bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0131274

PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
Cited by: 51
Author(s): Natalja Kurbatova, Justin C. Mason, Hugh W. Morgan, Terrence F. Meehan, Natasha A. Karp
Software Mentions: 4
Published: about 11 years ago

10.3390/genes11010034

Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions
Cited by: 3
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 4
Published: over 6 years ago

10.1186/s12931-016-0496-3

Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples
Cited by: 5
Author(s): Andre Koper, Leo Zeef, Leena Dennis Joseph, Keith M. Kerr, John R. Gosney, Mark A. Lindsay, Richard Booton
Software Mentions: 4
Published: over 9 years ago

10.1002/cam4.1397

Development and validation of an individualized diagnostic signature in thyroid cancer
Cited by: 16
Author(s): Li-ou Han, Xinyu Li, Mingming Cao, Yan Cao, Lihong Zhou
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.7313

Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma
Cited by: 37
Author(s): Tingting Guo, Hongwen Ma, Yuting Zhou
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2018.00265

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis
Cited by: 119
Author(s): Xinkui Liu, Jiarui Wu, Dan Zhang, Zhitong Bing, Jinhui Tian, Mengwei Ni, Xiaomeng Zhang, Ziqi Meng, Shuyu Liu
Software Mentions: 4
Published: about 8 years ago

10.1155/2014/145243

Integration of High-Volume Molecular and Imaging Data for Composite Biomarker Discovery in the Study of Melanoma
Cited by: 7
Author(s): Κωνσταντίνος Μούτσελος, Ilias Maglogiannis, Aristotelis Chatziioannou
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-60981-9

NBIA: a network-based integrative analysis framework – applied to pathway analysis
Cited by: 7
Author(s): Tin Nguyen, Adib Shafi, Tuan-Minh Nguyen, A. Grant Schissler, Sorin Drăghici
Software Mentions: 4
Published: over 6 years ago

10.1155/2019/7518374

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

10.7717/peerj.3394

SIX4 promotes metastasis via activation of the PI3K-AKT pathway in colorectal cancer
Cited by: 26
Author(s): Guodong Li, Fang Hu, Xuelai Luo, Jian Hu, Yongzeng Feng
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms20061370

Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver
Cited by: 3
Author(s): Stephenie D. Prokopec, Raimo Pohjanvirta, Selma Mahiout, Lars Pettersson, Paul C. Boutros
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.65760

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

10.1186/s12885-020-07532-7

Establishment of an immune-related gene pair model to predict colon adenocarcinoma prognosis
Cited by: 8
Author(s): Jihang Luo, Puyu Liu, Leibo Wang, Yi Huang, Yuanyan Wang, Wenjing Geng, Duo Chen, Yifeng Bai, Zichen Yang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2021.670777

Decidual NR2F2-Expressing CD4+ T Cells Promote TH2 Transcriptional Program During Early Pregnancy
Cited by: 2
Author(s): Yan Lin, Di Zhang, Yangyang Li, Yunyun Li, Bin Li, Meirong Du
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-44991-w

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

10.1002/cam4.3854

Identification of MEG8/miR‐378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis
Cited by: 7
Author(s): Jiang Lei, Zhen-Yu He, Jun Wang, Min Hu, Ping Zhou, Chen-Lu Lian, Hua Li, San‐Gang Wu, Juan Zhou
Software Mentions: 4
Published: over 5 years ago

10.1002/cam4.4022

A pharmacophore‐based classification better predicts the outcomes of HER2‐negative breast cancer patients receiving the anthracycline‐ and/or taxane‐based neoadjuvant chemotherapy
Cited by: 1
Author(s): Xuan Li, Hefen Sun, Qiqi Liu, Yang Liu, Yifeng Hou, Wei Jin
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.2478

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
Cited by: 13
Author(s): Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C. Kok, Yuan‐Chiang Chung, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Chi-Ying F. Huang, Ka-Lok Ng
Software Mentions: 4
Published: almost 10 years ago

