Ecosyste.ms: Papers

10.1186/s12885-021-08559-0

A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma
Cited by: 42
Author(s): Ying‐Kai Hong, Mingen Lin, Dehua Ou, Zhuangkai Huang, Peilin Shen
Software Mentions: 15
Published: about 3 years ago

10.1186/s12935-020-01362-0

Immune-related long non-coding RNA signature identified prognosis and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 40
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Ye Tian
Software Mentions: 13
Published: about 4 years ago

10.1371/journal.pcbi.1007753

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures
Cited by: 1
Author(s): Jacob Pfeil, Lauren Sanders, Ioannis N. Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 4 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: over 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: almost 4 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
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: almost 3 years ago

10.1111/jcmm.16619

Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: over 3 years ago

10.1002/cam4.4117

A comprehensive analysis of immune infiltration in the tumor microenvironment of osteosarcoma
Cited by: 17
Author(s): Hao Yang, Liang Zhao, Yang Zhang, Fangfang Li
Software Mentions: 10
Published: about 3 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

10.3389/fgene.2020.573515

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

10.3389/fimmu.2021.711337

Single-Cell RNA Sequencing Identifies New Inflammation-Promoting Cell Subsets in Asian Patients With Chronic Periodontitis
Cited by: 17
Author(s): Shu‐Jiao Qian, Qing-Guo Huang, Ruiying Chen, Jia-Ji Mo, Liyun Zhou, Yi Zhao, Bin Li, Hong-Chang Lai
Software Mentions: 8
Published: about 3 years ago

10.1007/s12282-020-01191-z

Immune-related gene data-based molecular subtyping related to the prognosis of breast cancer patients
Cited by: 1
Author(s): Guoyu Mu, Hong Ji, Hui He, Hongjiang Wang
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12885-021-08548-3

Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma
Cited by: 2
Author(s): Jinzhi Lai, Hainan Yang, Tianwen Xu
Software Mentions: 8
Published: about 3 years ago

10.3389/fonc.2020.614487

Distinguishable Prognostic miRNA Signatures of Head and Neck Squamous Cell Cancer With or Without HPV Infection
Cited by: 10
Author(s): Xinmei Luo, Min Zheng, Mingxin Cao, Weilong Zhang, Mengyuan Huang, Li Dai, Yaling Tang, Xin‐hua Liang
Software Mentions: 7
Published: over 3 years ago

10.1126/sciimmunol.abg0833

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Cited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: over 3 years ago

10.21203/rs.3.rs-131380/v2

Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets
Cited by: 3
Author(s): Young Il Kim, Kwang-Min Yu, June-Young Koh, Eunha Kim, Se‐Mi Kim, Young Ho Kim, Mark Anthony B. Casel, Rare Rollon, Seung-Gyu Jang, Min‐Suk Song, Su‐Jin Park, Hye Won Jeong, Eung‐Gook Kim, Ok-Jun Lee, Younho Choi, Shin-Ae Lee, Su–Hyung Park, Jae U. Jung, Young Ki Choi
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1008855

Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits
Cited by: 8
Author(s): Wei Cheng, Sohini Ramachandran, Lorin Crawford
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2021.674394

Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 3 years ago

10.3389/fonc.2021.733595

Identification of Glycolysis-Related lncRNAs and the Novel lncRNA WAC-AS1 Promotes Glycolysis and Tumor Progression in Hepatocellular Carcinoma
Cited by: 22
Author(s): Xigang Xia, Hao Zhang, Peng Xia, Yu Zhu, Jie Liu, Kequan Xu, Yufeng Yuan
Software Mentions: 7
Published: about 3 years ago

