cran: NMF | Projects | Ecosyste.ms: Papers

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1038/s41598-021-88209-4

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.15252/msb.20209498

Developmental function and state transitions of a gene expression oscillator in <i>Caenorhabditis elegans</i>
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago

10.1186/s12920-019-0578-4

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients
Cited by: 21
Author(s): Petr V. Nazarov, Anke Wienecke-Baldacchino, Andreï Zinovyev, Urszula Czerwińska, Arnaud Muller, Dorothée Nashan, Gunnar Dittmar, Francisco Azuaje, Stephanie Kreis
Software Mentions: 14
Published: over 5 years ago

10.1186/s12967-021-02894-3

Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responses
Cited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago

10.18632/oncotarget.6716

Integrative bioinformatic analyses of an oncogenomic profile reveal the biology of endometrial cancer and guide drug discovery
Cited by: 5
Author(s): Henry Sung Ching Wong, Yung‐Shun Juan, Mei-Shin Wu, Yan Feng Zhang, Yi‐Hsiang Hsu, Huang-Hui Chen, Weimin Liu, Wei Chiao Chang
Software Mentions: 13
Published: about 9 years ago

10.3389/fimmu.2021.698236

Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung Adenocarcinoma
Cited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: about 3 years ago

10.3389/fmolb.2021.684050

Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pgen.1007102

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Cited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: about 7 years ago

10.1534/g3.120.401436

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Cited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: about 4 years ago

10.3389/fonc.2021.711020

Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model
Cited by: 37
Author(s): Leilei Liang, Jing Yu, Jian Li, Ning Li, Jing Liu, Lin Xiu, Jia Zeng, Tiantian Wang, Lingying Wu
Software Mentions: 9
Published: over 3 years ago

10.3389/fphar.2021.608778

Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma
Cited by: 0
Author(s): Zhichao Liu, Xi Chen, Ruth Roberts, Ruili Huang, Mike Mikailov, Weida Tong
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1006378

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Cited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: over 6 years ago

10.1038/s41598-021-98966-x

Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy
Cited by: 4
Author(s): Xiangkuo Zheng, Yong Gao, Chunhua Yu, Guiquan Fan, Pengwu Li, Ming Zhang, Jian Yu, Mingqing Xu
Software Mentions: 8
Published: about 3 years ago

10.1186/s12964-019-0397-4

Subtyping of microsatellite instability-high colorectal cancer
Cited by: 28
Author(s): Wangxiong Hu, Yanmei Yang, Ling Qi, Jiani Chen, Weiting Ge, Shu Zheng
Software Mentions: 8
Published: over 5 years ago

10.1186/s12967-020-02697-y

A novel immune classification reveals distinct immune escape mechanism and genomic alterations: implications for immunotherapy in hepatocellular carcinoma
Cited by: 58
Author(s): Zaoqu Liu, Yuyuan Zhang, Chengcheng Shi, Xueliang Zhou, Kaihao Xu, Dechao Jiao, Zhenqiang Sun, Xinwei Han
Software Mentions: 7
Published: almost 4 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: almost 8 years ago

10.1242/dmm.039297

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Cited by: 10
Author(s): Christopher Nash, Nadia Boufaied, Dunarel Badescu, Yu Chang Wang, Miltiadis Paliouras, Mark Trifiro, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1009119

De novo mutational signature discovery in tumor genomes using SparseSignatures
Cited by: 21
Author(s): Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti
Software Mentions: 6
Published: over 3 years ago

10.1186/s12935-020-01552-w

Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population
Cited by: 7
Author(s): Qiang Zhao, Jian Xue, Bo Hong, Wubin Qian, Tiezhu Liu, Bin Fan, Jie Cai, Yunpeng Ji, Jia Liu, Yong Yang, Qi-Xiang Li, Sheng Guo, Ning Zhang
Software Mentions: 6
Published: over 4 years ago

10.3390/cancers13143394

Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma
Cited by: 7
Author(s): Fereshteh Izadi, Benjamin Sharpe, Stella P. Breininger, Maria Secrier, Jane Gibson, Robert Walker, S Rahman, Ginny Devonshire, Matthew G. Lloyd, Zoë S. Walters, Rebecca Fitzgerald, Matthew Rose-Zerilli, Tim Underwood
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.53618

Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth
Cited by: 15
Author(s): Caroline Contat, Pierre‐Benoit Ancey, Nadine Zangger, Silvia Sabatino, Justine Pascual, Stéphane Escrig, Linda Jensen, Christine Goepfert, Bernard Lanz, Mario Lepore, Rolf Gruetter, A. Rossier, Sabina Berezowska, Christina Neppl, Inti Zlobec, Stéphanie Clerc-Rosset, Graham Knott, Jeffrey C. Rathmell, E. Dale Abel, A. Meibom, Etienne Meylan
Software Mentions: 6
Published: over 4 years ago

10.3389/fonc.2021.632430

Genomic Alteration Characterization in Colorectal Cancer Identifies a Prognostic and Metastasis Biomarker: FAM83A|IDO1
Cited by: 29
Author(s): Zaoqu Liu, Yuyuan Zhang, Qin Dang, Kunpeng Wu, Dechao Jiao, Zhen Li, Zhenqiang Sun, Xinwei Han
Software Mentions: 6
Published: over 3 years ago

10.3389/fmolb.2020.608368

Identification and Development of a Novel 4-Gene Immune-Related Signature to Predict Osteosarcoma Prognosis
Cited by: 12
Author(s): Mingde Cao, Junhui Zhang, Haiyan Xu, Zhujian Lin, Hong Chang, Yuchen Wang, Xusheng Huang, Xiang Chen, Hua Wang, Yancheng Song
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2017.02102

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession
Cited by: 17
Author(s): Miao Wang, Erqin Li, Chen Liu, Alexandre Jousset, Joana Falcão Salles
Software Mentions: 6
Published: about 7 years ago

10.1186/s12915-021-01071-8

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma
Cited by: 17
Author(s): Wenqin Luo, Guan Ning Lin, Weichen Song, Yu Zhang, Huadong Lai, Man Zhang, Juju Miao, Xiaomu Cheng, Yongjie Wang, Wang Li, Wenxiang Wei, Wei‐Qiang Gao, Ru Yang, Jia Wang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1009256

A murine model of Lyme disease demonstrates that Borrelia burgdorferi colonizes the dura mater and induces inflammation in the central nervous system
Cited by: 23
Author(s): Timothy Casselli, Ali Divan, Emilie E. Vomhof-DeKrey, Yvonne Tourand, Heidi L. Pecoraro, Catherine A. Brissette
Software Mentions: 5
Published: almost 4 years ago

10.1155/2021/9998697

Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19
Cited by: 12
Author(s): Shaocong Mo, Leijie Dai, Yulin Wang, Biao Song, Zongcheng Yang, Wenchao Gu
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.22169

Immunological landscape of consensus clusters in colorectal cancer
Cited by: 49
Author(s): Paweł Karpiński, Joanna Rossowska, Maria M. Sasiadek
Software Mentions: 5
Published: about 7 years ago

10.7150/jca.51812

Identification of an apoptosis-related prognostic gene signature and molecular subtypes of clear cell renal cell carcinoma (ccRCC)
Cited by: 3
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmolb.2021.682084

Comprehensive Molecular Analyses of a Novel Mutational Signature Classification System with Regard to Prognosis, Genomic Alterations, and Immune Landscape in Glioma
Cited by: 26
Author(s): Xinwei Han, Taoyuan Lu, Libo Wang, Long Liu, Lifeng Li, Xinwei Han
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-13-59

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
Cited by: 97
Author(s): Joanna Zhuang, Martin Widschwendter, Andrew E. Teschendorff
Software Mentions: 5
Published: over 12 years ago

10.1186/s13073-021-00952-5

Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes
Cited by: 39
Author(s): Bethany Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I‐Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan, Stephen S. Taylor
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21239169

Development and Validation of a Novel 11-Gene Prognostic Model for Serous Ovarian Carcinomas Based on Lipid Metabolism Expression Profile
Cited by: 28
Author(s): Mingjun Zheng, Heather Mullikin, Anna Hester, Bastian Czogalla, H Heidegger, Theresa� Vilsmaier, Aurelia Vattai, Anca Chelariu-Raicu, Udo Jeschke, Fabian Trillsch, Sven Mahner, Till Kaltofen
Software Mentions: 5
Published: about 4 years ago