10.21203/rs.3.rs-539712/v1

Plasma Proteomics of COVID-19 Associated Cardiovascular Complications: Implications for Pathophysiology and Therapeutics
Cited by: 2
Author(s): Jason D. Roh, Robert Kitchen, James S. Guseh, Jenna McNeill, Malika Aïd, Amanda J. Martinot, Andy Yu, Colin Platt, James Rhee, Brittany Weber, Lena Trager, Margaret H. Hastings, Sarah Ducat, Peng Xia, Claire Castro, Bjarni Atlason, Timothy W. Churchill, Marcelo Di Carli, Patrick T. Ellinor, Dan H. Barouch, Jennifer E. Ho, Anthony Rosenzweig
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07646-7

Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii
Cited by: 18
Author(s): Victoria A. Ingham, Faye Brown, Hilary Ranson
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/8047146

A Novel Schizophrenia Diagnostic Model Based on Statistically Significant Changes in Gene Methylation in Specific Brain Regions
Cited by: 3
Author(s): Donghua Zou, Yufen Qiu, Rongjie Li, Youshi Meng, Yuan Wu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-53471-0

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

10.7717/peerj.6985

Simphony: simulating large-scale, rhythmic data
Cited by: 7
Author(s): Jordan M. Singer, Darwin Y. Fu, Jacob J. Hughey
Software Mentions: 4
Published: over 7 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2021.600506

Molecular and Clinicopathological Characterization of a Prognostic Immune Gene Signature Associated With MGMT Methylation in Glioblastoma
Cited by: 5
Author(s): Liang Zhao, Jiayue Zhang, Shurui Xuan, Zhiyuan Liu, Yu Wang, Peng Zhao
Software Mentions: 4
Published: over 5 years ago

10.1155/2019/1742341

Based on Integrated Bioinformatics Analysis Identification of Biomarkers in Hepatocellular Carcinoma Patients from Different Regions
Cited by: 9
Author(s): Linxin Teng, Kaiyuan Wang, Yu Liu, Yanxia Ma, Weiping Chen, Lei Bi
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12859-020-3366-4

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Cited by: 4
Author(s): Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich A. Maus, Thomas Illig, David S. DeLuca
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.11074

Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
Cited by: 6
Author(s): Jian Duan, Youming Lei, Guoli Lv, Yinqiang Liu, Zhao Wei, Qingmei Yang, Xin Su, Zhijian Song, Leilei Lu, Yunfei Shi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-67743-7

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

10.1186/s13148-021-01161-y

Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes
Cited by: 12
Author(s): Lyndsey E. Shorey‐Kendrick, Cindy T. McEvoy, Shannon M. O’Sullivan, Kristin Milner, Brittany Vuylsteke, Robert S. Tepper, David M. Haas, Byung Park, Lina Gao, Annette Vu, Cynthia D. Morris, Eliot R. Spindel
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-020-00990-7

DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome
Cited by: 25
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Kathleen Rooney, Jennifer Kerkhof, Michael A. Levy, Haley McConkey, R. Curtis Rogers, Katy Phelan, Sara M. Sarasua, Lavanya Jain, Rini Pauly, Luigi Boccuto, Barbara R. DuPont, Gerarda Cappuccio, Nicola Brunetti‐Pierri, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/4582082

Identification of a Two-m6A RNA Methylation Regulator Risk Signature as an Independent Prognostic Biomarker in Papillary Renal Cell Carcinoma by Bioinformatic Analysis
Cited by: 5
Author(s): Fusheng Yang, Guojiang Zhao, Liyuan Ge, Yimeng Song, Kai Hong, Hongxian Zhang, Cheng Liu, Hong Peng, Lulin Ma
Software Mentions: 4
Published: over 5 years ago

10.1111/acel.13366

Clonal hematopoiesis associated with epigenetic aging and clinical outcomes
Cited by: 57
Author(s): Daniel Nachun, Ake T. Lu, Alexander Bick, Pradeep Natarajan, Joshua Weinstock, Mindy D Szeto, Sekar Kathiresan, Gonçalo Abecasis, Kent D. Taylor, Xiuqing Guo, Russ Tracy, Peter Durda, Yongmei Liu, Craig W. Johnson, Stephen S. Rich, David Van Den Berg, Cecilia A. Laurie, Tom Blackwell, George Papanicolaou, Adolfo Correa, Laura M. Raffield, Andrew D. Johnson, Joanne M. Murabito, JoAnn E. Manson, Pinkal Desai, Charles Kooperberg, Themistocles L. Assimes, Daniel Levy, Jerome I. Rotter, Alex P. Reiner, Eric A. Whitsel, James G. Wilson, Steve Horvath, Siddhartha Jaiswal
Software Mentions: 4
Published: over 5 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-57542-5

Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects
Cited by: 11
Author(s): И. В. Медведева, Matthew E. Stokes, Dominic Eisinger, Samuel T. LaBrie, Jing Ai, Matthew Trotter, Peter Schäfer, Robert Yang
Software Mentions: 4
Published: over 6 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/fimmu.2019.02512

Selective Histone Deacetylase 6 Inhibition Normalizes B Cell Activation and Germinal Center Formation in a Model of Systemic Lupus Erythematosus
Cited by: 26
Author(s): Jingjing Ren, Michelle D. Catalina, Kristin Eden, Xiaofeng Liao, Kaitlin A. Read, Xin Luo, Ryan P. McMillan, Matthew W. Hulver, Matthew Jarpe, Prathyusha Bachali, Amrie C. Grammer, Peter E. Lipsky, Christopher M. Reilly
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-020-00877-7

Methylome profiling of young adults with depression supports a link with immune response and psoriasis
Cited by: 10
Author(s): Coral Lapsley, Rachelle E Irwin, Margaret McLafferty, Sara Jayne Thursby, Siobhan O’Neill, Anthony J. Bjourson, Colum P. Walsh, Elaine Murray
Software Mentions: 4
Published: about 6 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 11 years ago

10.1155/2021/6616434

Weighted Gene Coexpression Network Analysis Uncovers Critical Genes and Pathways for Multiple Brain Regions in Parkinson’s Disease
Cited by: 4
Author(s): Jianjun Huang, Li Liu, Lingling Qin, Hehua Huang, Li Xue
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.11931

Establishment of a ferroptosis-related gene signature for prognosis in lung adenocarcinoma patients
Cited by: 4
Author(s): Jingjing Cai, Chunyan Li, Hongsheng Li, Xiaoxiong Wang, Yunyun Zhou
Software Mentions: 4
Published: about 5 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

10.3389/fcell.2020.00808

Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration
Cited by: 10
Author(s): Dhanach Dhirachaikulpanich, Xin Li, Louise F. Porter, Luminita Paraoan
Software Mentions: 4
Published: about 6 years ago

10.3390/ani11082165

Comprehensive Transcriptomic Comparison between Porcine CD8− and CD8+ Gamma Delta T Cells Revealed Distinct Immune Phenotype
Cited by: 7
Author(s): Sang–Wook Kim, Bee-Oh Lim, Sameer-ul-Salam Mattoo, Eunyoung Oh, Chang-Gi Jeong, Won-Il Kim, Kyung-Tai Lee, Sang-Myeong Lee, Junmo Kim
Software Mentions: 4
Published: about 5 years ago

10.1002/reg2.48

Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in<i>Xenopus</i>embryos, axolotl regeneration, and human mesenchymal cell differentiation
Cited by: 51
Author(s): Vaibhav P. Pai, Christopher J. Martyniuk, Karen Echeverri, Sarah Sundelacruz, David L. Kaplan, Michael Levin
Software Mentions: 4
Published: almost 11 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: about 5 years ago

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

10.1371/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

10.1186/s13148-021-01115-4

Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells
Cited by: 7
Author(s): Johanna Huoman, David Martínez-Enguita, Elin Olsson, Jan Ernerudh, Lennart Nilsson, Karel Duchén, Mika Gustafsson, Maria C. Jenmalm
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0046045

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

10.3389/fimmu.2021.702877

Mapping Autoantibodies in Children With Acute Rheumatic Fever
Cited by: 7
Author(s): Reuben McGregor, Mei Lin Tay, Lauren H. Carlton, Paulina Hanson‐Manful, Jeremy M Raynes, Wasan Forsyth, Diane Brewster, Martin Middleditch, Julie Bennett, William J. Martin, Nigel Wilson, Polly Atatoa Carr, Michael G Baker, Nicole J. Moreland
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-019-1918-6

