10.3389/fcell.2021.710558

Construction and Validation of a Novel Immunosignature for Overall Survival in Uveal Melanoma
Cited by: 3
Author(s): Chufeng Gu, Xiaohong Gu, Yujie Wang, Zhixian Yao, Chuandi Zhou
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-018-2053-1

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
Cited by: 176
Author(s): Pedro Russo, Gustavo Rodrigues Ferreira, Lucas Esteves Cardozo, Matheus Carvalho Bürger, Raúl Arias‐Carrasco, Sandra Regina Maruyama, Thiago Dominguez Crespo Hirata, Diógenes Saulo de Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João Silva, Vinicius Maracaja‐Coutinho, Hidehiko Nakaya
Software Mentions: 4
Published: over 8 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: over 7 years ago

10.1155/2013/187509

Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data
Cited by: 8
Author(s): Ai-Di Zhang, Shao‐Xing Dai, Jing‐Fei Huang
Software Mentions: 4
Published: over 13 years ago

10.1186/s12915-020-00775-7

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions
Cited by: 114
Author(s): Federico Baldini, Johannes Hertel, Estelle Sandt, Cyrille C. Thinnes, Lorieza Neuberger-Castillo, Lukas Pavelka, Fay Betsou, Rejko Krüger, Ines Thiele
Software Mentions: 4
Published: about 6 years ago

10.3390/life11050367

Activation of Blood Vessel Development in Endometrial Stromal Cells In Vitro Cocultured with Human Peri-Implantation Embryos Revealed by Single-Cell RNA-Seq
Cited by: 4
Author(s): Bo Lv, Xiaoyu Xu, Xunyi Zhang, Lingbin Qi, He We, Lu Wang, Xian Chen, Luying Peng, Jinfeng Xue, Yao Ji, Zhigang Xue
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 6 years ago

10.1186/1752-0509-6-65

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
Cited by: 49
Author(s): Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz‐Sloan, Mark R. Chance
Software Mentions: 4
Published: about 14 years ago

10.1038/s41421-021-00271-4

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response
Cited by: 90
Author(s): Yu Wang, Yongfeng Liang, Haiyan Xu, Xiao Zhang, Tiebo Mao, Jiujie Cui, Jiyong Yao, Yongchao Wang, Feng Jiao, Xiuying Xiao, Jiong Hu, Qing Xia, Xiaofei Zhang, Xujun Wang, Yongwei Sun, Deliang Fu, Lei Shen, Ximing Xu, Jing Xue, Liwei Wang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-021-04180-x

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets
Cited by: 15
Author(s): Teresita M. Porter, Mehrdad Hajibabaei
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.630215

Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/3641231

Immune-Related Four-lncRNA Signature for Patients with Cervical Cancer
Cited by: 19
Author(s): Jianfeng Zheng, Benben Cao, Xia Zhang, Zhenbin Niu, Jinyi Tong
Software Mentions: 4
Published: almost 6 years ago

10.1155/2016/4241293

Differential Regulatory Analysis Based on Coexpression Network in Cancer Research
Cited by: 12
Author(s): Junyi Li, Yixue Li, Yuanyuan Li
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-017-08796-z

Surface PD-L1, E-cadherin, CD24, and VEGFR2 as markers of epithelial cancer stem cells associated with rapid tumorigenesis
Cited by: 42
Author(s): Goodwin G. Jinesh, Ganiraju C. Manyam, Chinedu O. Mmeje, Keith A. Baggerly, Ashish M. Kamat
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12862-019-1420-5

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore
Cited by: 6
Author(s): Rita Gomes Rocha, Vanessa Magalhães, José V. López‐Bao, W. van der Loo, Luís Llaneza, Francisco Álvares, Pedro J. Esteves, Raquel Godinho
Software Mentions: 4
Published: over 7 years ago

10.1107/S1399004715011426

From deep TLS validation to ensembles of atomic models built from elemental motions
Cited by: 14
Author(s): Alexandre Urzhumtsev, Pavel V. Afonine, A.H. Van Benschoten, James S. Fraser, Paul D. Adams
Software Mentions: 4
Published: about 11 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-017-04300-9