10.1038/s42003-021-02595-z

Single-cell profiling defines the prognostic benefit of CD39high tissue resident memory CD8+ T cells in luminal-like breast cancer
Cited by: 9
Author(s): Agnese Losurdo, Caterina Scirgolea, Giorgia Alvisi, Jolanda Brummelman, Valentina Errico, Luca Di Tommaso, Karolina Pilipow, Federico Colombo, Bethania Fernandes, Clelia Peano, Alberto Testori, Corrado Tinterri, Massimo Roncalli, Armando Santoro, Emilia Maria Cristina Mazza, Enrico Lugli
Software Mentions: 6
Published: almost 3 years ago

10.3389/fonc.2021.635324

Construction and Validation of a Universal Applicable Prognostic Signature for Gastric Cancer Based on Seven Immune-Related Gene Correlated With Tumor Associated Macrophages
Cited by: 14
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2021.705646

On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers
Cited by: 9
Author(s): Aarón Vázquez-Jiménez, Ugo Enrique Avila-Ponce De León, Meztli Matadamas-Guzmán, Erick Andrés Muciño-Olmos, Yoscelina Estrella Martínez-López, Thelma Escobedo-Tapia, Osbaldo Reséndis-Antonio
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-015-0815-x

The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1
Cited by: 48
Author(s): Florian Duclot, Mohamed Kabbaj
Software Mentions: 6
Published: almost 9 years ago

10.1038/s41392-021-00745-7

Melatonin enhances radiofrequency-induced NK antitumor immunity, causing cancer metabolism reprogramming and inhibition of multiple pulmonary tumor development
Cited by: 19
Author(s): Ming Li, Bingjie Hao, Menghuan Zhang, Russel J. Reíter, Shumeng Lin, Tiansheng Zheng, Xiangyun Chen, Yanru Ren, Liduo Yue, Аbay Baigenzhin, Guojie Chen, Xiao Xu, Yufeng Shi, Lihong Fan
Software Mentions: 6
Published: about 3 years ago

10.18632/aging.102683

DNAH10 mutation correlates with cisplatin sensitivity and tumor mutation burden in small-cell lung cancer
Cited by: 19
Author(s): Man Li, Anqi Lin, Peng Luo, Weitao Shen, Dan Xiao, Lan-ying Gou, Jian Zhang, Linlang Guo
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2021.665870

Prognostic and Predictive Value of Immune-Related Gene Pair Signature in Primary Lower-Grade Glioma Patients
Cited by: 2
Author(s): Kunjian Lei, Jingying Li, Zewei Tu, Feng Liu, Minhua Ye, Minxian Wu, Yue Zhu, Min Luo, Lin Li, Chuming Tao, Kai Huang, Xingen Zhu
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.632934

RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma
Cited by: 19
Author(s): Yimin Pan, Kai Xiao, Yue Li, Yuzhe Li, Qing Liu
Software Mentions: 6
Published: over 3 years ago

10.7150/thno.60031

Astrocytic YAP protects the optic nerve and retina in an experimental autoimmune encephalomyelitis model through TGF-β signaling
Cited by: 27
Author(s): Wei Qian, Xuemeng Miao, Jingjing Zhang, Ludan Xiang, Xiuchun Li, Xiaomei Bao, Siyu Du, Mianxian Wang, Shuangda Miao, Yiren Fan, Wei Wang, Xingxing Xu, Xiya Shen, Dongren Yang, Xiwu Wang, Yuanyuan Fang, Li‐Xin Hu, Xuyi Pan, Haoru Dong, Hui Wang, Ying Wang, Jia Li, Zhihui Huang
Software Mentions: 5
Published: over 3 years ago

10.1038/s41438-021-00487-1

Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development
Cited by: 34
Author(s): Anzhen Fu, Qing Wang, Jianlou Mu, Lili Ma, Changlong Wen, Xiaoyan Zhao, Lipu Gao, Jian Li, Kai Shi, Yunxiang Wang, Xuechuan Zhang, Xuewen Zhang, Fengling Wang, Donald Grierson, Jinhua Zuo
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evab099