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Cited by: 4
Author(s): Maroun Bou Sleiman, Michael Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigó, Bart Deplancke
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.202170

A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adults
Cited by: 10
Author(s): Chun-Kai Wen, Hongxue Wang, Han Wang, Hao Yuan Mo, Weiying Zhong, Jing Tang, Yuefeng Lu, Wenxian Zhou, Aihua Tan, Yan Liu, Weimin Xie
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/8886914

An Integrative Analysis Reveals the Potential Mechanism between Herbal Medicine Yinchen and Immunoregulation in Hepatocellular Carcinoma
Cited by: 3
Author(s): Zhuomao Mo, Zhirui Cao, Ling Yu, Yongdan Wang, Pan Li, You-Wu Lin, Shijun Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13014-021-01853-y

Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burden
Cited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-15-763

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate
Cited by: 5
Author(s): Dominik Mojžita, Merja Oja, Eija Rintala, Marilyn G. Wiebe, Merja Penttilä, Laura Ruohonen
Software Mentions: 4
Published: over 12 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

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: almost 7 years ago

10.1080/15476286.2019.1621625

NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution
Cited by: 5
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 4
Published: over 7 years ago

10.1038/s41431-021-00854-5

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

10.1111/pbi.13339

Balancing the double‐edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms
Cited by: 33
Author(s): Sabiha Parween, Joanne Jerenice Añonuevo, Vito M. Butardo, Gopal Misra, Roslen Anacleto, Cindy Llorente, Ondřej Kosík, Marissa V. Romero, E.H. Bandonill, Merlyn S. Mendioro, Alison Lovegrove, Alisdair R. Fernie, Yariv Brotman, Nese Sreenivasulu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms19103265

Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites
Cited by: 19
Author(s): Bernardus C. J. Schimmel, Juan M. Alba, Nicky Wybouw, Joris J. Glas, Tomas Meijer, Robert C. Schuurink, Merijn R. Kant
Software Mentions: 4
Published: almost 8 years ago

10.18632/aging.202228

Identification of SCARA3 with potential roles in metabolic disorders
Cited by: 7
Author(s): Hui Peng, Qi Guo, Tian Su, Ye Xiao, Changjun Li, Yan Huang, Xiang‐Hang Luo
Software Mentions: 4
Published: almost 6 years ago

10.3390/cells8101117

Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles
Cited by: 8
Author(s): Stefaan Verhulst, Tania Roskams, Pau Sancho–Bru, Leo A. van Grunsven
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2021.737867

Genomic Instability-Related LncRNA Signature Predicts the Prognosis and Highlights LINC01614 Is a Tumor Microenvironment-Related Oncogenic lncRNA of Papillary Thyroid Carcinoma
Cited by: 6
Author(s): Xubin Dong, Cong Jin, Danxiang Chen, Yizuo Chen, Zhiqiang Ye, Xiaohua Zhang, Xiaoli Huang, Wei Zhang, Di Gu
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-60175-3

The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts
Cited by: 18
Author(s): Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, James N. D. Battey, Athanasios Kondylis, Marja Talikka, Bjoern Titz, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Sonia Ouadi, Rendy Yanuar, Ching Keong Tung, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0054961

Host Responses to Melioidosis and Tuberculosis Are Both Dominated by Interferon-Mediated Signaling
Cited by: 57
Author(s): Gavin Koh, M. Fernanda Schreiber, Rubén Bautista, Rapeephan R. Maude, Susanna Dunachie, Direk Limmathurotsakul, Nicholas P. J. Day, Gordon Dougan, Sharon J. Peacock
Software Mentions: 4
Published: over 13 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

10.3389/fimmu.2021.704655

An Immune-Associated Genomic Signature Effectively Predicts Pathologic Complete Response to Neoadjuvant Paclitaxel and Anthracycline-Based Chemotherapy in Breast Cancer
Cited by: 4
Author(s): Changfang Fu, Yu Liu, Xinghua Han, Yueyin Pan, Hongqiang Wang, Hongzhi Wang, Haiming Dai, Wulin Yang
Software Mentions: 4
Published: about 5 years ago