Altered miRNA expression network in locus coeruleus of depressed suicide subjects
Cited by: 59
Author(s): Bhaskar Roy, Qingzhong Wang, M. Palkóvits, Gábor Faludi, Yogesh K. Dwivedi
Software Mentions: 4
Published: about 9 years ago

10.1186/s12935-020-01632-x

Targeting Lymphotoxin Beta and Paired Box 5: a potential therapeutic strategy for soft tissue sarcoma metastasis
Cited by: 0
Author(s): Runzhi Huang, Zhiwei Zeng, Penghui Yan, Huabin Yin, Xiaolong Zhu, Peng Hu, Juanwei Zhuang, Jiaju Li, Siqi Li, Dianwen Song, Tong Meng, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: about 7 years ago

10.1155/2021/9921195

A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs
Cited by: 0
Author(s): Aimin Hu, Wei Zheng, Zuxiang Zheng, Bichao Luo, Jieming Yi, Xinhong Zhou, Changjiang Zeng
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12870-020-02637-4

Revealing the full-length transcriptome of caucasian clover rhizome development
Cited by: 13
Author(s): Xiujie Yin, Kun Yi, Yihang Zhao, Yue Hu, Li Xu, Taotao He, Jiaxue Liu, Guowen Cui
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/4612158

<i>CCNB2</i>, <i>TOP2A</i>, and <i>ASPM</i> Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis
Cited by: 9
Author(s): Yuping Zeng, He He, Yu Zhang, Xia Wang, Yang Lin-de, Zhenmei An
Software Mentions: 4
Published: about 6 years ago

10.1016/j.celrep.2017.08.010

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
Cited by: 92
Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalvès, Clara Alsinet, Martín Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michaël Schubert, Stacey Price, James C. Wright, Lu Yu, Meizhu Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrão, Alvis Brāzma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Jyoti S. Choudhary
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-015-1522-4

Transcriptomic profiles of aging in purified human immune cells
Cited by: 57
Author(s): Lindsay M. Reynolds, Jingzhong Ding, Jeanette Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig W. Johnson, R. Graham Barr, Thomas C. Register, Kathleen Donohue, Monica V. Talor, Daniela Čiháková, C. Charles Gu, Jasmin Divers, David S. Siscovick, Gregory L. Burke, Wendy S. Post, Steven Shea, David R. Jacobs, Ina Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David M. Herrington, Russell P. Tracy, Yongmei Liu
Software Mentions: 4
Published: over 11 years ago

10.3389/fimmu.2021.716075

Transcriptome Analysis of Peripheral Blood Mononuclear Cells Reveals Distinct Immune Response in Asymptomatic and Re-Detectable Positive COVID-19 Patients
Cited by: 10
Author(s): Jiaqi Zhang, Dan Lin, Kui Li, Xiangming Ding, Lin Li, Yuntao Liu, Dongdong Liu, Jing Lin, Xiangyun Teng, Yizhe Li, Ming Liu, Jian Shen, Xiaodan Wang, He Dan, Yawei Shi, Dawei Wang, Jianhua Xu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12918-015-0155-1

Spatially-resolved metabolic cooperativity within dense bacterial colonies
Cited by: 69
Author(s): John A. Cole, Lars Köhler, Jamila Hedhli, Zaida Luthey‐Schulten
Software Mentions: 3
Published: over 11 years ago

10.3389/fcell.2021.702112

Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration
Cited by: 5
Author(s): Fengjiao Wang, Yuanfu Zhang, Yangyang Hao, Xuexin Li, Yue Qi, Mengyu Xin, Qifan Xiao, Peng Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-12-315

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs
Cited by: 83
Author(s): Hui Yu, Baohong Liu, Zhiqiang Ye, Chun Liang, Yixue Li, Yuanyuan Li
Software Mentions: 3
Published: about 15 years ago

10.3389/fcell.2020.620164

Analysis of Cyclin-Dependent Kinase 1 as an Independent Prognostic Factor for Gastric Cancer Based on Statistical Methods
Cited by: 7
Author(s): Xu Zhang, Hua Ma, Quan Zou, Jin Wu
Software Mentions: 3
Published: over 5 years ago

10.1155/2017/8347085

Identification of Transcriptional Modules and Key Genes in Chickens Infected with Salmonella enterica Serovar Pullorum Using Integrated Coexpression Analyses
Cited by: 7
Author(s): Baohong Liu, Jianping Cai
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2407-12-426

Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients
Cited by: 5
Author(s): Siv Kjølsrud Bøhn, Kjell Magne Russnes, Amrit Kaur Sakhi, Magne Thoresen, Matthew T. G. Holden, Jan Øivind Moskaug, Mari Myhrstad, Ole Kristoffer Olstad, Sigbjørn Smeland, Rune Blomhoff
Software Mentions: 3
Published: almost 14 years ago

10.3389/fendo.2020.571151

Microarray Data of Lacrimal Gland Implicates Dysregulated Protein Processing in Endoplasmic Reticulum in Graves’ Ophthalmopathy
Cited by: 1
Author(s): Wenling Tu, Jia Yao, Zhanjun Mei, Xue Jiang, Yu-Hong Shi
Software Mentions: 3
Published: over 5 years ago

10.3389/fendo.2020.00138

Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity
Cited by: 10
Author(s): Jana Breitfeld, Stephanie Kehr, Luise Müller, Peter F. Stadler, Yvonne Böttcher, Matthias Blüher, Michael Stümvoll, Peter Kovacs
Software Mentions: 3
Published: over 6 years ago

10.1155/2021/8836243

Altered Genes and Biological Functions in Response to Severe Burns
Cited by: 2
Author(s): Xinheng Liu, Yong-Xian Rong, Deng-Shing Huang, Zheng Liang, Xiao-Lin Yi, Fengyao Wu, Dandan Zhu, Steven Mo, Wenhai Nong, Hong-Mian Li
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers11121967

Pannexin1 Is Associated with Enhanced Epithelial-To-Mesenchymal Transition in Human Patient Breast Cancer Tissues and in Breast Cancer Cell Lines
Cited by: 25
Author(s): Nour Jalaleddine, Layal El-Hajjar, Hassan Dakik, Abdullah Shaito, Jessica Saliba, Rémi Safi, Kazem Zibara, Marwan El-Sabban
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2019.00036

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo
Cited by: 45
Author(s): Tingxian Deng, Aixin Liang, Shasha Liang, Xiaoya Ma, Xingrong Lu, Anqin Duan, Chaoyou Pang, Guohua Hua, Shenhe Liu, Giuseppe Campanile, Angela Salzano, B. Gasparrini, Xianwei Liang, Liguo Yang
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.558725

Transcriptome Analysis of the Cerebellum of Mice Fed a Manganese-Deficient Diet
Cited by: 3
Author(s): Young Ah Seo, Eun‐Kyung Choi, Luisa Aring, Molly Paschall, Shigeki Iwase
Software Mentions: 3
Published: over 5 years ago

10.1016/j.bioflm.2021.100051

Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle
Cited by: 7
Author(s): Brian J. Eddie, Anthony P. Malanoski, Elizabeth L. Onderko, Daniel A. Phillips, Sarah M. Glaven
Software Mentions: 3
Published: over 4 years ago

10.3390/molecules25040904

Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis
Cited by: 26
Author(s): Arnold Amusengeri, Rolland Bantar Tata, Özlem Tastan Bishop
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.690264

Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis ‘Old Blush’ After Exposure to a Gradual Drought Stress Followed by Recovery
Cited by: 7
Author(s): Xin Jia, Hui Feng, Yingjie Bu, Naizhe Ji, Yingmin Lyu, Shiwei Zhao
Software Mentions: 3
Published: about 5 years ago

10.1186/s12919-021-00223-6

Proceedings of ‘FETP-ICON 2020’ Conference
Cited by: 0
Author(s):
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers13102452

Efficacy and Safety of Durvalumab Combined with Daratumumab in Daratumumab-Refractory Multiple Myeloma Patients
Cited by: 9
Author(s): Kristine A. Frerichs, Christie P.M. Verkleij, Meletios Α. Dimopoulos, Jhon A. Marin Soto, Sonja Zweegman, Mary Young, Kathryn J. Newhall, Tuna Mutis, Niels W.C.J. van de Donk
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00903

SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes
Cited by: 12
Author(s): Zishuai Wang, Xikang Feng, Shuai Cheng Li
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2018.00453

