bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2020.00611

Human Regulatory T Cells From Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood
Cited by: 19
Author(s): Keshav Motwani, Leeana D. Peters, Willem H Vliegen, Ahmed G Elsayed, Howard R. Seay, Maria-Cecilia Lopez, Henry V. Baker, Amanda L. Posgai, Todd M. Brusko, Daniel J. Perry, Rhonda Bacher, Joseph Larkin, Michael J. Haller
Software Mentions: 8
Published: over 4 years ago

10.1186/s13058-021-01445-4

Single cell transcriptome atlas of mouse mammary epithelial cells across development
Cited by: 19
Author(s): Bhupinder Pal, Yunshun Chen, Michael J. G. Milevskiy, François Vaillant, Lexie Prokopuk, Caleb A. Dawson, Bianca D. Capaldo, Xiaoyu Song, Felicity C. Jackling, Paul Timpson, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 8
Published: over 3 years ago

10.3389/fcimb.2020.00194

Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections
Cited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: over 4 years ago

10.3389/fcell.2021.710207

Immunological Value of Prognostic Signature Based on Cancer Stem Cell Characteristics in Hepatocellular Carcinoma
Cited by: 14
Author(s): Qianhui Xu, Hao Xu, Shaohuai Chen, Wen Huang
Software Mentions: 8
Published: over 3 years ago

10.1016/j.ebiom.2021.103444

A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach
Cited by: 24
Author(s): Niamh Errington, James Iremonger, Josephine Pickworth, Sokratis Kariotis, Christopher J. Rhodes, Alexander Rothman, Robin Condliffe, Charles Elliot, David G. Kiely, Luke Howard, John Wharton, A. A. Roger Thompson, Nicholas W. Morrell, Martin R. Wilkins, Dennis Wang, Allan Lawrie
Software Mentions: 8
Published: over 3 years ago

10.3389/fcell.2021.642650

A Novel CpG Methylation Risk Indicator for Predicting Prognosis in Bladder Cancer
Cited by: 9
Author(s): Yufeng Guo, Jun Yin, Yuanheng Dai, Yu-Dong Guan, Pinjin Chen, Yongqiang Chen, Chen‐Zheng Huang, Yong‐Jie Lu, Lirong Zhang, Dae‐Kyu Song
Software Mentions: 8
Published: about 3 years ago

10.3389/fcell.2021.681745

Comprehensive Analysis of the Immune Infiltrates and PD-L1 of m6A RNA Methylation Regulators in Hepatocellular Carcinoma
Cited by: 9
Author(s): Yali Xu, Xueling He, Junjian Deng, Lin Xiong, Yue Li, Xiaoyu Zhang, Wenliang Chen, Xin Liu, Ximing Xu
Software Mentions: 8
Published: over 3 years ago

10.3389/fimmu.2020.558757

Molecular and Clinical Characterization of PD-1 in Breast Cancer Using Large-Scale Transcriptome Data
Cited by: 16
Author(s): Qiang Liu, Ran Cheng, Xiangyi Kong, Zhongzhao Wang, Yi Fang, Jing Wang
Software Mentions: 8
Published: about 4 years ago

10.1186/1471-2105-14-133

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis
Cited by: 23
Author(s): Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka M. Axmann, Ralf Steuer
Software Mentions: 8
Published: over 11 years ago

10.3389/fmolb.2021.661661

A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation
Cited by: 2
Author(s): Yicun Wang, Di Zhang, Xiaosong Hu
Software Mentions: 8
Published: over 3 years ago

10.3390/ijms21072337

Differential Targeting of Gr-MDSCs, T Cells and Prostate Cancer Cells by Dactolisib and Dasatinib
Cited by: 10
Author(s): Guoqiang Lü, Zhijian Jin, Xin Lü
Software Mentions: 8
Published: over 4 years ago

10.1186/s13058-016-0758-5

Patient survival and tumor characteristics associated with CHEK2:p.I157T – findings from the Breast Cancer Association Consortium
Cited by: 37
Author(s): Taru Muranen, Carl Blomqvist, Thilo Dörk, Anna Jakubowska, Päivi Heikkilä, Rainer Fagerholm, Dario Greco, Kristiina Aittomäki, Stig E. Bojesen, Mitul Shah, Alison M. Dunning, Valerie Rhenius, Per Hall, Kamila Czene, Judith S. Brand, Hatef Darabi, Jenny Chang–Claude, Anja Rudolph, Børge G. Nordestgaard, Fergus J. Couch, Steven N. Hart, Jonine D. Figueroa, Montserrat García‐Closas, Peter A. Fasching, Matthias W. Beckmann, Jingmei Li, Jing Liu, Irene L. Andrulis, Robert Winqvist, Katri Pylkäs, Arto Mannermaa, Vesa Kataja, Annika Lindblom, Sara Margolin, Jan Lubiński, Natalia Dubrowinskaja, Manjeet K. Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Douglas F. Easton, Paul D.P. Pharoah, Marjanka K. Schmidt, Heli Nevanlinna
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pgen.1009744