10.1186/s12935-020-01283-y

Identification and validation of m6A RNA methylation regulators with clinical prognostic value in Papillary thyroid cancer
Cited by: 34
Author(s): Xinyi Wang, Xiaorui Fu, Junjia Zhang, Xiong Cai, Shuyong Zhang, Yali Lv
Software Mentions: 5
Published: over 4 years ago

10.1186/s13024-020-00405-4

Integrated analysis of the aging brain transcriptome and proteome in tauopathy
Cited by: 20
Author(s): Carl Grant Mangleburg, Timothy Wu, Hari Krishna Yalamanchili, Caiwei Guo, Yi-Cheng Hsieh, Duc Duong, Eric B. Dammer, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Zhandong Liu
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0188842

Markers of epithelial-to-mesenchymal transition reflect tumor biology according to patient age and Gleason score in prostate cancer
Cited by: 31
Author(s): Dorota Jędroszka, Magdalena Orzechowska, R. Hamouz, Karolina Górniak, Andrzej K. Bednarek
Software Mentions: 5
Published: about 7 years ago

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-020-75062-0

MutSignatures: an R package for extraction and analysis of cancer mutational signatures
Cited by: 27
Author(s): Damiano Fantini, Vania Vidimar, Yu Yu, Salvatore Condello, Joshua J. Meeks
Software Mentions: 5
Published: about 4 years ago

10.3390/cancers11040489

Functional Effects of let-7g Expression in Colon Cancer Metastasis
Cited by: 9
Author(s): Che Mai Chang, Henry Sung Ching Wong, Chien‐Yu Huang, Wen Li Hsu, Zhi Feng Maio, Siou Jin Chiu, Yao Ting Tsai, Ben Kuen Chen, Yu Wan, Jaw‐Yuan Wang, Wei Chiao Chang
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.736540

Characterization of Molecular Heterogeneity Associated With Tumor Microenvironment in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy
Cited by: 9
Author(s): Weimin Zhong, Yinan Li, Yazhou Yuan, Hongbin Zhong, Chaoqun Huang, Jiwei Huang, Yao Lin, Jian Huang
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.ppat.1009097

Vaginal microbiome-hormonal contraceptive interactions associate with the mucosal proteome and HIV acquisition
Cited by: 17
Author(s): Laura Noël‐Romas, Michelle Perner, Refilwe P. Molatlhegi, Christina Farr Zuend, Amanda Mabhula, Sarah Hoger, Alana Lamont, Kenzie Birse, Alicia R. Berard, Stuart McCorrister, Garett Westmacott, Al Leslie, Vanessa Poliquin, Renee Heffron, Lyle R. McKinnon, Adam Burgener
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-67743-7

Multivariate analysis reveals differentially expressed genes among distinct subtypes of diffuse astrocytic gliomas: diagnostic implications
Cited by: 10
Author(s): Nerea González‐García, Ana Belén Nieto Librero, Ana Luísa Vital, Hermínio Tão, María González-Tablas, Álvaro Otero, Purificación Galindo-Villardón, Alberto Órfão, María Dolores Tabernero
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms18030627

Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens
Cited by: 14
Author(s): Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert T. Greenlee, Deborah Multerer, Stacey Honda, Yihe G. Daida, Heather Spencer Feigelson, Andrew G. Glass, Fergus J. Couch, Thomas E. Rohan, Iddo Z. Ben‐Dov
Software Mentions: 4
Published: almost 8 years ago

10.1155/2019/9523719

Attention-Based Multi-NMF Deep Neural Network with Multimodality Data for Breast Cancer Prognosis Model
Cited by: 13
Author(s): Hongling Chen, Mingyan Gao, Ying Zhang, Wenbin Liang, Xuan Zou
Software Mentions: 4
Published: over 5 years ago

10.1186/s40793-019-0346-2

Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease
Cited by: 20
Author(s): Viviane Radl, Jana Barbro Winkler, Susanne Kublik, Luhua Yang, Traud Winkelmann, Gisle Vestergaard, Peter Schröder, Michael Schloter
Software Mentions: 4
Published: about 5 years ago

10.1186/s13045-017-0462-7

Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs
Cited by: 56
Author(s): Todd P. Knutson, Thu H. Truong, Shihong Ma, Nicholas J. Brady, Megan Sullivan, Ganesh V. Raj, Kathryn L. Schwertfeger, Carol A. Lange
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2017.01284