Weighted Gene Co-expression Network Analysis of Endometriosis and Identification of Functional Modules Associated With Its Main Hallmarks
Cited by: 58
Author(s): Mohammad Reza Bakhtiarizadeh, Batool Hosseinpour, Maryam Shahhoseini, Arthur Korte, Peyman Gifani
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-017-3237-1

Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue
Cited by: 26
Author(s): Bojana Jovanović, Quanhu Sheng, Robert S. Seitz, Kasey Lawrence, Stephan W. Morris, Lance R. Thomas, David R. Hout, Brock L. Schweitzer, Yan Guo, Jennifer A. Pietenpol, Brian D. Lehmann
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2021.696591

Identification of Atrial Fibrillation-Associated Genes ERBB2 and MYPN Using Genome-Wide Association and Transcriptome Expression Profile Data on Left–Right Atrial Appendages
Cited by: 3
Author(s): Xiangkun Meng, Yali Nie, Keke Wang, Chongxi Fan, Juntao Zhao, Yuan Yang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2021.620740

Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People
Cited by: 5
Author(s): Zhenhua Lu, Ling‐Bing Meng, Zhen Sun, Xiaolei Shi, Weiwei Shao, Yangyang Zheng, Xinglei Yao, Jianguo Song
Software Mentions: 3
Published: over 5 years ago

10.3762/bjnano.6.252

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials
Cited by: 49
Author(s): Andrew Williams, Sabina Halappanavar
Software Mentions: 3
Published: over 10 years ago

10.3390/cancers10080273

Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer
Cited by: 26
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Sahib Zada, Jin Seok Hwang, Trang Minh Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.591079

Identifying M1 Macrophage-Related Genes Through a Co-expression Network to Construct a Four-Gene Risk-Scoring Model for Predicting Thyroid Cancer Prognosis
Cited by: 14
Author(s): Gaojian Zhuang, Yu Zeng, Qun Tang, Qian He, Guoqing Luo
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.610350

Construction of an RNA-Binding Protein-Related Prognostic Model for Pancreatic Adenocarcinoma Based on TCGA and GTEx Databases
Cited by: 14
Author(s): Xin Wen, Zhaogang Shao, Shuyi Chen, Wei Wang, Yan Wang, Jeng Kai Jiang, Qinggong Ma, Longzhen Zhang
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00970

Hub Genes Identification in a Murine Model of Allergic Rhinitis Based on Bioinformatics Analysis
Cited by: 5
Author(s): Chen Le, Le Shi, Yue Ma, Cheng Zheng
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2021.616388

Transcriptome Characterization of Short Distance Transport Stress in Beef Cattle Blood
Cited by: 14
Author(s): Hailin Zhao, Xiaoqin Tang, Mingli Wu, Qi Li, Xiaohua Yi, Shirong Liu, Junyi Jiang, Shuhui Wang, Xiuzhu Sun
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-020-00943-9

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia
Cited by: 45
Author(s): Hao Song, Ximing Guo, Lina Sun, Qianghui Wang, Fengming Han, Haiyan Wang, Gregory A. Wray, Phillip L. Davidson, Qing Wang, Zhi Hu, Cong Zhou, Zhi Yu, Mei‐Jie Yang, Jie Feng, Shi Pu, Yi Zhou, Libin Zhang, Tao Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s10020-019-0116-z

Inhibition of phosphatidylinositol 3-kinase by PX-866 suppresses temozolomide-induced autophagy and promotes apoptosis in glioblastoma cells
Cited by: 24
Author(s): Bryan Harder, Sen Peng, Chris Sereduk, Andrej M. Sodoma, Gaspar J. Kitange, Joseph C. Loftus, Jann N. Sarkaria, Nhan L. Tran
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2020.01481

Pediatric Burn Survivors Have Long-Term Immune Dysfunction With Diminished Vaccine Response
Cited by: 8
Author(s): Blair Z. Johnson, Sonia McAlister, Helen M. McGuire, Vetrichevvel Thirthar Palanivelu, Andrew Stevenson, Peter Richmond, Debra J. Palmer, Jessica Metcalfe, Susan L. Prescott, Fiona Wood, Barbara Fazekas de St Groth, Matthew D. Linden, Mark W. Fear, Vanessa S. Fear
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2019.00869