The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila
Cited by: 25
Author(s): A. Lukacs, Andreas W. Thomae, P. Krueger, Tamás Schauer, Anuroop Venkateswaran Venkatasubramani, Natalia Y. Kochanova, Wasim Aftab, Rupam Choudhury, Ignasi Forné, Axel Imhof
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-021-93034-w

Altered expression of genes controlling metabolism characterizes the tissue response to immune injury in lupus
Cited by: 20
Author(s): Kathryn M. Kingsmore, Prathyusha Bachali, Michelle D. Catalina, Andrea R. Daamen, Sarah Heuer, Robert Robl, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 8
Published: over 3 years ago

10.3389/fcell.2021.653357

Combination of Immune-Related Genomic Alterations Reveals Immune Characterization and Prediction of Different Prognostic Risks in Ovarian Cancer
Cited by: 2
Author(s): Xibo Zhao, Shanshan Cong, Qiuyan Guo, Yan Cheng, Tian Liang, Jing Wang, Guangmei Zhang
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-020-3506-x

Negative binomial additive model for RNA-Seq data analysis
Cited by: 16
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-018-24758-5

Applications of Bayesian network models in predicting types of hematological malignancies
Cited by: 47
Author(s): Rupesh Agrahari, Amir Foroushani, T. Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
Software Mentions: 8
Published: over 6 years ago

10.3389/fcell.2021.712230

A Novel Ferroptosis-Related Prognostic Signature Reveals Macrophage Infiltration and EMT Status in Bladder Cancer
Cited by: 19
Author(s): Yi‐Lin Yan, Jinming Cai, Zhengnan Huang, Xiangqian Cao, Pengyu Tang, Zeyi Wang, Fang Zhang, Shujie Xia, Bing Shen
Software Mentions: 8
Published: over 3 years ago

10.3389/fmolb.2021.613359

Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer
Cited by: 10
Author(s): Minxiao Jiang, Ren Lang, Yuanlei Chen, Huan Wang, Haiyang Wu, Sheng Cheng, Gonghui Li, Shicheng Yu
Software Mentions: 8
Published: over 3 years ago

10.1186/s12906-020-02939-y

A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies
Cited by: 3
Author(s): Mengwei Ni, Xinkui Liu, Ziqi Meng, Shuyu Liu, Shanshan Jia, Yingying Liu, Wei Zhou, Jiarui Wu, Jingyuan Zhang, Siyu Guo, Jialin Li, Haojia Wang, Xiaomeng Zhang
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pcbi.1009148

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
Cited by: 12
Author(s): Pol Castellano‐Escuder, Raúl González‐Domínguez, Francesc Carmona-Pontaque, Cristina Andrés‐Lacueva, Álex Sánchez-Pla
Software Mentions: 8
Published: over 3 years ago

10.1111/jcmm.15601

Novel gene signatures for prognosis prediction in ovarian cancer
Cited by: 25
Author(s): Mingyang Bao, Lihua Zhang, Yue‐Qing Hu
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj.10682

Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis
Cited by: 7
Author(s): Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Software Mentions: 8
Published: over 3 years ago

10.7150/jca.49266

Establishment of the Prognostic Index Reflecting Tumor Immune Microenvironment of Lung Adenocarcinoma Based on Metabolism-Related Genes
Cited by: 13
Author(s): Jianguo Zhang, Jianzhong Zhang, Cheng Yuan, Yuan Luo, Yangyi Li, Panpan Dai, Wenjie Sun, Nannan Zhang, Jiangbo Ren, Mengjie Zhang, Yan Gong, Conghua Xie
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-021-95068-6

CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer
Cited by: 17
Author(s): Jun Yin, Chen Lin, Meng Jiang, Xuhai Tang, Danlin Xie, Jingwen Chen, Rongqin Ke
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.11599

