cran: pheatmap | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.00968

Systematic Transcriptome Analysis of Noise-Induced Hearing Loss Pathogenesis Suggests Inflammatory Activities and Multiple Susceptible Molecules and Pathways
Cited by: 6
Author(s): Quan Wang, Yilin Shen, Hongbo Hu, Fan Cui, Andi Zhang, Rui Ding, Bin Ye, Ming Xiang
Software Mentions: 12
Published: about 4 years ago

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: over 4 years ago

10.3389/fphar.2021.726529

CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients
Cited by: 8
Author(s): Junqin Lu, Yihui Bi, Yapeng Zhu, Hanyu Shi, Wenxiu Duan, Jian Zhou
Software Mentions: 12
Published: about 3 years ago

10.3389/fgene.2021.620705

Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma
Cited by: 6
Author(s): Dongjun Dai, Lanyu Xie, Yongjie Shui, Jinfan Li, Qichun Wei
Software Mentions: 11
Published: almost 4 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: over 3 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-021-96712-x

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
Cited by: 12
Author(s): César A. Medina, Deborah A. Samac, Long‐Xi Yu
Software Mentions: 11
Published: about 3 years ago

10.3390/ijms221910302

The Impact of m1A Methylation Modification Patterns on Tumor Immune Microenvironment and Prognosis in Oral Squamous Cell Carcinoma
Cited by: 17
Author(s): Li Gao, Ru Chen, Masahiro Sugimoto, Masanobu Mizuta, Yo Kishimoto, Koichi Omori
Software Mentions: 11
Published: about 3 years ago

10.3389/fgene.2021.733715

Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer
Cited by: 2
Author(s): Jing Yu, Leilei Liang, Jing Liu, Tingting Liu, Jian Li, Lin Xiu, Jia Zeng, Tiantian Wang, Di Wang, Lijun Liang, Dawei Xie, Ding-Xiong Chen, Jusheng An, Lingying Wu
Software Mentions: 11
Published: about 3 years ago

10.3389/fonc.2021.672928

Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune Microenvironment
Cited by: 13
Author(s): Xiangming Cai, Feng Yuan, Junhao Zhu, Jin Yang, Chao Tang, Zixiang Cong, Chiyuan Ma
Software Mentions: 11
Published: over 3 years ago

10.1038/s41392-021-00753-7

Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients
Cited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: about 3 years ago

10.1242/jeb.210302

Time-critical influences of gestational diet in a seahorse model of male pregnancy
Cited by: 7
Author(s): Francisco Otero‐Ferrer, Freddy Lättekivi, James Ord, Ene Reimann, Sulev Kõks, Marisol Izquierdo, William V. Holt, Alireza Fazeli
Software Mentions: 11
Published: almost 6 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: over 4 years ago

10.1371/journal.pbio.3000595

A role for triglyceride lipase brummer in the regulation of sex differences in Drosophila fat storage and breakdown
Cited by: 69
Author(s): Lianna W Wat, Charlotte Chao, Rachael Bartlett, Justin Buchanan, Jason W Millington, Hui Ju Chih, Zahid Sadek Chowdhury, Puja Biswas, Vivian Huang, Leah J Shin, Lin Chuan Wang, Marie-Pierre Gauthier, Maria Cecilia Barone, Kristi L. Montooth, Michael A. Welte, Elizabeth J. Rideout
Software Mentions: 11
Published: almost 5 years ago

10.3389/fimmu.2021.599207

Molecular and Clinical Characterization of LAG3 in Breast Cancer Through 2994 Samples
Cited by: 15
Author(s): Qiang Liu, Yihang Qi, Jie Zhai, Xiangyi Kong, Xiangyu Wang, Zhongzhao Wang, Yi Fang, Jing Wang
Software Mentions: 11
Published: over 3 years ago

10.1038/s41408-019-0199-3

Deciphering the chronology of copy number alterations in Multiple Myeloma
Cited by: 35
Author(s): Anıl Aktaş Samur, Stéphane Minvielle, Masood A. Shammas, Mariateresa Fulciniti, Florence Magrangeas, Paul G. Richardson, Philippe Moreau, Michel Attal, Kenneth C. Anderson, Giovanni Parmigiani, Hervé Avet‐Loiseau, Nikhil C. Munshi, Mehmet K. Samur
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: almost 4 years ago