Rampant Genome-Wide Admixture across the <i>Heliconius</i> Radiation
Cited by: 28
Author(s): Krzysztof M. Kozak, Mathieu Joron, W. Owen McMillan, Chris D. Jiggins
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-02201-2

Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis
Cited by: 28
Author(s): Kohei Saeki, Gregory Chang, Noriko Kanaya, Xiwei Wu, Jinhui Wang, Lauren Bernal, Desiree Ha, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 5
Published: over 3 years ago

10.3389/fonc.2019.00898

Genome-Wide Identification of a Novel Eight-lncRNA Signature to Improve Prognostic Prediction in Head and Neck Squamous Cell Carcinoma
Cited by: 26
Author(s): Bowen Yang, Jiming Shen, Xu Lu, Ying Chen, Xiaofang Che, Xiujuan Qu, Yunpeng Liu, Yuee Teng, Zhi Li
Software Mentions: 5
Published: almost 5 years ago

10.3390/cancers13143638

SPTAN1 Expression Predicts Treatment and Survival Outcomes in Colorectal Cancer
Cited by: 2
Author(s): Christopher Schrecker, Sophia Behrens, Rebecca Schönherr, Anne Ackermann, Daniel Pauli, Guido Plotz, Stefan Zeuzem, Angela Brieger
Software Mentions: 5
Published: about 3 years ago

10.1155/2021/7922594

Identification of the Molecular Subgroups in Idiopathic Pulmonary Fibrosis by Gene Expression Profiles
Cited by: 4
Author(s): Ning Zhang, Yubiao Guo, Cong Wu, Bohan Jiang, Yuguang Wang
Software Mentions: 5
Published: almost 3 years ago

10.3389/fonc.2020.01119

Identification of RNA: 5-Methylcytosine Methyltransferases-Related Signature for Predicting Prognosis in Glioma
Cited by: 23
Author(s): Peng Wang, Minxian Wu, Zewei Tu, Chuming Tao, Qing Hu, Kuangxun Li, Xingen Zhu, Kai Huang
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-14-S19-S1

MaTSE: the gene expression time-series explorer
Cited by: 46
Author(s): P. Craig, Alan Cannon, Robert Kukla, Jessie Kennedy
Software Mentions: 5
Published: almost 11 years ago

10.7717/peerj.11342

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
Cited by: 6
Author(s): Qingqing Wang, Xiaoyan Yu, Zhewen Zheng, Fengxia Chen, Ningning Yang, Youwen Zhou
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.ppat.1009674

Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection
Cited by: 5
Author(s): Michelle Y.H. Lee, Amit A. Upadhyay, Hasse Walum, Chi N. Chan, Reem A. Dawoud, Christine Grech, Justin Harper, Kirti A. Karunakaran, Sydney A. Nelson, Ernestine Mahar, Kyndal Goss, Diane G. Carnathan, Barbara Cervasi, Kiran Gill, Gregory K. Tharp, Elizabeth R. Wonderlich, Vijayakumar Velu, Simon M. Barratt‐Boyes, Mirko Paiardini, Guido Silvestri, Jacob D. Estes, Steven E. Bosinger
Software Mentions: 5
Published: about 3 years ago

10.1172/jci.insight.142680

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Cited by: 33
Author(s): Kirsten E. Diggins, Elisavet Serti, Virginia S. Muir, Mario G. Rosasco, Tingting Lü, Elisa Balmas, Gerald T. Nepom, S. Alice Long, Peter S. Linsley
Software Mentions: 5
Published: over 3 years ago

10.1186/s12885-019-6391-9

Identification of recurrence marker associated with immune infiltration in prostate cancer with radical resection and build prognostic nomogram
Cited by: 39
Author(s): Rui Xin, Siliang Shao, Li Wang, Jiangyong Leng
Software Mentions: 5
Published: almost 5 years ago