A seven-lncRNA signature for predicting Ewing’s sarcoma
Cited by: 8
Author(s): Zhihui Chen, Xinyu Wang, Guozhu Wang, Bin Xiao, Zhe Ma, Hongliang Huo, Weiwei Li
Software Mentions: 8
Published: over 3 years ago

10.18632/aging.202670

A novel panel based on immune infiltration and tumor mutational burden for prognostic prediction in hepatocellular carcinoma
Cited by: 5
Author(s): Chengzhi Xie, Hewei Wu, Tao Pan, Xingrong Zheng, Xiaoàn Yang, Genglin Zhang, Yunwen Lian, Jiaxin Lin, Liang Peng
Software Mentions: 8
Published: over 3 years ago

10.1155/2020/2507074

A Network Pharmacology-Based Identification Study on the Mechanism of Xiao-Xu-Ming Decoction for Cerebral Ischemic Stroke
Cited by: 8
Author(s): Dehui Li, Yifan Su, Cheng-Yi Sun, Huanfang Fan, Weijuan Gao
Software Mentions: 8
Published: about 4 years ago

10.3389/fonc.2021.625007

Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid Cancer
Cited by: 7
Author(s): Yue Ma, Shi Yin, Xiaofeng Liu, Jing Hu, Ning Cai, Xiao-bei Zhang, Fu Li, Xuchen Cao, Yue Yu
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-021-04166-9

PTMViz: a tool for analyzing and visualizing histone post translational modification data
Cited by: 4
Author(s): Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-021-04123-6

The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma
Cited by: 19
Author(s): Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao, Yang Liu
Software Mentions: 8
Published: over 3 years ago

10.3389/fpls.2018.01632

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus
Cited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: about 6 years ago

10.1186/1471-2105-11-450

Filtering, FDR and power
Cited by: 43
Author(s): Maarten van Iterson, Judith M. Boer, Renée X. de Menezes
Software Mentions: 8
Published: about 14 years ago

10.3389/fonc.2019.01243

Identification of Subtype-Specific Three-Gene Signature for Prognostic Prediction in Diffuse Type Gastric Cancer
Cited by: 12
Author(s): Bowen Bao, Chunlei Zheng, Bowen Yang, Yue Jin, Kezuo Hou, Zhi Li, Xueying Zheng, Shitong Yu, Xiaojie Zhang, Yibo Fan, Xiujuan Qu, Yunpeng Liu, Xiaofang Che
Software Mentions: 8
Published: about 5 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: about 5 years ago

10.1186/s12957-021-02328-w

Identification of novel antioxidant gene signature to predict the prognosis of patients with gastric cancer
Cited by: 10
Author(s): Jianhua Wu, Xuan Wang, Nan Wang, Li Ma, Xin Xie, Hao Zhang, Huafeng Kang, Zhangjian Zhou
Software Mentions: 8
Published: over 3 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 3 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: over 3 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 3 years ago

10.1007/s00018-018-2898-5

Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: over 6 years ago

10.1097/MD.0000000000027374

Identification and validation of a hypoxia-related prognostic signature in clear cell renal cell carcinoma patients
Cited by: 7
Author(s): Zhengtian Li, Gang Du, Rong Zhao, Weibo Yang, Chan Li, Jun Huang, Zhenpei Wen, Hening Li, Bo Zhang
Software Mentions: 8
Published: about 3 years ago

10.1007/s00122-020-03667-0

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes
Cited by: 6
Author(s): Robert Richter, Susanne Rossmann, Doreen Gabriel, Reinhard Töpfer, Klaus Theres, Eva Zyprian
Software Mentions: 8
Published: over 4 years ago

10.7150/thno.55075

Single-cell transcriptome analysis of the heterogeneous effects of differential expression of tumor PD-L1 on responding TCR-T cells
Cited by: 2
Author(s): Renpeng Ding, Shang Liu, Shanshan Wang, Huanyi Chen, Fei Wang, Qumiao Xu, Linnan Zhu, Xuan Dong, Ying Gu, Xiuqing Zhang, Cheng‐Chi Chao, Qianqian Gao
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0164292

Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes
Cited by: 55
Author(s): T. Huibertus van Essen, Sake I. van Pelt, Inge H. G. Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J. van den Elsen, Pieter A. van der Velden, Didier Decaudin, Martine J. Jager
Software Mentions: 8
Published: about 8 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: about 6 years ago

10.1186/s12859-021-04114-7

Streamlining differential exon and 3′ UTR usage with diffUTR
Cited by: 3
Author(s): Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Software Mentions: 8
Published: over 3 years ago

