Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: edgeR

https://packages.ecosyste.ms/registries/bioconductor.org/packages/edgeR

Empirical Analysis of Digital Gene Expression Data in R
3 versions
Latest release: about 1 year ago
166 dependent packages
2,704,225 downloads total

Papers Mentioning edgeR 6,568

10.1038/s41598-021-90797-0
Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19
Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: over 3 years ago
10.1093/jxb/eraa124
Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: almost 5 years ago
10.1186/s40064-016-2743-y
Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis
Cited by: 9
Author(s): Jun Fan, Xiuping Chen, Wen-shun Hu, Shaoquan Zheng
Software Mentions: 5
Published: over 8 years ago
10.7150/thno.47081
Targeted inhibition of KDM6 histone demethylases eradicates tumor-initiating cells via enhancer reprogramming in colorectal cancer
Cited by: 20
Author(s): Junbao Zhang, Ying Ying, Meiqi Li, Maolin Wang, Xiaoyan Huang, Min Jia, Junhui Zeng, Canjie Ma, Yixiang Zhang, Chen Li, Xiaomei Wang, Xing-sheng Shu
Software Mentions: 5
Published: almost 5 years ago
10.3389/fmicb.2017.00398
Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines
Cited by: 30
Author(s): Brendan R E Ansell, Louise Baker, Samantha J. Emery, Malcolm J. McConville, Staffan G. Svärd, Robin B. Gasser, Aaron R. Jex
Software Mentions: 5
Published: almost 8 years ago
10.3389/fgene.2021.670749
Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression
Cited by: 5
Author(s): Haifeng Xu, Tonje G. Lien, Helga Bergholtz, Thomas Fleischer, Lounes Djerroudi, Anne Vincent‐Salomon, Thérese Sørlie, Tero Aittokallio
Software Mentions: 5
Published: over 3 years ago
10.1155/2021/6642939
Identification of a Potential PPAR-Related Multigene Signature Predicting Prognosis of Patients with Hepatocellular Carcinoma
Cited by: 7
Author(s): Wenfang Xu, Zhe Chen, Gang Liu, Yong Dai, Xuanfu Xu, Duan Ma, Lei Liu
Software Mentions: 5
Published: almost 4 years ago
10.3389/fphar.2020.599760
Modulation of the Gut Microbiota and Liver Transcriptome by Red Yeast Rice and Monascus Pigment Fermented by Purple Monascus SHM1105 in Rats Fed with a High-Fat Diet
Cited by: 10
Author(s): Hua Yang, Ronghua Pan, Jing Wang, Lizhong Zheng, Zhenjing Li, Qingbin Guo, Changlu Wang
Software Mentions: 5
Published: almost 4 years ago
10.3389/fimmu.2018.02406
Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome Sequencing
Cited by: 15
Author(s): Endika Varela-Martínez, Naiara Abendaño, Javier Asín, Maialen Sistiaga-Poveda, Marta Pérez, Ramsés Reina, D. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 5
Published: about 6 years ago
10.1002/ece3.6930
Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets
Cited by: 0
Author(s): Kristin L. Sikkink, Nathan W. Bailey, Marlene Zuk, Susan L. Balenger
Software Mentions: 5
Published: about 4 years ago
10.3389/fmicb.2020.00582
Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes
Cited by: 12
Author(s): Sainur Samad, Hyo‐Jung Lee, Sławek Cerbin, Marion Meima-Franke, Paul L. E. Bodelier
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2018.00441
Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: about 6 years ago
10.3389/fgene.2021.730003
Identification of Autophagy Related circRNA-miRNA-mRNA-Subtypes Network With Radiotherapy Responses and Tumor Immune Microenvironment in Non-small Cell Lung Cancer
Cited by: 12
Author(s): Limin Fan, Baosheng Li, Li Zhao, Liang Sun
Software Mentions: 5
Published: over 3 years ago
10.1155/2020/3817573
Diet Modifies Pioglitazone’s Influence on Hepatic PPAR<i>γ</i>-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: over 4 years ago
10.1155/2013/481545
Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: over 11 years ago
10.1098/rsos.200792
Tissue-specific developmental regulation and isoform usage underlie the role of<i>doublesex</i>in sex differentiation and mimicry in<i>Papilio</i>swallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-021-90095-9
miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta
Cited by: 1
Author(s): Iram P. Rodríguez‐Sánchez, Daniel Rafael Saldaña-Torres, Olga Karina Villanueva-Segura, María Lourdes Garza‐Rodríguez, Mayra A. Gómez‐Govea, Ghongwei Liang, María de Lourdes Ramírez‐Ahuja, Margarita L. Martínez‐Fierro, Iván Delgado‐Enciso, Laura Elia Martínez-de-Villarreal, Yu Zhou, Adriana E. Flores-Suárez, Xi Chen, Diana Reséndez‐Pérez, Chenyu Zhang, Gustavo Ponce‐García
Software Mentions: 5
Published: over 3 years ago
10.3389/fnins.2018.00136
Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
Cited by: 4
Author(s): Sofie Derycke, Loïc Kéver, Koen Herten, Koen Van Den Berge, Maarten Van Steenberge, Jeroen Van Houdt, Lieven Clement, Pascal Poncin, Éric Parmentier, Erik Verheyen
Software Mentions: 5
Published: almost 7 years ago
10.3389/fonc.2020.01088
MMP25 Regulates Immune Infiltration Level and Survival Outcome in Head and Neck Cancer Patients
Cited by: 8
Author(s): Yujie Liang, Chenyu Guan, Kan Li, Guanghui Zheng, Tao Wang, Sien Zhang, Guiqing Liao
Software Mentions: 5
Published: over 4 years ago
10.3389/fnins.2020.607215
Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer’s and Parkinson’s Brains With Digital Cytometry
Cited by: 5
Author(s): Marie Catherine Bordone, Nuno L. Barbosa‐Morais
Software Mentions: 5
Published: about 4 years ago
10.3389/fgene.2019.01347
Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating Sows
Cited by: 11
Author(s): Jiajie Sun, Haojie Zhang, Bao-Yu Hu, Yueqin Xie, Dongyang Wang, Jinzhi Zhang, Ting Chen, Junyi Luo, Songbo Wang, Qinyan Jiang, Qianyun Xi, Zujing Chen, Yongliang Zhang
Software Mentions: 5
Published: almost 5 years ago
10.3389/fgene.2019.01207
Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus
Cited by: 26
Author(s): Sarah-Anne David, Anaïs Vitorino Carvalho, Coralie Gimonnet, Aurélien Brionne, Christelle Hennequet-Antier, Benoît Piégu, Sabine Crochet, Nathalie Couroussé, Thierry Bordeau, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 5
Published: about 5 years ago
10.3389/fnins.2019.00002
A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Cited by: 51
Author(s): Shradha Mukherjee, Christine Klaus, Mihaela Pricop-Jeckstadt, Jeremy A. Miller, Felix L Struebing
Software Mentions: 5
Published: almost 6 years ago
10.3389/fgene.2015.00169
Identifying differential transcription factor binding in ChIP-seq
Cited by: 21
Author(s): Dai-Ying Wu, Danielle Bittencourt, Michael R. Stallcup, Kimberly D. Siegmund
Software Mentions: 5
Published: over 9 years ago
10.3389/fgene.2019.00766
Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: over 5 years ago
10.7554/eLife.27014
Regulation of life span by the gut microbiota in the short-lived African turquoise killifish
Cited by: 262
Author(s): Patrick M. Smith, David Willemsen, Miriam Popkes, Franziska Metge, Edson Gandiwa, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 5
Published: over 7 years ago
10.7554/eLife.33480
Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
Cited by: 86
Author(s): David A. Knowles, Courtney K Burrows, John Blischak, Kristen Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 5
Published: over 6 years ago
10.1007/s00442-019-04499-6
Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis
Cited by: 20
Author(s): Thomas M. Lilley, Jenni M. Prokkola, Anna Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomáš Bartonička, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 5