10.3389/fonc.2019.01147

Clinical and Expression Significance of AKT1 by Co-expression Network Analysis in Endometrial Cancer
Cited by: 19
Author(s): Xiao Huo, Hengzi Sun, Qian Liu, Xiangwen Ma, Peng Peng, Mei Yu, Ying Zhang, Dongyan Cao, Keng Shen
Software Mentions: 5
Published: almost 5 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 3 years ago

10.1186/s13637-016-0044-y

A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB
Cited by: 2
Author(s): Shriprakash Sinha
Software Mentions: 4
Published: about 8 years ago

10.1186/s12885-015-1179-z

Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma
Cited by: 57
Author(s): Yibin Hao, Wei Wu, Fachun Shi, Rodrigo Juliani Siqueira Dalmolin, Ming Yan, Fei Tian, Xiaobing Chen, Guoyong Chen, Wei Cao
Software Mentions: 4
Published: over 9 years ago

10.3389/fimmu.2020.590618

A TP53-Associated Immune Prognostic Signature for the Prediction of Overall Survival and Therapeutic Responses in Muscle-Invasive Bladder Cancer
Cited by: 32
Author(s): Xiangkun Wu, Daojun Lv, Chao Cai, Zhijian Zhao, Ming Wang, Wenzhe Chen, Yongda Liu
Software Mentions: 4
Published: almost 4 years ago

10.3389/fnins.2016.00390

Bidirectional Expression of Metabolic, Structural, and Immune Pathways in Early Myopia and Hyperopia
Cited by: 31
Author(s): Nina Riddell, Loretta Giummarra, Nathan E. Hall, Sheila G. Crewther
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0012548

The Proneural Molecular Signature Is Enriched in Oligodendrogliomas and Predicts Improved Survival among Diffuse Gliomas
Cited by: 130
Author(s): Lee Cooper, David Gutman, Qi Long, Brent A. Johnson, Sharath R. Cholleti, Tahsin Kurç, Joel Saltz, Daniel J. Brat, Carlos S. Moreno
Software Mentions: 4
Published: about 14 years ago

10.3389/fonc.2020.01065

Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling
Cited by: 28
Author(s): Marco Chierici, Nicole Bussola, Alessia Marcolini, Margherita Francescatto, Alessandro Zandonà, Lucia Trastulla, Claudio Agostinelli, Giuseppe Jurman, Cesare Furlanello
Software Mentions: 4
Published: about 4 years ago

10.18632/oncotarget.13814

The bromodomain inhibitor OTX015 (MK-8628) exerts anti-tumor activity in triple-negative breast cancer models as single agent and in combination with everolimus
Cited by: 74
Author(s): Ramiro Vàzquez, María E. Riveiro, Lucile Astorgues‐Xerri, Elodie Odore, Keyvan Rezai, Eugenio Erba, Nicolò Panini, Andrea Rinaldi, Ivo Kwee, Luca Beltrame, Mohamed Békradda, Esteban Cvitkovic, Francesco Bertoni, Roberta Frapolli, Maurizio D’Incalci
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12967-020-02279-y

Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease
Cited by: 9
Author(s): Li Ma, Wu Shi, Xiaoyan Ma, Ming‐Hui Zou, Weidan Chen, Wenlei Li, Rongjun Zou, Xinxin Chen
Software Mentions: 4
Published: over 4 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 6 years ago

10.7717/peerj.10812

Construction of an immune-related signature with prognostic value for colon cancer
Cited by: 2
Author(s): Yunxia Lv, Xinyi Wang, Yu Ren, Xiaorui Fu, Taiyuan Li, Qunguang Jiang
Software Mentions: 4
Published: over 3 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: about 7 years ago

10.7554/eLife.46919

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Cited by: 63
Author(s): Kirsty Sawicka, Caryn Hale, Christopher Y. Park, John Fak, Jodi Gresack, Sarah J. Van Driesche, Jaw Jou Kang, Jennifer C. Darnell, Robert B. Darnell
Software Mentions: 4
Published: over 4 years ago

