenvironment of Breast Cancer
Cited by: 15
Author(s): Yajie Zhao, Chunrui Pu, Zhenzhen Liu
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-9-S2-S12

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Cited by: 30
Author(s): Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì Maria Victoria Grober, Maria Ravo, Angelo Facchiano, Claudia Angelini, Alessandro Weisz
Software Mentions: 4
Published: over 18 years ago

10.7554/eLife.13195

Resistome diversity in cattle and the environment decreases during beef production
Cited by: 88
Author(s): Noelle Noyes, Xiang Yang, Lyndsey Linke, Roberta J. Magnuson, Adam Dettenwanger, Shaun R. Cook, Ifigenia Geornaras, D. Woerner, Sheryl Gow, Tim A. McAllister, Hua Yang, Jaime Ruiz, Kenneth L. Jones, Christina Boucher, Paul S. Morley, K. E. Belk
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-017-1915-2

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder
Cited by: 10
Author(s): Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chenglian Feng, Guang Fan
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0057886

Integrative Genome-Wide Gene Expression Profiling of Clear Cell Renal Cell Carcinoma in Czech Republic and in the United States
Cited by: 94
Author(s): Magdalena B. Wozniak, Florence Le Calvez-Kelm, Behnoush Abedi-Ardekani, Graham Byrnes, G. Durand, Christine Carreira, Jocelyne Michelon, Vladimír Janout, Ivana Holcátová, Lenka Foretová, A. Brisuda, Fabienne Lesueur, James McKay, Paul Brennan, Ghislaine Scélo
Software Mentions: 4
Published: over 13 years ago

10.1186/gb-2008-9-11-r164

Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Cited by: 50
Author(s): Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux
Software Mentions: 4
Published: over 18 years ago

10.1371/journal.pone.0111637

miR-27 Negatively Regulates Pluripotency-Associated Genes in Human Embryonal Carcinoma Cells
Cited by: 14
Author(s): Heiko Fuchs, Matthias Theuser, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-7-511

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Cited by: 23
Author(s): Andrew Holloway, Alicia Oshlack, Dileepa S. Diyagama, David D.L. Bowtell, Gordon K. Smyth
Software Mentions: 4
Published: almost 20 years ago

10.1016/j.omto.2020.04.001

A Cross-Reactive Small Protein Binding Domain Provides a Model to Study Off-Tumor CAR-T Cell Toxicity
Cited by: 6
Author(s): Joanne A. Hammill, Jacek M. Kwiecień, Anna Dvorkin‐Gheva, Vivian Wing Chong Lau, Christopher L. Baker, Ying Wu, Ksenia Bezverbnaya, Craig Aarts, Christopher W. Heslen, Galina Denisova, Heather Derocher, Katy Milne, Brad H. Nelson, Jonathan L. Bramson
Software Mentions: 4
Published: over 6 years ago

10.1016/j.gdata.2016.10.006

Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model
Cited by: 15
Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Reneé C. Ireton, Martin T. Ferris, Duncan M. Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, Michael Gale
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-16-S17-S5

A computational method for drug repositioning using publicly available gene expression data
Cited by: 4
Author(s): K M Shabana, K. A. Abdul Nazeer, Meeta Pradhan, Mathew Palakal
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-019-2952-9

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data
Cited by: 19
Author(s): Savvas Kinalis, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0211705

Little cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper
Cited by: 11
Author(s): Suhana Chattopadhyay, Eoghan M. Smyth, Prachi Kulkarni, Kelsey R. Babik, Molly C. Reid, Lauren E. Hittle, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 4
Published: over 7 years ago

10.3390/vaccines9060664

In Vitro Characterization of the Innate Immune Pathways Engaged by Live and Inactivated Tick-Borne Encephalitis Virus
Cited by: 3
Author(s): Aurora Signorazzi, Jeroen L. A. Pennings, Marilena P. Etna, Malou Noya, Eliana M. Coccia, Anke Huckriede
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2018.00482

Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes
Cited by: 10
Author(s): Athar Khalil, Batoul Dekmak, Fouad Boulos, Jake Kantrowitz, Avrum Spira, Junya Fujimoto, Humam Kadara, Nehmé El-Hachem, Georges Nemer
Software Mentions: 4
Published: almost 8 years ago