Immunomodulatory Effects and Induction of Apoptosis by Different Molecular Weight Chitosan Oligosaccharides in Head Kidney Macrophages From Blunt Snout Bream (Megalobrama amblycephala)
Cited by: 17
Author(s): Changcai Wu, Yishan Dai, Gailing Yuan, Jian Su, Xiaoling Liu
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2020.604785

JNK1 Signaling Downstream of the EGFR Pathway Contributes to Aldara®-Induced Skin Inflammation
Cited by: 3
Author(s): Aurore Le, Abdulkader Azouz, Séverine Thomas, Nicolas Istaces, Muriel Nguyen, Stanislas Goriely
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.666370

lncRNA-HEIM Facilitated Liver Fibrosis by Up-Regulating TGF-β Expression in Long-Term Outcome of Chronic Hepatitis B
Cited by: 9
Author(s): Jian Yao, Changpo Lin, Jingjing Jiang, Xujun Zhang, Fengxia Li, Tianxing Liu, Hongyan Diao
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-9-561

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
Cited by: 250
Author(s): Wen Chi Chang, Tzong-Yi Lee, Hsien Da Huang, His Yuan Huang, Rong Pan
Software Mentions: 3
Published: over 17 years ago

10.1186/s12864-015-1675-1

Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs
Cited by: 36
Author(s): Carlos Villacorta-Martín, Francisco Gonzalez, Jorn de Haan, Kitty Huijben, Paul Passarinho, Maya Lugassi-Ben Hamo, Michèle Zaccai
Software Mentions: 3
Published: about 11 years ago

10.1042/BSR20200514

Identification of co-expressed genes associated with <i>MLL</i> rearrangement in pediatric acute lymphoblastic leukemia
Cited by: 2
Author(s): Hao Zhang, Bei Liu, Juan Cheng, Haizhen Ma, Zijian Li, Yuandi Xi
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2020.02039

Crosstalk Between the MSI Status and Tumor Microenvironment in Colorectal Cancer
Cited by: 160
Author(s): Anqi Lin, Jian Zhang, Peng Luo
Software Mentions: 3
Published: about 6 years ago

10.1186/s12917-019-1815-y

A spatial assessment of Nipah virus transmission in Thailand pig farms using multi-criteria decision analysis
Cited by: 7
Author(s): Weerapong Thanapongtharm, Mathilde Paul, Anuwat Wiratsudakul, Vilaiporn Wongphruksasoong, Wantanee Kalpravidh, Kachen Wongsathapornchai, Sudarat Damrongwatanapokin, Daniel Schar, Marius Gilbert
Software Mentions: 3
Published: over 7 years ago

10.3389/fmed.2020.606461

Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus
Cited by: 3
Author(s): Melissa A Nickles, Huang Kai, Yi-Shin Chang, Maria M. Tsoukas, Nadera J. Sweiss, David L. Perkins, Patricia W. Finn
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0177819

Network architecture associated with the highly specialized hindlimb of frogs
Cited by: 17
Author(s): Daniel Andrés Dos Santos, Jéssica Fratani, María Laura Ponssa, Virginia Abdala
Software Mentions: 3
Published: over 9 years ago

10.1186/s13068-021-02032-7

Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed
Cited by: 17
Author(s): Keqi Li, Jie Wang, Lieqiong Kuang, Ze Tian, Xinfa Wang, Xiaoling Dun, Jinxing Tu, Hanzhong Wang
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-10-405

Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients
Cited by: 151
Author(s): Christiaan G J Saris, Steve Horvath, Paul W.J. van Vught, Michael A. van Es, Hylke M. Blauw, Tova Fuller, Peter Langfelder, Joseph DeYoung, John H. J. Wokke, Jan H. Veldink, Leonard H van den Berg, Roel A. Ophoff
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.ppat.1004869

Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort Study
Cited by: 108
Author(s): Yijie Zhai, Luis M. Franco, Robert L. Atmar, John Quarles, Nancy H. Arden, Kristine L. Bucasas, Janet Wells, Diane Niño, Xueqing Wang, Gladys Zapata, Chad A. Shaw, John W. Belmont, Robert B. Couch
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.ppat.1007950