10.1186/s40880-018-0326-8

Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells
Cited by: 20
Author(s): Man‐Li Tong, Ziqian Deng, Mengying Yang, Chang Xu, Xiaolong Zhang, Qingzheng Zhang, Yuwei Liao, Xiaolong Deng, Dekang Lv, Xuehong Zhang, Yu Zhang, Peiying Li, Limei Song, Bi-Cheng Wang, Aisha Al-Dherasi, Chi Kong Li, Quentin Liu
Software Mentions: 3
Published: almost 6 years ago

10.1002/ctm2.138

Cell cycle progression score as a predictive biomarker for overall survival in patients with adrenocortical carcinoma
Cited by: 0
Author(s): Jing Sun, Run Shi, Felix Beuschlein, C. Belka, Minglun Li
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2020.586376

A Novel Apoptosis-Related Gene Signature Predicts Biochemical Recurrence of Localized Prostate Cancer After Radical Prostatectomy
Cited by: 5
Author(s): Qijie Zhang, Kai Zhao, Lebin Song, Chengjian Ji, Rong Cong, Jiaochen Luan, Xiang Zhou, Jun Xia, Ninghong Song
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2021.666833

MiR-3614-5p Is a Potential Novel Biomarker for Colorectal Cancer
Cited by: 9
Author(s): Han Lin, Yanjun Sun, Cansheng Lu, Chungeng Ma, Jian Shi, Dengqun Sun
Software Mentions: 3
Published: over 3 years ago

10.1186/s12862-015-0550-7

Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose
Cited by: 32
Author(s): Magriet A. van der Nest, Emma Theodora Steenkamp, Alistair R. McTaggart, Conrad Trollip, T. Godlonton, E. Sauerman, Danielle Roodt, Kershney Naidoo, Martin Petrus Albertus Coetzee, P. Markus Wilken, Michael J. Wingfield, Brenda D. Wingfield
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-13-105

Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures
Cited by: 41
Author(s): Ana I. Manzano, Jack J. W. A. van Loon, Peter C. M. Christianen, Juana María González-Rubio, F. Javier Medina, Raúl Herranz
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-015-1515-3

The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits
Cited by: 4
Author(s): Hao Mei, Lianna Li, Shijian Liu, Fan Jiang, Michael Griswold, Thomas H. Mosley
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-15-79

The characteristic direction: a geometrical approach to identify differentially expressed genes
Cited by: 142
Author(s): Neil R. Clark, Kevin Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma’ayan
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-11520-6

Identification of prognostic genes through expression differentiation during metastatic process in lung adenocarcinoma
Cited by: 2
Author(s): Ning An, Xue Yang
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-14-143

Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Cited by: 23
Author(s): Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li
Software Mentions: 3
Published: over 11 years ago

10.1186/s13068-018-1198-5

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass
Cited by: 31
Author(s): Shingo Miyauchi, Anaïs Rancon, Élodie Drula, Hayat Hage, Delphine Chaduli, Anne Favel, Sacha Grisel, Bernard Henrissat, Isabelle Herpoël-Gimbert, Francisco J. Ruíz-Dueñas, Didier Chevret, Matthieu Hainaut, Jinfeng Lin, Mei Wang, Jasmyn Pangilinan, Anna Lipzen, Laurence Lesage‐Meessen, David Navarro, Robert Riley, Igor V. Grigoriev, Simeng Zhou, Sana Raouche, Marie‐Noëlle Rosso
Software Mentions: 3
Published: about 6 years ago

10.1186/s13058-014-0482-y

A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes
Cited by: 29
Author(s): Richard Hill, Ravi Kiran Reddy Kalathur, Sergio Callejas, Laura Colaço, Ricardo Brandão, Beatriz G. Serelde, Antonio Cebriá, Carmen Blanco‐Aparicio, Joaquı́n Pastor, Matthias E. Futschik, Ana Dopazo, Wolfgang Link
Software Mentions: 3
Published: almost 10 years ago