10.1590/1678-4685-GMB-2019-0090

Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma
Cited by: 4
Author(s): Yongwei Wang, Yaxian Gao, Sen Guo, Zhihong Chen
Software Mentions: 4
Published: over 6 years ago

10.3389/fonc.2021.724655

Super-Enhancer Induced IL-20RA Promotes Proliferation/Metastasis and Immune Evasion in Colorectal Cancer
Cited by: 12
Author(s): Du Yu, Xiao Yang, Jia Wei Lin, Zichao Cao, Chenghao Lu, Zheyu Yang, Minhua Zheng, Ruijun Pan, Wei Cai
Software Mentions: 4
Published: about 5 years ago

10.18632/genesandcancer.133

Genetically transforming human osteoblasts to sarcoma: development of an osteosarcoma model
Cited by: 21
Author(s): Yi Yuan Yang, Rui Yang, Michael Roth, Sajida Piperdi, Wendong Zhang, Howard D. Dorfman, Pulivarthi H. Rao, Amy Park, Sandeep Tripathi, Carrie Freeman, Yunjia Zhang, Rebecca Sowers, Jeremy Rosenblum, David S. Geller, Bang H. Hoang, Jonathan Gill, Richard Görlick
Software Mentions: 4
Published: over 9 years ago

10.3390/genes12091363

Meta-Analysis of Brain Gene Expression Data from Mouse Model Studies of Maternal Immune Activation Using Poly(I:C)
Cited by: 4
Author(s): Aodán Laighneach, Lieve Desbonnet, John Kelly, Gary Donohoe, Derek W. Morris
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0199314

Novel classification for global gene signature model for predicting severity of systemic sclerosis
Cited by: 1
Author(s): Zariel I. Johnson, Jennifer A. Jones, Avinaba Mukherjee, Dianxu Ren, Carol Feghali‐Bostwick, Yvette P. Conley, Cecelia C. Yates
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pcbi.1001034

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

10.3389/fonc.2021.705547

Construction of Novel Methylation-Driven Gene Model and Investigation of PARVB Function in Glioblastoma
Cited by: 3
Author(s): Wanli Yu, Pengfei Wu, Fang Wang, Miao Li, Bo Han, Zhiqun Jiang
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-9-164

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Cited by: 32
Author(s): Richard D. Pearson
Software Mentions: 4
Published: over 18 years ago

10.1371/journal.pone.0045708

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions
Cited by: 32
Author(s): Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Blanca Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim Hui-Ming Huang, Pearlly S. Yan, Luis del Peso
Software Mentions: 4
Published: almost 14 years ago

10.7554/eLife.29156

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

10.3389/fonc.2021.674897

Analysis of Immune-Related Signatures Related to CD4+ T Cell Infiltration With Gene Co-Expression Network in Pancreatic Adenocarcinoma
Cited by: 3
Author(s): Zhen Tan, Yubin Lei, Bo Zhang, Si Shi, Jiang Liu, Xianjun Yu, Jin Xu, Chen Liang
Software Mentions: 4
Published: about 5 years ago

10.3389/fonc.2020.567931

A Ten-N6-Methyladenosine (m6A)-Modified Gene Signature Based on a Risk Score System Predicts Patient Prognosis in Rectum Adenocarcinoma
Cited by: 10
Author(s): Wei Huang, Gen Li, Zihang Wang, Lin Zhou, Xin Yin, Tianshu Yang, Pei Wang, Xu Teng, Yajuan Feng, Hefen Yu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0134168

Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment
Cited by: 19
Author(s): Benjawan Kaewseekhao, Vivek Naranbhai, Sittiruk Roytrakul, Wises Namwat, Atchara Paemanee, Viraphong Lulitanond, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 4
Published: about 11 years ago

10.3389/fonc.2020.592811

Exploration of the Prognostic and Immunotherapeutic Value of B and T Lymphocyte Attenuator in Skin Cutaneous Melanoma
Cited by: 6
Author(s): Xubin Dong, Jingjing Song, Buran Chen, Yufeng Qi, Wenjie Jiang, Huihui Li, Danni Zheng, Yinghao Wang, Xiaohua Zhang, Haiguang Liu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0104504

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

10.1186/s12864-019-5669-2

Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships
Cited by: 39
Author(s): Afshin Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey, David B. Lowry
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-341