10.3390/cells10010045

Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature
Cited by: 5
Author(s): Darío Rocha, Iris Alejandra García, Aldana González Montoro, Andrea S. Llera, Laura Beatriz Prato, María Romina Girotti, Gastón Soria, Elmer Fernández
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0021495

MicroRNA Expression Profiling Reveals MiRNA Families Regulating Specific Biological Pathways in Mouse Frontal Cortex and Hippocampus
Cited by: 70
Author(s): Juuso Juhila, Tessa Sipilä, Katherine Icay, Daniel Nicorici, Pekka Ellonen, Aleksi Kallio, Eija Korpelainen, Dario Greco, Iiris Hovatta
Software Mentions: 4
Published: about 15 years ago

10.3389/fendo.2021.674616

Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment
Cited by: 7
Author(s): Mingming Guo, Zhe Chen, Yayi Li, Sijin Li, Fei Shen, Xiao‐Xiong Gan, Jianhua Feng, Wei Cai, Qingzhi Liu, Bo Xu
Software Mentions: 4
Published: about 5 years ago

10.1155/2021/6680066

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

10.1186/s12864-017-3661-2

Detect tissue heterogeneity in gene expression data with BioQC
Cited by: 42
Author(s): Jitao David Zhang, Klas Hatje, Gregor Sturm, Clemens Broger, Martin Ebeling, Martine Burtin, Fabiola Terzi, Silvia Pomposiello, Laura Badi
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0244556

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

10.1186/s12885-015-1179-z

Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma
Cited by: 57
Author(s): Yibin Hao, Wei Wu, Fachun Shi, Rodrigo Juliani Siqueira Dalmolin, Ming Yan, Fei Tian, Xiaobing Chen, Guoyong Chen, Wei Cao
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.ppat.1009773

CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice
Cited by: 15
Author(s): Deniz Koyuncu, M. Khalid Khan Niazi, Thomas E. Tavolara, Claudia Abeijón, Melanie Ginese, Yanghui Liao, Carolyn Mark, Aubrey G. Specht, Adam C. Gower, Blanca I. Restrepo, Daniel M. Gatti, Igor Kramnik, Metin N. Gürcan, Bülent Yener, Gillian Beamer
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/6657013

Identification of a Prognostic Risk Signature of Kidney Renal Clear Cell Carcinoma Based on Regulating the Immune Response Pathway Exploration
Cited by: 2
Author(s): Guangzhen Wu, Yingkun Xu, Chenglin Han, Zilong Wang, Jiayi Li, Qifei Wang, Xiangyu Che
Software Mentions: 4
Published: over 5 years ago

10.1038/s41375-020-0965-z

A transcriptomic continuum of differentiation arrest identifies myeloid interface acute leukemias with poor prognosis
Cited by: 6
Author(s): Jonathan Bond, Aleksandra Krzywon, Ludovic Lhermitte, Christophe Roumier, Anne Roggy, Mohamed Belhocine, Alexander Abdulkader Kheirallah, Patrick Villarèse, Guillaume Hypolite, Francine Garnache‐Ottou, Sylvie Castaigné, Nicolas Boissel, Vahid Asnafi, Claude Preudhomme, Hervé Dombret, Elisa Laurenti, Elizabeth Macintyre
Software Mentions: 4
Published: about 6 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: about 10 years ago

10.1186/1756-8935-7-26

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

10.1371/journal.ppat.1009785

Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART
Cited by: 9
Author(s): Michael J. Corley, Carlo Sacdalan, Alina P.S. Pang, Nitiya Chomchey, Nisakorn Ratnaratorn, Victor Valcour, Eugène Kroon, Kyu S. Cho, Andrew C. Belden, Donn Colby, Merlin L. Robb, Denise C. Hsu, Serena Spudich, Robert Paul, Sandhya Vasan, Lishomwa C. Ndhlovu, Rv study groups
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0207952

RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns
Cited by: 8
Author(s): Gary P. Brennan, Dimitrios Vitsios, Sophie Casey, Ann-Marie Looney, Boubou Hallberg, David C. Henshall, Geraldine B. Boylan, Deirdre M. Murray, Catherine Mooney
Software Mentions: 4
Published: almost 8 years ago