Assessment of the Combined Effect of Epstein–Barr Virus and Plasmodium falciparum Infections on Endemic Burkitt Lymphoma Using a Multiplex Serological Approach
Cited by: 13
Author(s): Ruth Aguilar, Delphine Casabonne, Cristina O’Callaghan-Gordo, Marta Vidal, Joseph J. Campo, Nora Mutalima, Evelina Angov, Sandeep Dutta, Deepak Gaur, Chetan E. Chitnis, Virander S. Chauhan, Angelika Michel, Sílvia de Sanjosé, Tim Waterboer, Manolis Kogevinas, Rob Newton, Carlota Dobaño
Software Mentions: 4
Published: about 7 years ago

10.1186/s12967-015-0453-9

GLI2 inhibition abrogates human leukemia stem cell dormancy
Cited by: 81
Author(s): Anil Sadarangani, Gabriel Pineda, Kathleen M. Lennon, Hye Jung Chun, Alice Shih, Annelie Schairer, Angela C. Court, Daniel Goff, Sacha Prashad, Ifat Geron, Russell Wall, John Douglas Mcpherson, Richard A. Moore, Minya Pu, Lei Bao, Amy Jackson-Fisher, Michael J. Munchhof, Todd VanArsdale, Tannishtha Reya, Sheldon R. Morris, Mark D. Minden, Karen Messer, Hanna Mikkola, Marco A. Marra, Thomas J. Hudson, Catriona Jamieson
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-018-25604-4

Transcriptomic integration of D4R and MOR signaling in the rat caudate putamen
Cited by: 8
Author(s): Alejandra Valderrama-Carvajal, Haritz Irizar, Belén Gago, Haritz Jiménez-Urbieta, Kjell Fuxé, María C. Rodríguez‐Oroz, David Otaegui, Alicia Rivera
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-015-0485-4

NMF-mGPU: non-negative matrix factorization on multi-GPU systems
Cited by: 44
Author(s): Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoaín, Carlos Garcı́a, Francisco Tirado, Alberto Pascual-Montano
Software Mentions: 4
Published: almost 10 years ago

10.3390/nu11122973

Giardia intestinalis and Fructose Malabsorption: A Frequent Association
Cited by: 18
Author(s): María Trelis, Silvia Taroncher-Ferrer, Mónica Gozalbo, Vicente Ortiz, José Miguel Soriano del Castillo, Antonio Osuna, Juan Francisco Merino-Torres
Software Mentions: 3
Published: about 5 years ago

10.18632/aging.102736

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota
Cited by: 46
Author(s): Ning Liufu, Ling Liu, Shiqian Shen, Zengliang Jiang, Yuanlin Dong, Yanyan Wang, Deborah J. Culley, Gregory Crosby, Minghui Cao, Yuan Shen, Edward R. Marcantonio, Zhongcong Xie, Yiying Zhang
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.103202

Integrative analysis of genomic and epigenetic regulation of endometrial cancer
Cited by: 6
Author(s): Qihang Zhong, Junpeng Fan, Honglei Chu, Mujia Pang, Junsheng Li, Yong Fan, Ping Liu, Congying Wu, Jie Qiao, Rong Li, Jing Hang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12920-021-00876-4

Development and validation of prognostic markers in sarcomas base on a multi-omics analysis
Cited by: 4
Author(s): Yi Song, Kui Yang, Tuanhe Sun, Ruixiang Tang
Software Mentions: 3
Published: almost 4 years ago

10.1155/2018/6515670

Microbiota Composition in Upper Respiratory Tracts of Healthy Children in Shenzhen, China, Differed with Respiratory Sites and Ages
Cited by: 23
Author(s): Heping Wang, Wenkui Dai, Xin Feng, Qian Zhou, Hongmei Wang, Yonghong Yang, Shuai Cheng Li, Yuejie Zheng
Software Mentions: 3
Published: over 6 years ago

10.1002/cam4.3842

Subgrouping by gene expression profiles to improve relapse risk prediction in paediatric B‐precursor acute lymphoblastic leukaemia
Cited by: 1
Author(s): Qingsheng Huang, Jiayong Zhong, Huan Gao, Kuanrong Li, Huiying Liang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pbio.2005086

Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice
Cited by: 35
Author(s): Alberto Roselló-Díez, Linda Madisen, Sébastien Bastide, Hongkui Zeng, Alexandra L. Joyner
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1006581

