bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/jcm9092730

Metastatic Burden Defines Clinically and Biologically Distinct Subgroups of Stage 4 High-Risk Neuroblastoma
Cited by: 2
Author(s): Eun Seop Seo, Eun-Jin Lee, Boram Lee, Min Jae Shin, Young-Seok Cho, Hee Young Ju, Hee Won Cho, Hee Young Ju, Keon Hee Yoo, Hong Hoe Koo, Ji Won Lee, Ki Woong Sung
Software Mentions: 5
Published: over 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

10.1128/AEM.00338-19

Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in Rhodonia ( Postia ) placenta
Cited by: 13
Author(s): Inger Skrede, Monica Hongrø Solbakken, Jaqueline Hess, Carl Gunnar Fossdal, Olav A. Hegnar, Gry Alfredsen
Software Mentions: 5
Published: over 5 years ago

10.1002/jcp.28522

Comprehensive analysis of a ceRNA network reveals potential prognostic cytoplasmic lncRNAs involved in HCC progression
Cited by: 84
Author(s): Yi Bai, Junyu Long, Zhisong Liu, Jianzhen Lin, Hanchan Huang, Dongxu Wang, Yang Xu, Fei Miao, Yilei Mao, Xinting Sang, Hong Zhao
Software Mentions: 5
Published: over 5 years ago

10.1016/j.devcel.2020.11.013

Diverse Routes toward Early Somites in the Mouse Embryo
Cited by: 40
Author(s): Carolina Guibentif, J. B. Griffiths, Iván Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni
Software Mentions: 5
Published: almost 4 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

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: about 9 years ago

10.1242/dev.194761

Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns
Cited by: 30
Author(s): Milica Bulajić, Divyanshi Srivastava, Jeremy S. Dasen, Hynek Wichterle, Shaun Mahony, Esteban O. Mazzoni
Software Mentions: 5
Published: almost 5 years ago

10.1111/jcmm.14886

Expression signature of six‐snoRNA serves as novel non‐invasive biomarker for diagnosis and prognosis prediction of renal clear cell carcinoma
Cited by: 28
Author(s): Yimeng Zhao, Yuanyuan Yan, Rong Ma, Xuemei Lv, Liwen Zhang, Jinlong Wang, Wenjing Zhu, Liang Zhao, Longyang Jiang, Lin Zhao, Lijie Wen, Bo Yang, Yu Zong Chen, Miao He, Mingyan Liu, Minjie Wei
Software Mentions: 5
Published: almost 5 years ago

10.3390/v13061129

Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout
Cited by: 4
Author(s): Irene Cano, Eduarda M. Santos, Karen Moore, Audrey Farbos, Ronny van Aerle
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: almost 4 years ago

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22062901

Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen
Cited by: 7
Author(s): Fulin Liu, Christelle Simasotchi, Françoise Vibert, Wencan Zhu, Sophie Gil, Séverine A. Degrelle, Thierry Fournier
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-020-03691-3

Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Cited by: 31
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 5
Published: over 4 years ago

10.3390/insects11060326

Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects
Cited by: 0
Author(s): Yujun Wang, Hua-Ling Wang, Xiaowei Wang, Shu‐Sheng Liu
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 6 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.3390/biology10010039

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets
Cited by: 11
Author(s): Adeel Malik, Chang-Bae Kim
Software Mentions: 5
Published: almost 4 years ago

10.3389/fendo.2021.632060

Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Transcriptomic Stress Response
Cited by: 8
Author(s): Suzanne H. Austin, Rayna M. Harris, April M. Booth, Andrew S. Lang, Victoria S. Farrar, Jesse S. Krause, Tyler A. Hallman, Matthew D. MacManes, Rebecca M. Calisi
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-015-2040-0

Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study
Cited by: 27
Author(s): Philip Shaw, Sastra Chaotheing, Pavita Kaewprommal, Jittima Piriyapongsa, Chayaphat Wongsombat, Nattida Suwannakitti, Pongpisid Koonyosying, Chairat Uthaipibull, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-020-68949-5

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 4 years ago

10.7150/jca.52187

Centromere Protein F (CENPF) Serves as a Potential Prognostic Biomarker and Target for Human Hepatocellular Carcinoma
Cited by: 15
Author(s): Yugang Huang, Xiuwen Chen, Li Wang, Tieyan Wang, Xianbin Tang, Xiaomin Su
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-018-4987-0

PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans
Cited by: 16
Author(s): Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman, Stephan Schneider
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-021-07849-y

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat
Cited by: 7
Author(s): Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 5
Published: over 3 years ago

10.1002/cti2.1093

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus
Cited by: 39
Author(s): William A. Figgett, Katherine Monaghan, Milica Ng, Monther Alhamdoosh, Eugene Maraskovsky, Nicholas J. Wilson, Alberta Hoi, Eric F Morand, Fabienne Mackay
Software Mentions: 5
Published: almost 6 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

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
Software Mentions: 5
Published: over 3 years ago

10.1186/s12936-019-2659-4

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites
Cited by: 7
Author(s): Abhinay Ramaprasad, Amit Kumar Subudhi, Richard Culleton, Arnab Pain
Software Mentions: 5
Published: almost 6 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.2020.00505