10.3390/life11080835

Identification of Autophagy- and Ferroptosis-Related lncRNAs Functioned through Immune-Related Pathways in Head and Neck Squamous Carcinoma
Cited by: 9
Author(s): Qi Guo, Xuehan Zhang, Tao Shen, Xiangting Wang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.ppat.1009734

Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition
Cited by: 10
Author(s): Pieter C. Steketee, Emily A. Dickie, James Iremonger, Kathryn Crouch, Edith Paxton, Siddharth Jayaraman, Omar A. Alfituri, Georgina Awuah‐Mensah, Ryan Ritchie, Achim Schnaufer, T.G. Rowan, Harry P. de Koning, Catarina Gadelha, Bill Wickstead, Michael P. Barrett, Liam J. Morrison
Software Mentions: 4
Published: about 5 years ago

10.1007/s00401-021-02327-x

Targeting fibroblast growth factor receptors to combat aggressive ependymoma
Cited by: 9
Author(s): Daniela Lötsch, Dominik Kirchhofer, Bernhard Englinger, Li Jiang, Konstantin Okonechnikov, Daniel Senfter, Anna Laemmerer, Lisa Gabler, Christine Pirker, Andrew M. Donson, Peter Bannauer, Pia Korbel, Carola Jaunecker, Jens-Martin Hübner, Lisa Mayr, Sibylle Madlener, Maria Theresa Schmook, Gerda Ricken, Kendra K. Maaß, Michael Grusch, Klaus Holzmann, Bettina Grasl‐Kraupp, Sabine Spiegl-Kreinecker, Jennifer L. Hsu, Christian Dorfer, Karl Rössler, Amedeo A. Azizi, Nicholas Foreman, Andreas Peyrl, Christine Haberler, Thomas Czech, Irene Slavc, Mariella G. Filbin, Kristian W. Pajtler, Marcel Kool, Walter Berger, Johannes Gojo
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.56325

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

10.7554/eLife.38014

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

10.1371/journal.pbio.1001126

Sex Chromosome-Specific Regulation in the Drosophila Male Germline But Little Evidence for Chromosomal Dosage Compensation or Meiotic Inactivation
Cited by: 123
Author(s): Colin D. Meiklejohn, Emily L. Landeen, Jodi M. Cook, Sarah B. Kingan, Daven C. Presgraves
Software Mentions: 4
Published: about 15 years ago

10.1007/s00592-018-1223-y

Negative pressure wound therapy in the treatment of diabetic foot ulcers may be mediated through differential gene expression
Cited by: 12
Author(s): Sebastian Borys, Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Jerzy Hohendorff, Teresa Koblik, Julita Machlowska, Beata Kieć‐Wilk, Paweł Wołkow, Maciej Małecki
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pbio.3000976

Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain
Cited by: 33
Author(s): Gareth Ball, Jakob Seidlitz, Jonathan O’Muircheartaigh, Ralica Dimitrova, Daphna Fenchel, Antonios Makropoulos, Daan Christiaens, Andreas Schuh, Jonathan Passerat–Palmbach, Jana Hutter, Lucilio Cordero‐Grande, Emer Hughes, Anthony N. Price, Jo Hajnal, Daniel Rueckert, Emma C. Robinson, A. David Edwards
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-021-00393-9

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

10.1155/2020/2137319

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

10.7554/eLife.45310

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

10.1155/2020/4251761

Identification of Potential Hub Genes Related to Diagnosis and Prognosis of Hepatitis B Virus-Related Hepatocellular Carcinoma via Integrated Bioinformatics Analysis
Cited by: 28
Author(s): Yuqin Tang, Yongqiang Zhang, Xun Hu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0211854

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

10.1371/journal.pbio.2004986

Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids
Cited by: 10
Author(s): Ewa M. Michalak, Michael J. G. Milevskiy, Rachel Joyce, Johanna F. Dekkers, Paul Jamieson, Bhupinder Pal, Caleb A. Dawson, Yifang Hu, Stuart H. Orkin, Warren S. Alexander, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 4
Published: about 8 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776