Published: over 5 years ago
10.3389/fmicb.2021.705712
Dual Transcriptomic Analyses Unveil Host–Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks (Anas platyrhynchos)
Cited by: 1
Author(s): Yu Zhang, Lina Song, Li-e Hou, Zhen Cao, Wanwipa Vongsangnak, Guoqiang Zhu, Qi Xu, Guohong Chen
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0184471
Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: over 7 years ago
10.3389/fonc.2021.745166
A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma
Cited by: 6
Author(s): Yuan Fang, Yang Yang, Xiaoli Zhang, Na Li, Bo Yuan, Li Jin, Sheng Bao, Mengge Li, Dan Zhao, Lingrui Li, Zhong Zeng, Hanfei Huang
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0119027
Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: almost 10 years ago
10.3389/fimmu.2020.558036
The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models
Cited by: 14
Author(s): Qiu-Lan Ma, Cansheng Zhu, Marco Morselli, Trent Su, Matteo Pelligrini, Zhengqi Lu, Mychica Jones, Paul Denver, Daniel Castro, Xiaohong Gu, Frances Relampagos, Kaitlin Caoili, Bruce Teter, Sally A. Frautschy, Gregory M. Cole
Software Mentions: 5
Published: about 4 years ago
10.3389/fgene.2020.616998
Application of an Autophagy-Related Gene Prognostic Risk Model Based on TCGA Database in Cervical Cancer
Cited by: 16
Author(s): Huadi Shi, Fulan Zhong, Xiaoqiong Yi, Zhenyi Shi, Feiyan Ou, Zhonghua Xu, Yufang Zuo
Software Mentions: 5
Published: almost 4 years ago
10.1007/s00122-020-03712-y
The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding
Cited by: 38
Author(s): Liangliang Gao, Dal Hoe Koo, Philomin Juliana, Trevor W. Rife, Daljit Singh, Cristiano Lemes da Silva, Thomas Lux, Kevin M. Dorn, Marshall Clinesmith, Paula Silva, Xu Wang, Manuel Spannagl, Cécile Monat, Bernd Friebe, Burkhard Steuernagel, Gary J. Muehlbauer, Sean Walkowiak, Curtis Pozniak, Ravi P. Singh, Nils Stein, Martin Mascher, Allan K. Fritz, Jesse Poland
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0252685
Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2021.663556
Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer
Cited by: 14
Author(s): Yang Liu, Hefen Sun, Xuan Li, Qiqi Liu, Yuanyuan Zhao, Liangdong Li, Baojin Xu, Yifeng Hou, Wei Jin
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-85669-6
Transcriptome of rhesus macaque (Macaca mulatta) exposed to total-body irradiation
Cited by: 12
Author(s): Yaoxiang Li, Jatinder Singh, Rency S. Varghese, Yubo Zhang, Oluseyi O. Fatanmi, Amrita K. Cheema, Vijay K. Singh
Software Mentions: 5
Published: almost 4 years ago
10.3389/fonc.2020.01195
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model
Cited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2020.00055
Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma
Cited by: 14
Author(s): Wenjie Wang, Han Wang, Ting-yan Hua, Wei Song, Jie Zhu, Jingjing Wang, Yongzhen Huang, Zhi-Liang Ding
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41598-021-92610-4
Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-86544-0
An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.62850
Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.42819
Shank3 modulates sleep and expression of circadian transcription factors
Cited by: 56
Author(s): Ashley M Ingiosi, Hannah Schoch, Taylor Wintler, Kristan G. Singletary, Dario Righelli, Leandro Gabriel Roser, E Medina, Davide Risso, Marcos G. Frank, Lucı́a Peixoto
Software Mentions: 5
Published: over 5 years ago
10.3389/fonc.2021.637733
Low Expression of ADCY4 Predicts Worse Survival of Lung Squamous Cell Carcinoma Based on Integrated Analysis and Immunohistochemical Verification
Cited by: 3
Author(s): Zhicong Liu, Lixin Ru, Zhenchao Ma
Software Mentions: 5