10.1093/bib/bbx149

Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
Cited by: 20
Author(s): Francesca Vitali, Haiquan Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, Yves A. Lussier
Software Mentions: 3
Published: over 6 years ago

10.1038/s41419-018-0342-2

Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells
Cited by: 30
Author(s): Shariq Ansari, Ashwini Kumar Sharma, Himanshu Soni, Doaa M. Ali, Björn Tews, Rainer König, Hansjörg Eibl, Martin R. Berger
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-020-00414-w

The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy
Cited by: 3
Author(s): Peng Zhao, Guiliang Xin, Feng Yan, Huan Wang, Xiaolong Ren, Keith Woeste, Wenzhe Liu
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2407-13-585

The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts
Cited by: 10
Author(s): Pratiti Bandopadhayay, Anissa Jabbour, Christopher D. Riffkin, Marika Salmanidis, Lavinia Gordon, Dean Popovski, Lin Rigby, David M. Ashley, D. Neil Watkins, David M. Thomas, Elizabeth Algar, Paul G. Ekert
Software Mentions: 3
Published: almost 11 years ago

10.14814/phy2.14482

Modifying nutritional substrates induces macrovesicular lipid droplet accumulation and metabolic alterations in a cellular model of hepatic steatosis
Cited by: 5
Author(s): Pippa J. Gunn, Camilla Pramfalk, Val Millar, Thomas Cornfield, Matthew Hutchinson, Elspeth Johnson, Shilpa R. Nagarajan, Perla Troncoso‐Rey, Richard Mithen, Katherine E. Pinnick, Μαρία Τράκα, Charlotte Green, Leanne Hodson
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2020.563237

GelFAP: Gene Functional Analysis Platform for Gastrodia elata
Cited by: 6
Author(s): Jiaotong Yang, Qiaoqiao Xiao, Jin Xu, Lingling Da, Lan-Ping Guo, Luqi Huang, Yue Liu, Wenying Xu, Zhen Su, Shiping Yang, Qi Pan, Wei-Ke Jiang, Tao Zhou
Software Mentions: 3
Published: almost 4 years ago

10.18632/aging.103645

Bioinformatics analysis of the clinical value and potential mechanisms of AHNAK2 in papillary thyroid carcinoma
Cited by: 12
Author(s): Zhenyu Xie, Yu Lun, Xin Li, Yuzhen He, Song Wu, Shiyue Wang, Jing Sun, Yuchen He, Jian Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0038602

Gene Expression Changes in the Septum: Possible Implications for MicroRNAs in Sculpting the Maternal Brain
Cited by: 19
Author(s): Changjiu Zhao, Michael C. Saul, Terri M. Driessen, Stephen C. Gammie
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0015188

Genome-Wide Analysis of Glucocorticoid Receptor Binding Regions in Adipocytes Reveal Gene Network Involved in Triglyceride Homeostasis
Cited by: 151
Author(s): Chi-Yi Yu, Oleg Mayba, Joyce V. Lee, Joanna Tran, Charlie Harris, Terence P. Speed, Jen-Chywan Wang
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-021-97371-8

Compromised anti-tumor–immune features of myeloid cell components in chronic myeloid leukemia patients
Cited by: 1
Author(s): Ibuki Harada, Haruka Sasaki, Koichi Murakami, Akira Nishiyama, Jun Nakabayashi, Motohide Ichino, Tatsuya Miyazaki, Ken Kumagai, Kenji Matsumoto, Maki Hagihara, Wataru Kawase, Takayoshi Tachibana, Masatsugu Tanaka, T. Saito, Heiwa Kanamori, Hiroyuki Fujita, Shin Fujisawa, Hitoshi Nakajima, Tomohide Tamura
Software Mentions: 2
Published: about 3 years ago