10.3389/fnins.2021.613329

Integrated Transcriptional Profiling Analysis and Immune-Related Risk Model Construction for Intracranial Aneurysm Rupture
Cited by: 4
Author(s): Dezhi Shan, Xing Guo, Guozheng Yang, Zheng He, Rongrong Zhao, Hao Xue, Gang Li
Software Mentions: 8
Published: over 3 years ago

10.3389/fphys.2021.660906

Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek
Cited by: 6
Author(s): Ainash Childebayeva, Taylor Harman, Julien Weinstein, Trevor A. Day, Tom D. Brutsaert, Abigail W. Bigham
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0127163

Genetic Deletion of the Transcriptional Repressor NFIL3 Enhances Axon Growth In Vitro but Not Axonal Repair In Vivo
Cited by: 2
Author(s): L.R. van der Kallen, Ruben Eggers, Erich Ehlert, Joost Verhaagen, August B. Smit, Ronald E. van Kesteren
Software Mentions: 8
Published: over 9 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 3 years ago

10.1016/j.cell.2019.08.003

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Cited by: 170
Author(s): Rosina Pryor, Povilas Norvaišas, Γεώργιος Μαρίνος, Lena Best, Louise B. Thingholm, Leonor M. Quintaneiro, Wouter De Haes, Daniela Esser, Silvio Waschina, Celia Lujan, Reuben L. Smith, Timothy A. Scott, Daniel Martínez-Martínez, Orla Woodward, Kevin Bryson, Matthias Laudes, Wolfgang Lieb, Riekelt H. Houtkooper, André Franke, Liesbet Temmerman, Ivana Bjedov, Helena M. Cochemé, Christoph Kaleta, Filipe Cabreiro
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.00624

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma
Cited by: 53
Author(s): Nitish K. Mishra, Siddesh Southekal, Chittibabu Guda
Software Mentions: 8
Published: over 5 years ago

10.1016/j.isci.2021.102762

NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells
Cited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-48746-5

Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Cited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: about 5 years ago

10.1007/s13365-020-00931-3

Transcriptional signatures of Zika virus infection in astrocytes
Cited by: 3
Author(s): Blake Schouest, Tiffany A. Peterson, Dawn Szeltner, Elizabeth A. Scheef, Melody Baddoo, Nathan Ungerleider, Erik K. Flemington, Andrew G. MacLean, Nicholas J. Maness
Software Mentions: 8
Published: almost 4 years ago

10.3389/fgene.2019.00278

Identification of Prognostic Alternative Splicing Signature in Breast Carcinoma
Cited by: 25
Author(s): Dong Zhang, Yi Duan, Jinjing Cun, Qifeng Yang
Software Mentions: 8
Published: over 5 years ago

10.3390/cancers13143621

HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements
Cited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: over 3 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: about 4 years ago

10.1016/j.csbj.2020.06.023

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Cited by: 10
Author(s): Susan Idicula‐Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader
Software Mentions: 8
Published: almost 5 years ago

10.1002/1878-0261.12381

A pan‐cancer atlas of cancer hallmark‐associated candidate driver lnc <scp>RNA</scp> s
Cited by: 19
Author(s): Yulan Deng, Shangyi Luo, Xinxin Zhang, Chaoxia Zou, Huating Yuan, Gaoming Liao, Liwen Xu, Chunyu Deng, Yujia Lan, Tingting Zhao, Xu Gao, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-019-1855-4

Common DNA sequence variation influences 3-dimensional conformation of the human genome
Cited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: almost 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 4 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: over 9 years ago

10.1002/cam4.2493

Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidates
Cited by: 12
Author(s): Marco Antônio De Bastiani, Fábio Klamt
Software Mentions: 8
Published: about 5 years ago

10.3389/fonc.2020.00835

Development and Validation of a 12-Gene Immune Relevant Prognostic Signature for Lung Adenocarcinoma Through Machine Learning Strategies
Cited by: 14
Author(s): Xue Li, Guoshu Bi, Cheng Zhan, Yi Zhang, Yunfeng Yuan, Hong Fan
Software Mentions: 8
Published: over 4 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 6 years ago

10.3389/fonc.2020.574939

Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia Patients
Cited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: about 4 years ago

10.1186/s13059-019-1747-7

Cell type-specific epigenetic links to schizophrenia risk in the brain
Cited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
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 4 years ago