Published: over 3 years ago
10.7150/thno.47137
USP7 targeting modulates anti-tumor immune response by reprogramming Tumor-associated Macrophages in Lung Cancer
Cited by: 87
Author(s): Xiaomeng Dai, Lisen Lu, Suke Deng, Jingshu Meng, Chao Wan, Jing Huang, Yajie Sun, Yan Hu, Bian Wu, Gang Wu, Jonathan F. Lovell, Jin Huang, Kunyu Yang
Software Mentions: 5
Published: almost 5 years ago
10.3390/genes11050499
Unmasking Intra-Tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
Cited by: 2
Author(s): Chang In Moon, William Tompkins, Yuxi Wang, Abigail Godec, Xiaochun Zhang, Patrik Pipkorn, Christopher A. Miller, Carina Dehner, Sonika Dahiya, Angela C. Hirbe
Software Mentions: 5
Published: over 4 years ago
10.1186/s12931-019-1085-z
Airway host-microbiome interactions in chronic obstructive pulmonary disease
Cited by: 82
Author(s): Zhang Wang, Barbara Maschera, Simon Lea, Umme Kolsum, David Michalovich, Stephanie Van Horn, Christopher Traini, James R. Brown, Edith M. Hessel, Dave Singh
Software Mentions: 5
Published: over 5 years ago
10.3389/fonc.2021.691372
Prognostic Signature of Hepatocellular Carcinoma and Analysis of Immune Infiltration Based on m6A-Related lncRNAs
Cited by: 6
Author(s): Ting Guo, Kun He, Yifei Wang, Jingjing Sun, Yong Chen, Zelong Yang
Software Mentions: 5
Published: over 3 years ago
10.1534/g3.118.200852
Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant <i>Ferula assafoetida</i>
Cited by: 21
Author(s): Hajar Amini, Mohammad Reza Naghavi, Tong Shen, Yanhong Wang, Jaber Nasiri, Ikhlas A. Khan, Oliver Fiehn, Philipp Zerbe, Julin Maloof
Software Mentions: 5
Published: almost 6 years ago
10.1155/2018/7691794
Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse
Cited by: 6
Author(s): Minjung Kim, Yi Yin Yu, Ji-Hoi Moon, Insong Koh, Jae Hyung Lee
Software Mentions: 5
Published: almost 7 years ago
10.1186/s13029-017-0063-4
DEApp: an interactive web interface for differential expression analysis of next generation sequence data
Cited by: 63
Author(s): Yan Li, Jorge Andrade
Software Mentions: 5
Published: almost 8 years ago
10.3389/fimmu.2019.01463
Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats
Cited by: 17
Author(s): Sajad A. Wani, Anamika Sahu, Raja Ishaq Nabi Khan, Awadh Bihari Pandey, Shikha Saxena, Neelima Hosamani, Waseem Akram Malla, Dheeraj Chaudhary, Sonam Kanchan, V. K. Sah, Kaushal Kishor Rajak, D. Muthuchelvan, Bina Mishra, Ashok Kumar Tiwari, Aditya Prasad Sahoo, Basavaraj Sajjanar, Yash Pal Singh, Ravi Kumar Gandham, Bishnu Prasad Mishra, Raj Kumar Singh
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pone.0227303
Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: almost 5 years ago
10.3389/fonc.2021.616576
LncRNA FENDRR in Carcinoma-Associated Fibroblasts Regulates the Angiogenesis of Oral Squamous Cell Carcinoma Through the PI3K/AKT Pathway
Cited by: 4
Author(s): Yuming Xu, Erhui Jiang, Zhang Shao, Zhengjun Shang
Software Mentions: 5
Published: over 3 years ago
10.3389/fimmu.2021.640837
Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy
Cited by: 1
Author(s): Khushboo Singh, Hai Fang, Graham Davies, Benjamin Wright, Helen Lockstone, Richard O. Williams, Daniela Čiháková, Julian C. Knight, Shoumo Bhattacharya
Software Mentions: 5
Published: almost 4 years ago
10.3389/fonc.2021.626187
Dysregulation of Transcription Factor Networks Unveils Different Pathways in Human Papillomavirus 16-Positive Squamous Cell Carcinoma and Adenocarcinoma of the Uterine Cervix
Cited by: 9
Author(s): Saloê Bispo, Ticiana Della Justina Farias, Patrícia Savio de Araujo-Souza, Ricardo Cintra, Hellen Geremias dos Santos, Natasha Andressa Nogueira Jorge, Mauro A. A. Castro, Gabriel Wajnberg, Nicole de Miranda Scherer, Maria Luiza Nogueira Dias Genta, Jesus Paula Carvalho, Luísa Lina Villa, Laura Sichero, Fábio Passetti