10.18632/aging.203234

Prognostic signatures associated with high infiltration of Tregs in bone metastatic prostate cancer
Cited by: 4
Author(s): Fanbao Meng, Xu Han, Zhixue Min, Xiaotian He, Sha Zhu
Software Mentions: 2
Published: about 3 years ago

10.1186/s13075-017-1388-8

Anabolic role of lysyl oxidase like-2 in cartilage of knee and temporomandibular joints with osteoarthritis
Cited by: 27
Author(s): Weam Alshenibr, Mustafa Tashkandi, Saqer F. Alsaqer, Yazeed Alkheriji, Amelia Wise, Sadanand Fulzele, Pushkar Mehra, Mary B. Goldring, Louis C. Gerstenfeld, Manish V. Bais
Software Mentions: 2
Published: about 7 years ago

10.1186/s12885-021-08597-8

NR1D1 suppressed the growth of ovarian cancer by abrogating the JAK/STAT3 signaling pathway
Cited by: 12
Author(s): Huailin Wang, Yan Fu
Software Mentions: 2
Published: about 3 years ago

10.1186/s12885-021-08486-0

A novel immune-related gene pair prognostic signature for predicting overall survival in bladder cancer
Cited by: 4
Author(s): Yang Xin Fu, Shanshan Sun, Jianbin Bi, Chuize Kong, Lei Yin
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2148-13-133

Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis
Cited by: 8
Author(s): Raúl Herranz, Oliver Larkin, R. Hill, Irene López‐Vidriero, Jack J. W. A. van Loon, F. Javier Medina
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-10-210

Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2
Cited by: 19
Author(s): Alan L. Kwan, Linya Li, David Kulp, Susan K. Dutcher, Gary D. Stormo
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-14-226

Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis
Cited by: 13
Author(s): Élodie Darbo, Carl Herrmann, Thomas Lecuit, Denis Thieffry, Jacques van Helden
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-12-565

Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia
Cited by: 28
Author(s): Vivek Bhadri, Mark J. Cowley, Warren Kaplan, Toby N. Trahair, Richard B. Lock
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-13-686

A REST derived gene signature stratifies glioblastomas into chemotherapy resistant and responsive disease
Cited by: 14
Author(s): Matthew P. Wagoner, Avtar Roopra
Software Mentions: 2
Published: over 12 years ago

10.1093/bioinformatics/btx082

Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Cited by: 57
Author(s): Claudia Hernández-Armenta, David Ochoa, Emanuel Gonçalvès, Julio Sáez-Rodríguez, Pedro Beltrão
Software Mentions: 2
Published: over 7 years ago

10.1155/2020/8657468

Integrated Bioinformatics Analysis of the Clinical Value and Biological Function of ATAD2 in Hepatocellular Carcinoma
Cited by: 7
Author(s): Xiangyu Meng, Lu Wang, Bo Zhu, Jun Zhang, Shuai Guo, Qiang Li, Tao Zhang, Zhichao Zheng, Gang Wu, Yan Zhao
Software Mentions: 2
Published: over 4 years ago

10.1155/2021/8826286

Using Elevated Cholesterol Synthesis as a Prognostic Marker in Wilms’ Tumor: A Bioinformatic Analysis
Cited by: 2
Author(s): Yuanbin He, Xu Cui, Yu Lin, Yunjin Wang, Dianming Wu, Yifan Fang
Software Mentions: 2
Published: over 3 years ago

10.1155/2020/3962146

TPPP3 Associated with Prognosis and Immune Infiltrates in Head and Neck Squamous Carcinoma
Cited by: 9
Author(s): Zheng Yang, Xiaohong Li, Jingyu Li, Qingde Su, Yuling Qiu, Zunni Zhang, Liqian Zhang, Wuning Mo
Software Mentions: 2
Published: almost 4 years ago