10.1002/cam4.2983

Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm
Cited by: 30
Author(s): Jun Luo, Yi Xie, Yuxiao Zheng, Chenji Wang, Feng Qi, Jiateng Hu, Yixiang Xu
Software Mentions: 11
Published: over 4 years ago

10.1155/2021/2291899

Crosstalk between Heart Failure and Cognitive Impairment via hsa-miR-933/RELB/CCL21 Pathway
Cited by: 8
Author(s): Wenxiao Feng, Jie Yang, Wen‐Chao Song, Yi-Tao Xue
Software Mentions: 11
Published: about 3 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: about 4 years ago

10.3389/pore.2021.1609852

Identification of a Gene Prognostic Model of Gastric Cancer Based on Analysis of Tumor Mutation Burden
Cited by: 9
Author(s): Weijun Ma, Weidong Li, Xu Liu, Lu Liu, Xinbing Yu, Liping Yang, Mingxu Da
Software Mentions: 11
Published: about 3 years ago

10.3389/fcvm.2021.624714

Identification of Potential Biomarkers and Immune Infiltration Characteristics in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Analysis
Cited by: 21
Author(s): Haowei Zeng, Xiaoqin Liu, Yushun Zhang
Software Mentions: 11
Published: almost 4 years ago

10.3389/fcell.2021.707143

The Prognosis and Immune Checkpoint Blockade Efficacy Prediction of Tumor-Infiltrating Immune Cells in Lung Cancer
Cited by: 11
Author(s): Xiangzheng Liu, Xueqian Shang, Jian Li, Shijie Zhang
Software Mentions: 11
Published: over 3 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 3 years ago

10.7717/peerj.10680

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma
Cited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: over 3 years ago

10.3389/fonc.2021.646060

Immune-Related Gene SERPINE1 Is a Novel Biomarker for Diffuse Lower-Grade Gliomas via Large-Scale Analysis
Cited by: 20
Author(s): Xiaoming Huang, Fenglin Zhang, Dong He, Xiaoshuai Ji, Jiajia Gao, Wenqing Liu, Yunda Wang, Qian Liu, Tao Xin
Software Mentions: 11
Published: over 3 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: almost 5 years ago

10.1242/dev.177428

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
Cited by: 182
Author(s): Sandra Ruiz García, Marie Deprez, Kévin Lebrigand, Amélie Cavard, Agnès Paquet, Marie-Jeanne Arguel, Virginie Magnone, Marin Truchi, Ignacio Caballero, Sylvie Leroy, Charles‐Hugo Marquette, Brice Marcet, Pascal Barbry, Laure‐Emmanuelle Zaragosi
Software Mentions: 11
Published: about 5 years ago

10.3389/fmolb.2021.611508

CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic Adenocarcinoma
Cited by: 17
Author(s): Huimin Huang, Wangxiao Zhou, Renpin Chen, Bingfeng Xiang, Shipeng Zhou, Linhua Lan
Software Mentions: 11
Published: almost 4 years ago

10.18632/aging.203242

Glycolysis- and immune-related novel prognostic biomarkers of Ewing's sarcoma: glucuronic acid epimerase and triosephosphate isomerase 1
Cited by: 9
Author(s): Jie Jiang, Xinli Zhan, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Yuanlin Yao, Chong Liu
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-020-74909-w

Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria
Cited by: 19
Author(s): Shane Fitzgerald, Emer Duffy, Linda Holland, Aoife Morrin
Software Mentions: 10
Published: about 4 years ago

10.1099/mgen.0.000552

Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen
Cited by: 6
Author(s): Josephine Grützke, Mayada Gwida, Carlus Deneke, Holger Brendebach, Michaela Projahn, Alexander Schattschneider, Dirk Hofreuter, Maged El-Ashker, Burkhard Malorny, Sascha Al Dahouk
Software Mentions: 10
Published: over 3 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago

10.3389/fimmu.2021.622563

9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Cited by: 17
Author(s): Kexin Yan, Yuxiu Lu, Zhangyong Yan, Yutao Wang
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.597745