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/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 4 years ago

10.3390/vaccines8030438

Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection
Cited by: 4
Author(s): Kelsey O’Dowd, Mehdi Emam, Mohamed Reda El Khili, Amin Emad, Eveline M. Ibeagha‐Awemu, Carl A. Gagnon, Neda Barjesteh
Software Mentions: 5
Published: over 4 years ago

10.1016/j.isci.2020.101249

Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer
Cited by: 5
Author(s): Asha Nair, Xiaojia Tang, Kevin J. Thompson, Peter T. Vedell, Krishna R. Kalari, Subbaya Subramanian
Software Mentions: 5
Published: over 4 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

10.3389/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/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

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: about 5 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

10.3390/metabo10020066

EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models
Cited by: 6
Author(s): Chaitra Sarathy, Martina Kutmon, Michael Lenz, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
Software Mentions: 5
Published: almost 5 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

10.15252/msb.20199012

Sex‐dependent and sex‐independent regulatory systems of size variation in natural populations
Cited by: 4
Author(s): Hirokazu Okada, Ryuta Yagi, Vincent Gardeux, Bart Deplancke, Ernst Hafen
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-018-2122-5

IntEREst: intron-exon retention estimator
Cited by: 18
Author(s): Ali Oghabian, Dario Greco, Mikko J. Frilander
Software Mentions: 5
Published: over 6 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

10.1186/s12859-020-3416-y

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Cited by: 12
Author(s): Michelle L. Treiber, Diana H. Taft, Ian F Korf, David A. Mills, Danielle G. Lemay
Software Mentions: 5
Published: almost 5 years ago

10.15252/msb.20209888

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: about 4 years ago

10.18632/aging.102697

Identification of a nomogram based on long non-coding RNA to improve prognosis prediction of esophageal squamous cell carcinoma
Cited by: 45
Author(s): Wenli Li, Jun Li, Hetong Zhao
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-019-5801-3

Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum
Cited by: 15
Author(s): Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, C. Liang, Caixia Jia
Software Mentions: 5
Published: over 5 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: about 4 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: over 5 years ago

10.1002/1878-0261.12138

<scp>APE</scp>1/Ref‐1 knockdown in pancreatic ductal adenocarcinoma – characterizing gene expression changes and identifying novel pathways using single‐cell <scp>RNA</scp> sequencing
Cited by: 26
Author(s): Fenil Shah, Emery Goossens, Nadia M. Atallah, Michelle Grimard, Mark R. Kelley, Melissa L. Fishel
Software Mentions: 5
Published: about 7 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

10.3389/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

10.1007/s10456-021-09788-4

The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis
Cited by: 20
Author(s): Lanette Kempers, Yuki Wakayama, Ivo van der Bijl, Charita Furumaya, Iris M. De Cuyper, Aldo Jongejan, Marije Kat, Anne-Marieke D. van Stalborch, Antonius L. van Boxtel, Marvin Hubert, Dirk Geerts, Jaap D. van Buul, Dirk de Korte, Wiebke Herzog, Coert Margadant
Software Mentions: 5
Published: over 3 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

10.1002/1878-0261.12902

A novel prognostic mRNA/miRNA signature for esophageal cancer and its immune landscape in cancer progression
Cited by: 35
Author(s): Yue Zhao, Li Xu, Xinyu Wang, Shuai Niu, Hezhong Chen, Chunguang Li
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

10.1002/1878-0261.12853

Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancer
Cited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: about 4 years ago

10.1016/j.xcrm.2020.100039

Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer
Cited by: 27
Author(s): Shamin Li, Yannick Simoni, Étienne Becht, Chiew Yee Loh, Naisi Li, Daniel M. Lachance, Si-Lin Koo, Teck Por Lim, Emile Tan, Ronnie Mathew, Andrew Nguyen, Justin Golovato, Julia D. Berkson, Martin Prlic, Bernett Lee, Samuel S. Minot, Niranjan Nagarajan, Neelendu Dey, Daniel S.W. Tan, Iain Bee Huat Tan, Evan W. Newell
Software Mentions: 5
Published: over 4 years ago

10.1164/rccm.202003-0510OC

Whole-Blood RNA Profiles Associated with Pulmonary Arterial Hypertension and Clinical Outcome
Cited by: 36
Author(s): Christopher J. Rhodes, Pablo Otero-Núñez, John Wharton, Emilia M. Swietlik, Sokratis Kariotis, Lars Harbaum, Mark J. Dunning, Jason M. Elinoff, Niamh Errington, A. A. Roger Thompson, James Iremonger, J. Gerry Coghlan, Paul A. Corris, Luke Howard, David G. Kiely, Colin Church, Joanna Pepke‐Zaba, Mark Toshner, Stephen J. Wort, Ankit A. Desai, Marc Humbert, William C. Nichols, Laura Southgate, David‐Alexandre Trégouët, Richard Trembath, Inga Prokopenko, Stefan Gräf, Nicholas W. Morrell, Dennis Wang, Allan Lawrie, Martin R. Wilkins
Software Mentions: 5
Published: over 4 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