10.1084/jem.20201833

ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses
Cited by: 7
Author(s): Anna‐Maria Herzner, Zia Khan, Eric L. Van Nostrand, Sara M. Chan, Trinna Cuellar, Ronald Chen, Ximo Pechuan-Jorge, László G. Kömüves, Margaret Solon, Zora Modrušan, Benjamin Haley, G Yeo, Timothy W. Behrens, Matthew L. Albert
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2018.00100

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues
Cited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 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: over 6 years ago

10.3389/fmed.2021.644053

Comprehensive Analysis Identifies Potential Ferroptosis-Associated mRNA Therapeutic Targets in Ovarian Cancer
Cited by: 16
Author(s): Jiyan Zhang, Jie Xi, Ping Huang, Saitian Zeng
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: over 4 years ago

10.15252/msb.20199002

Endogenous fluctuations of <scp>OCT</scp> 4 and <scp>SOX</scp> 2 bias pluripotent cell fate decisions
Cited by: 35
Author(s): Daniel Strebinger, Cédric Deluz, Elias T Friman, Subashika Govindan, Andrea Brigitta Alber, David M. Suter
Software Mentions: 8
Published: about 5 years ago

10.1128/mBio.01369-21

HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 <sup>+</sup> T Cells Early Postinfection
Cited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.65508

Seroconversion stages COVID19 into distinct pathophysiological states
Cited by: 36
Author(s): Matthew D. Galbraith, Kohl T Kinning, Kelly D. Sullivan, Ryan M. Baxter, Paula Araya, Kimberly R. Jordan, Seth Russell, Keith P Smith, Ross E Granrath, Jessica Shaw, Monika Dzieciątkowska, Tusharkanti Ghosh, Andrew A. Monte, Angelo D’Alessandro, Kirk C. Hansen, Tellen D Benett, Elena W.Y. Hsieh, Joaquín M. Espinosa
Software Mentions: 8
Published: over 3 years ago

10.1128/mSystems.01356-20

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
Cited by: 26
Author(s): Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich
Software Mentions: 8
Published: over 3 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: almost 4 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 4 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: over 4 years ago

10.1186/s41065-021-00201-0

Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis
Cited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: about 3 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-017-3746-y

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
Cited by: 29
Author(s): Lihua Julie Zhu, Michael C. Lawrence, Ankit Gupta, Hervé Pagès, Alper Küçükural, Manuel Garber, Scot A. Wolfe
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 4 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: about 4 years ago

10.3389/fonc.2020.590006

AUNIP Expression Is Correlated With Immune Infiltration and Is a Candidate Diagnostic and Prognostic Biomarker for Hepatocellular Carcinoma and Lung Adenocarcinoma
Cited by: 14
Author(s): Chenxi Ma, Wenyan Kang, Lu Yu, Zongcheng Yang, Di Tian
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pmed.1002223

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
Cited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: almost 8 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: almost 5 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: about 5 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 3 years ago

10.1093/bib/bbv069

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
Cited by: 45
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 8
Published: about 9 years ago

10.3389/fendo.2020.561370

Adropin Stimulates Proliferation and Inhibits Adrenocortical Steroidogenesis in the Human Adrenal Carcinoma (HAC15) Cell Line
Cited by: 14
Author(s): Ewelina Stelcer, Paulina Milecka, Hanna Komarowska, Karol Jopek, Marianna Tyczewska, Marta Szyszka, Marta Leśniczak, Wiktoria Suchorska, Karlygash Bekova, Beata Szczepaniak, Marek Ruchała, Marek Karczewski, T Wierzbicki, Witold Szaflarski, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 8
Published: about 4 years ago

10.3390/cancers13051113

MPscore: A Novel Predictive and Prognostic Scoring for Progressive Meningioma
Cited by: 12
Author(s): Feili Liu, Jin Qian, Chenkai Ma
Software Mentions: 8
Published: over 3 years ago

10.1002/cam4.2665

Genome‐wide screening of abberant methylated drivers combined with relative risk loci in bladder cancer
Cited by: 2
Author(s): Chuanjie Zhang, Kangjie Shen, Yuxiao Zheng, Feng Qi, Jun Luo
Software Mentions: 8
Published: almost 5 years ago

10.3390/cancers13071561

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma
Cited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.ppat.1009602

Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire
Cited by: 5
Author(s): Ivy K. Brown, Nathan Dyjack, Mindy M. Miller, S. Harsha Krovi, Cydney Rios, Rachel A. Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P. O’Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A. Seibold, James Scott‐Browne, Radleigh Santos, R. Lee Reinhardt
Software Mentions: 8
Published: over 3 years ago

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