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: almost 4 years ago

10.1097/MD.0000000000026068

MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method
Cited by: 1
Author(s): Zhengtian Li, Lingling Jiang, Rong Zhao, Jun Huang, Weibo Yang, Zhenpei Wen, Bo Zhang, Gang Du
Software Mentions: 10
Published: over 3 years ago

10.1111/pbi.13299

Learning from methylomes: epigenomic correlates of<i>Populus balsamifera</i>traits based on deep learning models of natural DNA methylation
Cited by: 9
Author(s): Marc J. Champigny, Faride Unda, Oleksandr Skyba, Raju Soolanayakanahally, Shawn D. Mansfield, Malcolm M. Campbell
Software Mentions: 10
Published: almost 5 years ago

10.1002/cam4.4071

Integrative analysis of immune molecular subtypes and microenvironment characteristics of bladder cancer
Cited by: 5
Author(s): Jinlong Cao, Jianpeng Li, Xin Yang, Pan Li, Zhiqiang Yao, Dali Han, Lijun Ying, Lijie Wang, Junqiang Tian
Software Mentions: 10
Published: over 3 years ago

10.3389/fonc.2021.704038

Fatty Acid Metabolism-Related lncRNAs Are Potential Biomarkers for Predicting the Overall Survival of Patients With Colorectal Cancer
Cited by: 13
Author(s): Yue Peng, Chang Xu, Jun Wen, Yuanchuan Zhang, Meng Wang, Xiaoxiao Liu, Kang Zhao, Zheng Wang, Yanjun Liu, Tongtong Zhang
Software Mentions: 10
Published: over 3 years ago

10.18632/aging.202279

Exploration of the immune cell infiltration-related gene signature in the prognosis of melanoma
Cited by: 19
Author(s): Yongquan Zeng, Yue Zeng, Hang Yin, Fengxia Chen, Qingqing Wang, Xiaoyan Yu, Youwen Zhou
Software Mentions: 10
Published: almost 4 years ago

10.1007/s00262-020-02817-z

Immune signature-based risk stratification and prediction of immune checkpoint inhibitor’s efficacy for lung adenocarcinoma
Cited by: 85
Author(s): Ming Yi, An‐Ping Li, Linghui Zhou, Qian Chu, Suxia Luo, Kongming Wu
Software Mentions: 10
Published: almost 4 years ago

10.3389/fonc.2021.644956

A New Oxaliplatin Resistance-Related Gene Signature With Strong Predicting Ability in Colon Cancer Identified by Comprehensive Profiling
Cited by: 6
Author(s): Qiu Sheng Lin, Liang Luo, Hua Wang
Software Mentions: 10
Published: over 3 years ago

10.1002/cam4.3632

Analyzing and predicting the LNM rate and prognosis of patients with intraductal papillary mucinous neoplasm of the pancreas
Cited by: 1
Author(s): Chao‐Tao Tang, Bi‐Xia Liu, Youxiang Chen, Chunyan Zeng
Software Mentions: 10
Published: over 3 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: over 3 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12864-019-6181-4

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)
Cited by: 12
Author(s): Jianjun Fu, Wenbin Zhu, Lanmei Wang, Ming Luo, Fei Song, Zaijie Dong
Software Mentions: 10
Published: about 5 years ago

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 6 years ago

10.1155/2021/1031906

Development of a Ferroptosis-Related lncRNA Signature to Predict the Prognosis and Immune Landscape of Bladder Cancer
Cited by: 14
Author(s): Ranran Zhou, Jingjing Liang, Haijun Tian, Qi Chen, Cheng Yang, Cundong Liu
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.43257

Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 5 years ago

10.1016/j.celrep.2019.10.024

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Cited by: 227
Author(s): Ross Dobie, John Wilson-Kanamori, Beth E. P. Henderson, J. F. Smith, Kylie P. Matchett, Jordan Raymond Portman, Karolina Wallenborg, Simone Picelli, Анна Загорска, Swetha Pendem, Thomas E. Hudson, Max C. Wu, Grant R. Budas, David G. Breckenridge, Ewen M Harrison, Damian J. Mole, Stephen J. Wigmore, Prakash Ramachandran, Chris P. Ponting, Sarah A. Teichmann, John C. Marioni, Neil C. Henderson
Software Mentions: 10
Published: about 5 years ago