Equine arteritis virus long-term persistence is orchestrated by CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis
Cited by: 19
Author(s): Mariano Carossino, Pouya Dini, Theodore S. Kalbfleisch, Alan T. Loynachan, Igor F. Canisso, R. Frank Cook, Peter J. Timoney, Udeni B. R. Balasuriya
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-3198-9

Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems
Cited by: 81
Author(s): Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean G. Byars, Taru Tukiainen, Johannes Kettunen, Luz D. Orozco, Matteo Pellegrini, Aldons J. Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville Mäkinen, Xia Yang
Software Mentions: 3
Published: almost 10 years ago

10.1590/1414-431X20198333

Screening potential prognostic biomarkers of long non-coding RNAs for predicting the risk of chronic kidney disease
Cited by: 11
Author(s): Na Li, Yan Cui, Min Yin, Feng Liu
Software Mentions: 3
Published: over 7 years ago

10.1098/rsos.190958

Low connectivity between shallow, mesophotic and rariphotic zone benthos
Cited by: 18
Author(s): Paris V. Stefanoudis, Molly Rivers, Struan R. Smith, Craig W. Schneider, Daniel Wagner, Helen Ford, Alex D. Rogers, Lucy C. Woodall
Software Mentions: 3
Published: almost 7 years ago

10.1186/1752-0509-2-95

Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Cited by: 152
Author(s): Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath
Software Mentions: 3
Published: almost 18 years ago

10.1186/s12931-019-0995-0

Identification of differentially expressed proteins in the injured lung from zinc chloride smoke inhalation based on proteomics analysis
Cited by: 13
Author(s): Xiaowei Xie, Jiemin Zhao, Lei Xie, Haiyan Wang, Yan Xiao, Yingjia She, Lingyun Ma
Software Mentions: 3
Published: over 7 years ago

10.1186/1742-4690-8-18

Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease
Cited by: 53
Author(s): Jing Qin Wu, Dominic E. Dwyer, Wayne B. Dyer, Jean Yee Hwa Yang, Binbin Wang, Nitin K. Saksena
Software Mentions: 3
Published: over 15 years ago

10.1186/s12977-016-0248-y

TLR8 regulation of LILRA3 in monocytes is abrogated in human immunodeficiency virus infection and correlates to CD4 counts and virus loads
Cited by: 8
Author(s): Hui Zhi Low, Gerrit Ahrenstorf, Claudia Pommerenke, Nadine Habermann, Klaus Schughart, David Ordóñez, Renata Stripecke, Esther Wilk, Torsten Witte
Software Mentions: 3
Published: over 10 years ago

10.1186/s12918-016-0336-6

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus
Cited by: 51
Author(s): Jason McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Liu, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2105-15-162

A multivariate approach to the integration of multi-omics datasets
Cited by: 214
Author(s): Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0203275

Genetic diversity and biogeography of T. officinale inferred from multi locus sequence typing approach
Cited by: 3
Author(s): Mahdi Jafari, Waheed Akram, Yanju Pang, Aqeel Ahmad, Shakeel Ahmed, Nasim Ahmad Yasin, Tehmina Anjum, Basharat Ali, Xiangdong Hu, Xiaohua Li, Shuang-Lin Dong, Qian Cai, Matteo Ciprian, Monika Bielec, Sheng Hu, Fatemeh Sefidkon, Xuebo Hu
Software Mentions: 3
Published: almost 8 years ago

10.1038/srep12872

Geochemical influences and mercury methylation of a dental wastewater microbiome
Cited by: 17
Author(s): Asha Rani, Karl J. Rockne, James L. Drummond, Muntasar Al-Hinai, Ravi Ranjan
Software Mentions: 3
Published: about 11 years ago

10.1111/cns.13380

Molecular and clinical characterization of PARP9 in gliomas: A potential immunotherapeutic target
Cited by: 13
Author(s): Hao Xu, Songshan Chai, Yihao Wang, Jiajing Wang, Dongdong Xiao, Junjun Li, Nanxiang Xiong
Software Mentions: 3
Published: over 6 years ago

10.1111/cns.13254

High expression of <i>COPB2</i> predicts adverse outcomes: A potential therapeutic target for glioma
Cited by: 13
Author(s): Yan Zhou, Xuan Wang, Xing Huang, Xu‐Dong Li, Kai Chen, Hao Yu, Yujie Zhou, Ping Lv, Xiao Jiang
Software Mentions: 3
Published: almost 7 years ago