10.3390/biom10101377

Omics-Based Platforms: Current Status and Potential Use for Cholangiocarcinoma
Cited by: 4
Author(s): Yu‐Chan Chang, Ming-Huang Chen, Chun‐Nan Yeh, Michael Hsiao
Software Mentions: 2
Published: almost 4 years ago

10.1186/bcr3689

Parity-related molecular signatures and breast cancer subtypes by estrogen receptor status
Cited by: 35
Author(s): Melissa Rotunno, Xuezheng Sun, Jonine D. Figueroa, Mark E. Sherman, Montserrat García-Closas, Paul S. Meltzer, Tyisha Williams, Sallie S. Schneider, D. Joseph Jerry, Xiaohong R. Yang, Melissa A. Troester
Software Mentions: 2
Published: over 10 years ago

10.1002/mgg3.515

Gene coexpression network analysis identified potential biomarkers in gestational diabetes mellitus progression
Cited by: 11
Author(s): Xuefei Zhao, Wen Li
Software Mentions: 2
Published: almost 6 years ago

10.1002/1878-0261.12317

Genomewide binding of transcription factor Snail1 in triple‐negative breast cancer cells
Cited by: 21
Author(s): Varun Maturi, Anita Morén, Stefan Enroth, Carl‐Henrik Heldin, Aristidis Moustakas
Software Mentions: 2
Published: over 6 years ago

10.1002/1878-0261.12012

Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer
Cited by: 36
Author(s): Yuka Suzuki, Sarah Boonhsi Ng, Clarinda Chua, Wei Qiang Leow, Jermain Chng, Shi Yang Liu, R. Kalpana, Anna Gan, Dan Liang Ho, Rachel Ten, Yan Shu, A. Lezhava, Jiunn Herng Lai, David Koh, Kiat Hon Lim, Patrick Tan, Steven G. Rozen, Iain Beehuat Tan
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.8348

Prognostic value of CLIC3 mRNA overexpression in bladder cancer
Cited by: 9
Author(s): Mei Chen, Shufang Zhang, Xiaohong Wen, Hui Cao, Yuanhui Gao
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1003291

miR-199a-5p Is Upregulated during Fibrogenic Response to Tissue Injury and Mediates TGFbeta-Induced Lung Fibroblast Activation by Targeting Caveolin-1
Cited by: 209
Author(s): Christian L. Lino Cardenas, Imène Sarah Hénaoui, Elisabeth Courcot, Christoph Roderburg, Christelle Cauffiez, Sébastien Aubert, Marie‐Christine Copin, B. Wallaert, François Glowacki, Edmone Dewaeles, Jadranka Milošević, Julien Maurizio, John Tedrow, Brice Marcet, Jean-Marc Lo-Guidice, Naftali Kaminski, Pascal Barbry, Tom Luedde, Michaël Perrais, Bernard Mari, Nicolas Pottier
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0224086

Double triage to identify poorly annotated genes in maize: The missing link in community curation
Cited by: 9
Author(s): Marcela K. Tello-Ruiz, Cristina F. Marco, Fei‐Man Hsu, Rajdeep S. Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay Barone, Cornel Ghiban, Demitri Muna, Andrew Olson, Liya Wang, Doreen Ware, David Micklos
Software Mentions: 2
Published: almost 5 years ago

10.15252/embr.201642198

Capture‐C reveals preformed chromatin interactions between <scp>HIF</scp> ‐binding sites and distant promoters
Cited by: 58
Author(s): James L. Platt, Rafik Salama, James Smythies, Hani Choudhry, James O. J. Davies, Jim R. Hughes, Peter J. Ratcliffe, David R. Mole
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2021.616073

Comprehensive Analysis of Tumor Microenvironment Identified Prognostic Immune-Related Gene Signature in Ovarian Cancer
Cited by: 13
Author(s): Na Li, Biao Li, Xianquan Zhan
Software Mentions: 2
Published: over 3 years ago