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Cited by: 34
Author(s): Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cécile Segonzac, Graham J. Etherington, Kee Hoon Sohn, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 4
Published: over 12 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-017-3797-0

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
Cited by: 20
Author(s): Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam, Marc R. Wilkins
Software Mentions: 4
Published: over 9 years ago

10.1186/s13046-019-1228-6

Extracellular lipid loading augments hypoxic paracrine signaling and promotes glioma angiogenesis and macrophage infiltration
Cited by: 18
Author(s): Svenja Offer, Julien A. Menard, Julio Enríquez Pérez, Kelin Gonçalves de Oliveira, Vineesh Indira Chandran, Martin Johansson, Anna Bång-Rudenstam, Peter Siesjö, Anna Ebbesson, Ingrid Hedenfalk, Pia C. Sundgren, Anna Darabi, Mattias Belting
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-017-3745-z

The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model
Cited by: 20
Author(s): Martijn van Hagen, Diewertje G. E. Piebes, Wim C. de Leeuw, Ilona M. Vuist, Willeke M. C. van Roon‐Mom, Perry D. Moerland, Pernette J. Verschure
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-020-07327-x

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development
Cited by: 5
Author(s): Juliet M. Wong, Gretchen E. Hofmann
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4011-0

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Cited by: 54
Author(s): Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Young Ho Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant
Software Mentions: 4
Published: about 9 years ago

10.3389/fonc.2021.603556

Pharmacological Inhibition and Genetic Knockdown of BCL9 Modulate the Cellular Landscape of Cancer-Associated Fibroblasts in the Tumor-Immune Microenvironment of Colorectal Cancer
Cited by: 5
Author(s): Ming Yang, Wei Zhuang, Mei Feng, Yuanyuan Zhu, Yong Chen, Di Zhu
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.104119

Vascular endothelial growth factor receptor-2 and its association with tumor immune regulatory gene expression in hepatocellular carcinoma
Cited by: 5
Author(s): Ze-Long Liu, Lingling Zhu, Jinghua Liu, Zhaoxia Pu, Zhiping Ruan, Chen Jiang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: almost 8 years ago

10.7150/ijbs.60674

Ailanthus Altissima-derived Ailanthone enhances Gastric Cancer Cell Apoptosis by Inducing the Repression of Base Excision Repair by Downregulating p23 Expression
Cited by: 7
Author(s): Chunming Wang, Hua-Fu Li, Xiaokun Wang, Wu-Guo Li, Shan Qiao, Xing Xiao, Tong Hao, Wei Chen, Yawei Zhang, Haiyong Zhang, Wei Wu, Zhenran Hu, Guochao Zhao, Mingyu Huo, Yulong He, Changhua Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13046-020-01752-2

MiRNA-340-5p mediates the functional and infiltrative promotion of tumor-infiltrating CD8+ T lymphocytes in human diffuse large B cell lymphoma
Cited by: 9
Author(s): Yangyang Xu, Zhenchuan Liu, Lixin Lv, Ping Li, Bing Xu, Wenbin Qian, Aibin Liang
Software Mentions: 4
Published: almost 6 years ago

10.1080/21623945.2020.1829852

Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations
Cited by: 7
Author(s): Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007603

SuperFreq: Integrated mutation detection and clonal tracking in cancer
Cited by: 34
Author(s): Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.15842

Identifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysis
Cited by: 29
Author(s): Zhong He, Min Sun, Ke Yuan, Rongjie Lin, Youde Xiao, Shaosheng Zhou, Hong Zhao, Yan Wang, Fuxiang Zhou, Youwen Zhou
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-016-2695-1

Improving microRNA target prediction with gene expression profiles
Cited by: 22
Author(s): Cesaré Ovando-Vázquez, Daniel Lepe-Soltero, Cei Abreu‐Goodger
Software Mentions: 4
Published: over 10 years ago

10.1186/s12902-021-00709-6

Identification of hub genes related to the progression of type 1 diabetes by computational analysis
Cited by: 10
Author(s): G Prashanth, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Iranna Kotturshetti
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.202781

One potential biomarker for teratozoospermia identified by in-depth integrative analysis of multiple microarray data
Cited by: 3
Author(s): Baoquan Han, Lu Wang, Shuai Yu, Wei Ge, Yaqi Li, Hui Jiang, Wei Shen, Zhongyi Sun
Software Mentions: 4
Published: over 5 years ago