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2021.640272
Identification of Novel Alternative Splicing Events Associated With Tumorigenesis, Protein Modification, and Immune Microenvironment in Early-Onset Gastric Cancer
Cited by: 4
Author(s): Jian Zhang, Ajay Goel, Lin Zhu
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2021.632571
Prediction of Biochemical Recurrence-Free Survival of Prostate Cancer Patients Leveraging Multiple Gene Expression Profiles in Tumor Microenvironment
Cited by: 10
Author(s): Rui Zhou, Yuanfa Feng, Jian‐Heng Ye, Zhengxue Han, Yu‐Xiang Liang, Qing-Biao Chen, Xiaoming Xu, Yuhan Huang, Zhenyu Jia, Weide Zhong
Software Mentions: 5
Published: about 3 years ago
10.1093/hmg/ddab031
Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma
Cited by: 10
Author(s): Ruhina Shirin Laskar, Peng Li, Szilvia Ecsedi, Behnoush Abedi‐Ardekani, G. Durand, Nivonirina Robinot, Jean-Noël Hubert, Vladimí­r Janout, Давид Заридзе, Anush Mukeria, Dana Mateș, Ivana Holcátová, Lenka Foretová, Beata Świątkowska, Zoran Džamić, Saša Milosavljević, Robert Olaso, Anne Boland, Jean‐François Deleuze, David C. Muller, James McKay, Paul Brennan, Florence Le Calvez-Kelm, Ghislaine Scélo, Estelle Chanudet
Software Mentions: 5
Published: almost 4 years ago
10.3389/fmicb.2020.562775
Response of Soil Fungal Community to Drought-Resistant Ea-DREB2B Transgenic Sugarcane
Cited by: 7
Author(s): Xue Zhao, Qi Liu, Sasa Xie, Yuke Jiang, Hao Yang, Ziting Wang, Muqing Zhang
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.ppat.1009346
Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors
Cited by: 27
Author(s): Stuart R. Jefferys, Samuel D. Burgos, Jackson J Peterson, Sara R. Selitsky, Anne-Marie W. Turner, Lindsey I. James, Yi-Hsuan Tsai, Alisha R. Coffey, David M. Margolis, Joel S. Parker, Edward P. Browne
Software Mentions: 5
Published: almost 4 years ago
10.3389/fimmu.2019.00330
Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: almost 6 years ago
10.3389/fimmu.2018.02055
Molecular and Cellular Response to Experimental Anisakis pegreffii (Nematoda, Anisakidae) Third-Stage Larval Infection in Rats
Cited by: 19
Author(s): Ivana Bušelić, Željka Trumbić, Jerko Hrabar, Anamarija Vrbatović, Ivana Bočina, Ivona Mladineo
Software Mentions: 5
Published: over 6 years ago
10.3390/genes11050504
Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory Intervals
Cited by: 5
Author(s): Ruoyu Tian, Yidan Pan, Thomas H A Etheridge, Harshavardhan Deshmukh, Dalia Gulick, Greg Gibson, Gang Bao, Ciaran M. Lee
Software Mentions: 5
Published: over 4 years ago
10.1186/s13072-021-00417-4
Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Cited by: 2
Author(s): Ning Liu, Wai Yee Low, Hamid Alinejad‐Rokny, Stephen Pederson, Timothy Sadlon, Simon C. Barry, James Breen
Software Mentions: 5
Published: over 3 years ago
10.1002/ece3.6308
Oxidative stress delays development and alters gene expression in the agricultural pest moth, <i>Helicoverpa armigera</i>
Cited by: 7
Author(s): Nonthakorn Apirajkamol, Bill James, Karl Gordon, Tom Walsh, Angela McGaughran
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-018-36471-4
Astrocytoma progression scoring system based on the WHO 2016 criteria
Cited by: 12
Author(s): Zhen-Hang Li, Yanlei Guan, Qiang Liu, Yao Wang, Run Cui, Yunjie Wang
Software Mentions: 5
Published: almost 6 years ago
10.1126/sciadv.abd7819
High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: almost 4 years ago
10.1530/ERC-19-0474
A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/− rats
Cited by: 15