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1008831

Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens
Cited by: 18
Author(s): Trieu-Duc Vu, Yoshiaki Iwasaki, Shuji Shigenobu, Akiko Maruko, Koichiro Oshima, Erica Iioka, Chao Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Sheng Lin, Chih Kuan Chen, Mei-Yeh Jade Lu, Masaru Hojo, Hao Ven Wang, Shun Fen Tzeng, Hao Huang, Akio Kanai, Takashi Gojobori, Tzen‐Yuh Chiang, Han Sun, Wen-Hsiung Li, Norihiro Okada
Software Mentions: 10
Published: over 4 years ago

10.3390/ijms22179601

In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia
Cited by: 7
Author(s): Hande Öngün Yılmaz, Halil Ibrahim Toy, Stephan Marquardt, Gökhan Karakülah, Can Küçük, Panagiota I. Kontou, Stella Logotheti, Athanasia Pavlopoulou
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.ppat.1005996

A Mouse Model of Chronic West Nile Virus Disease
Cited by: 44
Author(s): Jessica B. Graham, Jessica L. Swarts, Courtney Wilkins, Sunil Thomas, Richard Green, Aimee Sekine, Kathleen Voss, Reneé C. Ireton, Michael A. Mooney, Gabrielle Choonoo, Darla R. Miller, Piper M. Treuting, Fernando Pardo Manuel de Villena, Martin T. Ferris, Shannon K. McWeeney, Michael Gale, Jennifer M. Lund
Software Mentions: 10
Published: about 8 years ago

10.3389/fgene.2021.739520

Construction of a Prognostic Model in Lung Adenocarcinoma Based on Ferroptosis-Related Genes
Cited by: 6
Author(s): Min Liang, Mafeng Chen, Yao Zhong, Satwant Singh, Sandeep Singh
Software Mentions: 10
Published: about 3 years ago

10.1016/j.isci.2021.102768

Spatially resolved sampling for untargeted metabolomics: A new tool for salivomics
Cited by: 4
Author(s): Alessio Ciurli, Maximiliam Liebl, Rico Derks, Jacques Neefjes, Martin Giera
Software Mentions: 10
Published: over 3 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.1038/s41598-021-96236-4

A novel prognostic signature of immune-related lncRNA pairs in lung adenocarcinoma
Cited by: 5
Author(s): Yang Liu, Qiuhong Wu, Xuejiao Fan, Wen Li, Yong Li, Hui Zhu, Qinghua Zhou, Jinming Yu
Software Mentions: 10
Published: over 3 years ago

10.3390/cancers13133371

Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: over 3 years ago

10.3390/ijms22063200

Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens
Cited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: over 3 years ago

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: over 3 years ago

10.1186/s12974-018-1113-9

Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 6 years ago

10.3389/fgene.2019.00880

LINC00460 Hypomethylation Promotes Metastasis in Colorectal Carcinoma
Cited by: 15
Author(s): Hui Zhang, Ya Lu, Jianzhong Wu, Jifeng Feng
Software Mentions: 9
Published: about 5 years ago

10.3389/fgene.2020.576566

Systematic Profiling of Immune Risk Model to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 9
Author(s): Xingyu Liu, Jiarui Chen, Wei Lu, Zhao-Yi Zeng, Jiali Li, Xueping Jiang, Yanping Gao, Yan Gong, Qiuji Wu, Conghua Xie
Software Mentions: 9
Published: about 4 years ago

10.3390/ijms21093139

The Dark Side of Orchid Symbiosis: Can Tulasnella calospora Decompose Host Tissues?
Cited by: 21
Author(s): Martino Adamo, Matteo Chialva, Jacopo Calevo, Silvia De Rose, Mariangela Girlanda, Silvia Perotto, Raffaella Balestrini
Software Mentions: 9
Published: over 4 years ago

10.3389/fncel.2020.00065

Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses
Cited by: 29
Author(s): Kee Wui Huang, Bernardo L. Sabatini
Software Mentions: 9
Published: over 4 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: almost 4 years ago

10.3389/fonc.2020.573141

Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma
Cited by: 57
Author(s): Kai Kang, Fucun Xie, Jianshan Mao, Yi Bai, Xiang Wang
Software Mentions: 9
Published: about 4 years ago