10.1186/s40246-019-0247-x

Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms
Cited by: 6
Author(s): David R. Lorenz, Vikas Misra, Dana Gabuzda
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13046-021-02122-2

Mutant NPM1-regulated lncRNA HOTAIRM1 promotes leukemia cell autophagy and proliferation by targeting EGR1 and ULK3
Cited by: 19
Author(s): Yipei Jing, Xueke Jiang, Lei Li, Meixi Peng, Jun Ren, Qiaoling Xiao, Tao Yao, Yonghong Tao, Junpeng Huang, Lu Wang, Yuting Tang, Zailin Yang, Yang Zhou, Ling Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-1716-9

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system
Cited by: 66
Author(s): Rodrigo Pulgar, Christian Hödar, Dante Travisany, Alejandro Zúñiga, Cristina Ruesca Domínguez, Alejandro Maass, Maurício González, Verónica Cambiazo
Software Mentions: 4
Published: about 11 years ago

10.1155/2019/1785042

Low GAS5 Levels as a Predictor of Poor Survival in Patients with Lower-Grade Gliomas
Cited by: 18
Author(s): Yanfang Wang, Xin Shan, Kai Zhang, Run Shi, Xuanwen Bao
Software Mentions: 4
Published: over 7 years ago

10.1186/s40246-021-00344-1

High-throughput screening of circRNAs reveals novel mechanisms of tuberous sclerosis complex-related renal angiomyolipoma
Cited by: 2
Author(s): Yupei Zhao, Hao Guo, Wenda Wang, Guoyang Zheng, Zhan Wang, Xu Wang, Yushi Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s40246-020-00270-8

A potential prognostic prediction model of colon adenocarcinoma with recurrence based on prognostic lncRNA signatures
Cited by: 14
Author(s): Lipeng Jin, Chenyao Li, Tao Liu, Lei Wang
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.203049

Construction of a novel mRNA-miRNA-lncRNA network and identification of potential regulatory axis associated with prognosis in colorectal cancer liver metastases
Cited by: 8
Author(s): Lu Chen, Xiaochun Luo, Xing Cheng, Yonghuan Mao, Yuting Xu, Wenjie Gao, Wulin Wang, Tian Zhan, Guoguang Wang, Zhengxia Liu, Chang-Feng Yu
Software Mentions: 4
Published: over 5 years ago

10.1084/jem.20201290

Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation
Cited by: 16
Author(s): Marcel S Woo, Friederike Ufer, Nicola Rothammer, Giovanni Di Liberto, Lars Binkle, Undine Haferkamp, Jana K. Sonner, Jan Broder Engler, Sönke Hornig, Simone Bauer, Ingrid Wagner, Kristóf Égervári, Jacob Raber, Robert M. Duvoisin, Ole Pleß, Doron Merkler, Manuel A. Friese
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2121-14-43

In vitro three-dimensional modeling of fallopian tube secretory epithelial cells
Cited by: 39
Author(s): Kate Lawrenson, Maria Notaridou, Nathan Lee, E. Benjamin, Ian Jacobs, Christopher S. Jones, Simon A. Gayther
Software Mentions: 4
Published: almost 13 years ago

10.3389/fonc.2021.701500

Development and Validation of a Radiosensitivity Prediction Model for Lower Grade Glioma Based on Spike-and-Slab Lasso
Cited by: 3
Author(s): Zixuan Du, Shang Cai, Derui Yan, Huijun Li, Xinyan Zhang, Wei Yang, Jianping Cao, Nengjun Yi, Zaixiang Tang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: about 11 years ago

10.1128/mSystems.00215-21

Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation
Cited by: 5
Author(s): Marlène S Birk, Rina Ahmed-Begrich, Stefan Tran, Alexander K. W. Elsholz, Christian K. Frese, Emmanuelle Charpentier
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/9587084

Development of an Individualized Immune Prognostic Signature for Clear Cell Renal Cell Carcinoma through the Identification of Differential Immune Genes
Cited by: 1
Author(s): Jianfeng Wang, Chaozhi Tang, Xiaowu Liu
Software Mentions: 4
Published: about 5 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776