Author(s): James F. Powers, Brent Cochran, James D. Baleja, Hadley D. Sikes, Andrew Pattison, Xue Zhang, Inna Lomakin, Annette Shepard-Barry, Karel Pacák, Sun Jin Moon, Troy F. Langford, Kassi T. Stein, Richard W. Tothill, Ying-Bin Ouyang, Arthur S. Tischler
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.ppat.1008986
Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: about 4 years ago
10.1186/s13072-021-00399-3
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome
Cited by: 8
Author(s): William T. Jordan, Erica Larschan
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2021.663787
Integrated Analysis of Microarray and RNA-Seq Data for the Identification of Hub Genes and Networks Involved in the Pancreatic Cancer
Cited by: 10
Author(s): Maryum Nisar, Rehan Zafar Paracha, Iqra Arshad, Sidra Adil, Sabaoon Zeb, Rumeza Hanif, Mehak Rafiq, Zamir Hussain
Software Mentions: 5
Published: over 3 years ago
10.1186/s13072-017-0137-1
Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid
Cited by: 32
Author(s): Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry, Gaël Le Trionnaire
Software Mentions: 5
Published: over 7 years ago
10.1167/iovs.18-24101
Ascorbate Suppresses VEGF Expression in Retinal Pigment Epithelial Cells
Cited by: 20
Author(s): David W. Sant, Vladimir Camarena, Sushmita Mustafi, Yiwen Li, Zachary Wilkes, Derek Van Booven, Rong Wen, Gaofeng Wang
Software Mentions: 5
Published: over 6 years ago
10.1186/s13072-018-0230-0
CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands
Cited by: 19
Author(s): Louie N. van de Lagemaat, Maria Flenley, Magnus Lynch, David Garrick, Simon R. Tomlinson, Kamil R. Kranc, Douglas Vernimmen
Software Mentions: 5
Published: about 6 years ago
10.1186/s13045-020-01005-x
RNA sequencing: new technologies and applications in cancer research
Cited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: about 4 years ago
10.1080/15592294.2019.1710913
A regulatory role for CHD2 in myelopoiesis
Cited by: 5
Author(s): Farzaneh Shahin Varnoosfaderani, Anna M. Palau, Wenbo Dong, Jenna Persson, Mickaël Durand-Dubief, J. Peter Svensson, Andreas Lennartsson
Software Mentions: 5
Published: almost 5 years ago
10.1534/g3.118.200540
Regulation of Root Angle and Gravitropism
Cited by: 19
Author(s): Ted Toal, Mily Ron, Donald J Gibson, Kaisa Kajala, Bessie L. Splitt, Logan Johnson, Nathan D. Miller, Radka Slovak, Allison Gaudinier, Rohan Patel, Miguel de Lucas, Nicholas J. Provart, Edgar P. Spalding, Wolfgang Busch, Daniel J. Kliebenstein, Siobhán M. Brady
Software Mentions: 5
Published: about 6 years ago
10.3389/fmolb.2021.689037
Analyzing and Validating the Prognostic Value of a TNF-Related Signature in Kidney Renal Clear Cell Carcinoma
Cited by: 5
Author(s): Wenhao Zhang, Chang-Jiu Li, Fanding Wu, Ning Li, Yuwei Wang, Yixuan Hu, Tiantian Fang, Yuan Hui, Honghua He
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2019.01497
Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment
Cited by: 27
Author(s): Rongfang Shen, Ping Li, Bing Li, Botao Zhang, Feng Li, Shujun Cheng
Software Mentions: 5
Published: almost 5 years ago
10.3389/fmicb.2020.00360
Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants
Cited by: 16
Author(s): Maria Petronella Human, David Kenneth Berger, Bridget Genevieve Crampton
Software Mentions: 5
Published: almost 5 years ago
10.1186/s13072-020-00359-3
UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells
Cited by: 5
Author(s): Beisi Xu, Brett B. Mulvey, Muneeb Salie, Xiaoyang Yang, Yurika Matsui, Anjana Nityanandam, Yiping Fan, Jamy C. Peng
Software Mentions: 5
Published: about 4 years ago
10.3389/fmolb.2021.716544
GeneTrail: A Framework for the Analysis of High-Throughput Profiles
Cited by: 1
Author(s): Nico Gerstner, Tim Kehl, Kerstin Lenhof, Lea Eckhart, Lara Schneider, Daniel Stöckel, Christina Backes, Eckart Meese, Andreas Keller, Hans‐Peter Lenhof