10.1111/jcmm.14767

An EMT‐related gene signature for the prognosis of human bladder cancer
Cited by: 113
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Wei Qiu, Ye Tian
Software Mentions: 9
Published: about 5 years ago

10.1126/sciadv.abc8492

Persistent epigenetic reprogramming of sweet taste by diet
Cited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: about 4 years ago

10.3390/cancers12051076

Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women
Cited by: 31
Author(s): Yong Won Jin, Pingzhao Hu
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-71521-w

Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples
Cited by: 9
Author(s): Leah C. Wehmas, Susan Hester, Charles E. Wood
Software Mentions: 9
Published: about 4 years ago

10.1186/s12890-021-01588-2

A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma
Cited by: 9
Author(s): Fēi Li, Dongcen Ge, Shulan Sun
Software Mentions: 9
Published: over 3 years ago

10.18632/aging.203040

Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension
Cited by: 16
Author(s): Haoru Dong, Xiuchun Li, Mengsi Cai, Chi Zhang, Mao Wei-qi, Ying Wang, Qinying Xu, Mayun Chen, Liangxing Wang, Xiaoying Huang
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-76792-x

Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific
Cited by: 3
Author(s): Hillary A. Smith, Jessica A. Conlan, F. Joseph Pollock, Naohiro Wada, Amanda Shore, Julia Yun-Hsuan Hung, Greta S. Aeby, Bette L. Willis, David S. Francis, David G. Bourne
Software Mentions: 9
Published: about 4 years ago

10.3389/fmicb.2019.02320

Saccharomyces cerevisiae Induces Immune Enhancing and Shapes Gut Microbiota in Social Wasps
Cited by: 18
Author(s): Niccolò Meriggi, Monica Di Paola, Francesco Vitali, Damaríz Rivero, Federico Cappa, Francesco Turillazzi, Agnese Gori, Leonardo Dapporto, L. Beani, Stefano Turillazzi, Duccio Cavalieri
Software Mentions: 9
Published: about 5 years ago

10.1186/s12935-021-02215-0

Identification of the prognostic value of a 2-gene signature of the WNT gene family in UCEC using bioinformatics and real-world data
Cited by: 9
Author(s): Yuexin Hu, Mingjun Zheng, Dandan Zhang, Rui Gou, Ouxuan Liu, Shuang Wang, Bei Lin
Software Mentions: 9
Published: about 3 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: almost 5 years ago

10.18632/aging.203290

Expression mode and prognostic value of FXYD family members in colon cancer
Cited by: 8
Author(s): Ming Jin, Hui Zhang, Jun Yang, Zheng Zhao, Kaitai Liu
Software Mentions: 9
Published: over 3 years ago

10.1016/j.celrep.2020.107732

Variable Outcomes in Neural Differentiation of Human PSCs Arise from Intrinsic Differences in Developmental Signaling Pathways
Cited by: 43
Author(s): Alessio Strano, Eleanor J. Tuck, Victoria Stubbs, Frederick J. Livesey
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: almost 5 years ago

10.18632/aging.202614

BDKRB2 is a novel EMT-related biomarker and predicts poor survival in glioma
Cited by: 8
Author(s): Ying Yang, Jin Wang, Fei Shi, Aijun Shan, Shi‐Hai Xu, Wen Lv
Software Mentions: 9
Published: over 3 years ago

10.3389/fimmu.2021.709173

The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters
Cited by: 6
Author(s): Afshin Derakhshani, Hossein Safarpour, Behzad Baradaran, Nima Hemmat, Patrizia Leone, Zahra Asadzadeh, Mehrdad Pashazadeh, Behzad Baradaran, Vito Racanelli
Software Mentions: 9
Published: about 3 years ago

10.1172/jci.insight.138729

CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation
Cited by: 45
Author(s): Kathryn E. Beckermann, Rachel Hongo, Xiang Ye, Kirsten Young, Katie Carbonell, Diana C Contreras Healey, Peter J. Siska, Sierra Barone, Caroline E. Roe, Christof C. Smith, Benjamin G. Vincent, Frank M. Mason, Jonathan M. Irish, W. Kimryn Rathmell, Jeffrey C. Rathmell
Software Mentions: 9
Published: over 4 years ago