10.1002/psp4.12091

Model-Based Network Meta-Analysis: A Framework for Evidence Synthesis of Clinical Trial Data
Cited by: 48
Author(s): David Mawdsley, Meg Bennetts, Sofia Dias, Martin Boucher, Nicky J Welton
Software Mentions: 3
Published: about 10 years ago

10.1038/srep24964

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Cited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0224477

Are we ready for scaling up restoration actions? An insight from Mediterranean macroalgal canopies
Cited by: 21
Author(s): Laura Tamburello, Loredana Papa, Giuseppe Guarnieri, Laura Basconi, Serena Zampardi, Maria Beatrice Scipione, Antonio Terlizzi, Valerio Zupo, Simonetta Fraschetti
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5833-8

Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups
Cited by: 26
Author(s): Claudia Hemsley, Paul O’Neill, Angela Essex-Lopresti, Isobel H. Norville, Tim Atkins, Richard W. Titball
Software Mentions: 3
Published: about 7 years ago

10.1016/j.ccell.2018.08.015

The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation
Cited by: 75
Author(s): N Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasińska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Dan Coleman, Sirintra Nakjang, Salam A. Assi, Victoria J. Forster, Mojgan Reza, Edward Law, Philip Berry, Dorothée Mueller, Cameron S. Osborne, Alex Elder, Simon Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, Olaf Heidenreich
Software Mentions: 3
Published: almost 8 years ago

10.15252/msb.20188462

Enzyme promiscuity shapes adaptation to novel growth substrates
Cited by: 47
Author(s): Gabriela I. Guzmán, Troy E. Sandberg, Ryan A. LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A. King, Ying Hefner, Trent Northen, Richard A. Notebaart, Csaba Pál, Bernhard Palsson, Balázs Papp, Adam M. Feist
Software Mentions: 3
Published: over 7 years ago

10.1186/s12935-020-01587-z

Identified IGSF9 association with prognosis and hypoxia in nasopharyngeal carcinoma by bioinformatics analysis
Cited by: 6
Author(s): Danxia Huang, Qianqian Liu, Weijun Zhang, Chunyue Huang, Ronghui Zheng, Gaoqiang Xie, Hongmei Wang, Baochang Jia, Jianjun Shi, Yawei Yuan, Min Deng
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep44849

Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease
Cited by: 39
Author(s): Davina J. Hensman Moss, Michael Flower, Kitty Lo, James R. C. Miller, G.J.B. van Ommen, Peter A.C. ’t Hoen, Timothy Stone, Amelia Guinee, Douglas R. Langbehn, Lesley Jones, Vincent Plagnol, Willeke M. C. van Roon‐Mom, Peter Holmans, Sarah J. Tabrizi
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-01468-y

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin
Cited by: 15
Author(s): Richard Ahn, Keyon Taravati, Kevin Lai, Kristina M. Lee, Joanne Nititham, Rashmi Gupta, David S. Chang, Sarah T. Arron, Michael D. Rosenblum, Wilson Liao
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-03121-0

Echo-Planar J-resolved Spectroscopic Imaging using Dual Read-outs: Implementation and Quantitation of Human Brain Metabolites
Cited by: 4
Author(s): Manoj K. Sarma, Rajakumar Nagarajan, Zohaib Iqbal, Paul M. Macey, M. Albert Thomas
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0037108

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: about 14 years ago

10.1038/s41598-017-07015-z

Biochemical profiling of diabetes disease progression by multivariate vibrational microspectroscopy of the pancreas
Cited by: 9
Author(s): Christoffer Nord, Maria Eriksson, Andrea Dicker, Anna Eriksson, Eivind Grong, Erwin Ilegems, Ronald Mårvik, Bård Kulseng, Per Olof Berggren, András Gorzsás, Ulf Ahlgren
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-07297-3

Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum
Cited by: 37
Author(s): Bei Gao, Xiaoshuang Li, Daoyuan Zhang, Yuqing Liang, Yang Hong-yuan, Moxian Chen, Yuanming Zhang, Jianhua Zhang, Andrew J. Wood
Software Mentions: 3
Published: about 9 years ago