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: about 6 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: over 3 years ago

10.1002/1878-0261.12314

Induced <scp>PTF</scp> 1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment
Cited by: 17
Author(s): Brad L. Jakubison, Patrick G. Schweickert, Sarah E. Moser, Yi Yang, Hongyu Gao, Kathleen M. Scully, Pamela Itkin-Ansari, Yunlong Liu, Stephen F. Konieczny
Software Mentions: 5
Published: over 6 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 4 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-017-3810-7

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Cited by: 27
Author(s): Ezra Lencer, Wesley C. Warren, Richard G. Harrison, Amy R. McCune
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-019-2697-5

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
Cited by: 5
Author(s): Karl Stamm, Aoy Tomita‐Mitchell, Serdar Bozdag
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: about 4 years ago

10.1186/s13229-020-00359-w

IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism
Cited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: over 4 years ago

10.1186/s13100-021-00236-0

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa
Cited by: 26
Author(s): Guillaume Wos, Rimjhim Roy Choudhury, Filip Kolář, Christian Parisod
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0242073

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data
Cited by: 14
Author(s): Xinyan Zhang, Boyi Guo, Nengjun Yi
Software Mentions: 5
Published: about 4 years ago

10.1074/mcp.TIR119.001646

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis
Cited by: 109
Author(s): Yong Zhu, Lukas M. Orre, Yan Zhou Tran, Georgios Mermelekas, Henrik J. Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö
Software Mentions: 5
Published: over 4 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

10.3389/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

10.1038/s41421-020-00214-5

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression
Cited by: 67
Author(s): Guohe Song, Yang Shi, Meiying Zhang, Shyamal Goswami, Saifullah Afridi, Ling Meng, Jiaqiang Ma, Yi Chen, Youpei Lin, Juan Zhang, Yuming Liu, Zijie Jin, Shenghong Yang, Dongning Rao, Shu Zhang, Aiwu Ke, Xiaoying Wang, Yang Cao, Jian Zhou, Jia Fan, Xiaoming Zhang, Ruibin Xi, Qiang Gao
Software Mentions: 5
Published: about 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

10.1186/s12864-016-2386-y

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
Cited by: 103
Author(s): Viktor Jönsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Software Mentions: 5
Published: almost 9 years ago

10.3389/fgene.2021.648701

Multiomics Analysis Reveals Molecular Abnormalities in Granulosa Cells of Women With Polycystic Ovary Syndrome
Cited by: 14
Author(s): Ru-Song Zhao, Yonghui Jiang, Shigang Zhao, Han Zhao
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.625466

Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome
Cited by: 1
Author(s): Karissa Barthelson, Lachlan Baer, Yang Dong, Melanie L. Hand, Zac Pujic, Morgan Newman, Geoffrey J. Goodhill, Robert I. Richards, Stephen Pederson, Michael Lardelli
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0205427

Identification of gene expression predictors of occupational benzene exposure
Cited by: 11
Author(s): Courtney Schiffman, Cliona M. McHale, Alan Hubbard, Luoping Zhang, Reuben Thomas, Roel Vermeulen, Guilan Li, Min Shen, Stephen M. Rappaport, Shu Yin, Qing Lan, Martyn T. Smith, Nathaniel Rothman
Software Mentions: 5
Published: about 6 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

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: almost 9 years ago

10.1186/s40168-021-01129-3

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Cited by: 7
Author(s): Wodan Ling, Ni Zhao, Anna Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer, Michael C. Wu
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

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: almost 4 years ago

10.1007/s00424-021-02582-7

Abnormal neonatal sodium handling in skin precedes hypertension in the SAME rat
Cited by: 2
Author(s): L. J. Mullins, Jessica R. Ivy, Mairi Ward, Olav Tenstad, Helge Wiig, Kento Kitada, Jonathan Manning, Natalia Rakova, Dominik N. Müller, John J. Mullins
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.67714

The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia
Cited by: 13
Author(s): Katalin Skrapits, Miklós Sárvári, Imre Farkas, Balázs Göcz, Szabolcs Takács, Éva Rumpler, Viktória Váczi, Csaba Vastagh, Gergely Rácz, András Matolcsy, Norbert Solymosi, Szilárd Póliska, Blanka Tóth, Ferenc Erdélyi, Gábor Szabó, Michael D. Culler, Cécile Allet, Ludovica Cotellessa, Vincent Prévot, Paolo Giacobini, Erik Hrabovszky
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

10.3390/plants9091176

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
Cited by: 19
Author(s): Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova, Alexander A. Kamnev
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.65574

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Cited by: 16
Author(s): Anthony A Ruberto, Aline Gréchez-Cassiau, Sabrina Guérin, Luc Martin, Johana S. Revel, Mohamed Mehiri, Malayannan Subramaniam, Franck Delaunay, Michèle Teboul
Software Mentions: 5
Published: over 3 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/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: about 4 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPARγ-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

10.7150/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

10.7150/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

10.1371/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

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: about 5 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568