10.1172/jci.insight.141683

CD84 is a regulator of the immunosuppressive microenvironment in Multiple Myeloma
Cited by: 15
Author(s): Hadas Lewinsky, Emine Gulsen Gunes, Keren David, Lihi Radomir, Matthias P. Kramer, Bianca Pellegrino, Michal Perpinial, Jing Chen, Ting He, Anthony G. Mansour, Kun yu Teng, Supriyo Bhattacharya, Enrico Caserta, Estelle Troadec, Peter Lee, Mingye Feng, Jonathan J. Keats, Amrita Krishnan, Michael Rosenzweig, Jianhua Yu, Michael A. Caligiuri, Yosef Cohen, Olga Shevetz, Shirly Becker-Herman, Flavia Pichiorri, Steven T. Rosen, Idit Shachar
Software Mentions: 9
Published: almost 4 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago

10.18632/aging.101795

Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models
Cited by: 4
Author(s): Zhiliang Wang, Zheng Zhao, Zheng Wang, Chuanbao Zhang, Tao Jiang
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-019-53903-x

Proteome characterization of used nesting material and potential protein sources from group housed male mice, Mus musculus
Cited by: 16
Author(s): Amanda J. Barabas, Uma K. Aryal, Brianna N. Gaskill
Software Mentions: 9
Published: almost 5 years ago

10.26508/lsa.202101108

Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo
Cited by: 11
Author(s): Karen N. McFarland, Carolina Wiesner Ceballos, Awilda M. Rosario, Thomas B. Ladd, Brenda D. Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilufer Ertekin‐Taner, Cory C. Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, Todd E. Golde
Software Mentions: 9
Published: over 3 years ago

10.3389/fcell.2021.654504

Role of CXCR4 as a Prognostic Biomarker Associated With the Tumor Immune Microenvironment in Gastric Cancer
Cited by: 5
Author(s): Yuyang Gu, Wenyue Gu, Rongrong Xie, Zhi Chen, Tongpeng Xu, Zhenghua Fei
Software Mentions: 9
Published: about 3 years ago

10.7717/peerj.10008

A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
Cited by: 3
Author(s): Zhenyu Zhao, Boxue He, Qidong Cai, Pengfei Zhang, Ping Xiong, Yuqian Zhang, Hui Xie, Xiang Wang
Software Mentions: 9
Published: about 4 years ago

10.3390/genes12070995

Effects of the Developmental Regulator BOLITA on the Plant Metabolome
Cited by: 3
Author(s): Hugo Gerardo Lazcano-Ramírez, Roberto Gamboa-Becerra, Irving Jair Garcia-Lopez, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martı́nez de la Vega, José Juan Ordaz-Ortíz, Stefan de Folter, Axel Tiessen-Favier, Robert Winkler, Nayelli Marsch-Martínez
Software Mentions: 9
Published: over 3 years ago

10.1155/2021/8864436

Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer
Cited by: 10
Author(s): Xuening Zhang, Xiaoguang Shi, Hao Zhao, Xiaocan Jia, Yongli Yang
Software Mentions: 9
Published: over 3 years ago

10.1002/cam4.2774

Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods
Cited by: 39
Author(s): Xiao Li, Yang Gao, Zicheng Xu, Zheng Zhang, Yuxiao Zheng, Feng Qi
Software Mentions: 9
Published: almost 5 years ago

10.7717/peerj.9017

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon
Cited by: 10
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, Cecilia Conaco
Software Mentions: 9
Published: over 4 years ago

10.3389/fonc.2020.593760

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue
Cited by: 4
Author(s): Rihards Saksis, Ivars Silamiķelis, Pola Laksa, Kaspars Megnis, Raitis Pečulis, Ilona Mandrika, Olesja Rogoza, Ramona Petrovska, Inga Balcere, Ilze Konrāde, Liva Steina, Jānis Stukēns, Austra Breikša, Jurijs Nazarovs, Jeļizaveta Sokolovska, Valdis Pīrāgs, Jānis Kloviņš, Vita Rovīte
Software Mentions: 9
Published: almost 4 years ago

Projects: cran: pheatmap

Papers Mentioning pheatmap 2,572