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2021.634116
A Novel Six-mRNA Signature Predicts Survival of Patients With Glioblastoma Multiforme
Cited by: 8
Author(s): Zhentao Liu, Hao Zhang, Haitao Hu, Zengyu Cai, Chengyin Lu, Qiang Liang, Jun Qian, Chunhui Wang, Lei Jiang
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-018-33718-y
A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: about 6 years ago
10.1002/eji.201847897
Expression of IL‐7Rα and KLRG1 defines functionally distinct CD8 <sup>+</sup> T‐cell populations in humans
Cited by: 24
Author(s): Ester B. M. Remmerswaal, Pleun Hombrink, Benjamin Nota, Hanspeter Pircher, Ineke J. M. ten Berge, René A. W. van Lier, Michiel C. van Aalderen
Software Mentions: 5
Published: over 5 years ago
10.3389/fgene.2020.00505
Analysis of Circular RNA-Related Competing Endogenous RNA Identifies the Immune-Related Risk Signature for Colorectal Cancer
Cited by: 16
Author(s): Wei Song, Jun Ren, Chuntao Wang, Yuhang Ge, Tao Fu
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-018-36768-4
Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: almost 6 years ago
10.1093/femsyr/foab011
Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production
Cited by: 2
Author(s): Leonie Baumann, Tyler W. Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.51796
A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brain
Cited by: 44
Author(s): Lihong Zhan, Li Fan, Lay Kodama, Peter Sohn, Man Ying Wong, Gergey Alzaem Mousa, Yungui Zhou, Yaqiao Li, Li Gan
Software Mentions: 5
Published: about 4 years ago
10.3389/fonc.2021.685980
Role of NRP1 in Bladder Cancer Pathogenesis and Progression
Cited by: 15
Author(s): Yun Dong, Weiming Ma, Zengliang Shi, Zhiguo Zhang, Jing Zhou, Yang Li, Shaoqi Zhang, Kun Pang, Bibo Li, Wen-da Zhang, Tao Fan, Guanghao Zhu, Xue Li, Rui Li, Ying Liu, Lin Hao, Conghui Han
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2019.00912
Construction of a Competitive Endogenous RNA Network and Identification of Potential Regulatory Axis in Gastric Cancer
Cited by: 21
Author(s): Hongda Pan, Chen Guo, Jianji Pan, Dongwei Guo, Shibo Song, Ye Zhou, Dazhi Xu
Software Mentions: 5
Published: about 5 years ago
10.1038/s41598-018-29993-4
Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: over 6 years ago
10.3389/fnmol.2018.00481
Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency
Cited by: 30
Author(s): A. Ayanna Wade, Kenneth J. Lim, Rinaldo Catta-Preta, Alexander Nord
Software Mentions: 5
Published: almost 6 years ago
10.1002/ece3.7434
Tree diversity and functional leaf traits drive herbivore‐associated microbiomes in subtropical China
Cited by: 1
Author(s): Yang Li, Douglas Chesters, Ming‐Qiang Wang, Tesfaye Wubet, Andreas Schuldt, Perttu Anttonen, Pengfei Guo, Jing‐Ting Chen, Qianxiong Zhou, Nai‐Li Zhang, Keping Ma, Helge Bruelheide, Chunsheng Wu, Chao‐Dong Zhu
Software Mentions: 5
Published: over 3 years ago
10.1155/2021/8880585
Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2019.00689
Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle
Cited by: 6
Author(s): Anna Lewandowska-Sabat, Е. В. Кирсанова, Christophe Klopp, T. R. Solberg, B. Heringstad, Olav Østerås, Preben Boysen, I. Olsaker
Software Mentions: 5
Published: over 5 years ago
10.3390/genes10070552
Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation
Cited by: 14
Author(s): Xitong Zhao, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Ai Hong, Kai Xing, Chuduan Wang
Software Mentions: 5
Published: over 5 years ago
10.1111/eva.12278
Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tracts
Cited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: over 9 years ago