Differences in the rare variant spectrum among human populations
Cited by: 90
Author(s): Iain Mathieson, David Reich
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0238742

A hypothetical trivalent epigenetic code that affects the nature of human ESCs
Cited by: 2
Author(s): Yasuhisa Ishikawa, Kenta Nakai
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0179945

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major)
Cited by: 21
Author(s): Lucie Kropáčková, Hana Pechmanová, Michal Vinkler, Jana Svobodová, Hana Velová, Martin Těšičký, Jean‐François Martin, Jakub Kreisinger
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0192775

Functional characterization and genomic studies of a novel murine submandibular gland epithelial cell line
Cited by: 6
Author(s): Sang‐Won Min, Eun-Ah Christine Song, Akinsola Oyelakin, Christian Gluck, Kirsten Smalley, Rose‐Anne Romano
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0188900

FGMD: A novel approach for functional gene module detection in cancer
Cited by: 6
Author(s): Dao‐Chao Jin, Hyunju Lee
Software Mentions: 3
Published: about 7 years ago

10.1186/s13072-017-0131-7

A computational approach for the functional classification of the epigenome
Cited by: 3
Author(s): Francesco Gandolfi, Anna Tramontano
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.669400

Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies
Cited by: 4
Author(s): Abhinandan Devaprasad, Timothy R D J Radstake, Aridaman Pandit
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.01622

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica
Cited by: 20
Author(s): Fatma Karray, Mahmoud Gargouri, Asma Chebaane, Najla Mhiri, Ahmed Mliki, Sami Sayadi
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2020.566430

Hypoxia Correlates With Poor Survival and M2 Macrophage Infiltration in Colorectal Cancer
Cited by: 33
Author(s): Ling Qi, Jiani Chen, Yanmei Yang, Wangxiong Hu
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-11552-y

Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax
Cited by: 34
Author(s): Tânia Pimentel, Joana Marcelino, Fernando Ricardo, Amadeu M.V.M. Soares, Ricardo Calado
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: over 5 years ago

10.1002/jev2.12110

Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV‐CATCHER): A customizable purification assay designed for small‐RNA biomarker identification and evaluation of circulating small‐EVs
Cited by: 23
Author(s): Megan I. Mitchell, Iddo Z. Ben‐Dov, Christina Liu, Kenny Ye, Kar Fai Chow, Y.G. Kramer, Anju Gangadharan, Steven Park, Sean Fitzgerald, Andrew Ramnauth, David S. Perlin, Michèle Donato, Emily Bhoy, Ehsan Manouchehri Doulabi, Michael G. Poulos, Masood Kamali‐Moghaddam, Olivier Loudig
Software Mentions: 3
Published: over 3 years ago

10.1038/onc.2015.499

Enhanced MAPK signaling drives ETS1-mediated induction of miR-29b leading to downregulation of TET1 and changes in epigenetic modifications in a subset of lung SCC
Cited by: 26
Author(s): Molly A. Taylor, Mark Wappett, Oona Delpuech, Helen Brown, Christine Chresta
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.43079

Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body
Cited by: 116
Author(s): Michael J. Dolan, Shahar Frechter, Alexander Shakeel Bates, Chuntao Dan, Paavo Huoviala, Ruairí J.V. Roberts, Philipp Schlegel, Serene Dhawan, Remy Tabano, Heather Dionne, Christina Christoforou, Kari Close, Ben Sutcliffe, B Giuliani, Feng Li, Marta Costa, Gudrun Ihrke, Geoffrey W. Meissner, Davi D. Bock, Yoshinori Aso, Gerald M. Rubin, Gregory Jefferis
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.61082

Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer
Cited by: 9
Author(s): Bahman Afsari, Albert Kuo, Yifan Zhang, Lu Li, Kamel Lahouel, Ludmila Danilova, Alexander V. Favorov, Thomas A. Rosenquist, Arthur P. Grollman, Ken W Kinzler, Leslie Cope, Bert Vogelstein, Cristian Tomasetti
Software Mentions: 3
Published: almost 4 years ago

10.18632/aging.101871

Anesthesia and surgery induce cognitive dysfunction in elderly male mice: the role of gut microbiota
Cited by: 46
Author(s): Gaofeng Zhan, Hua Duan, Niannian Huang, Yue Wang, Shan Li, Zhiqiang Zhou, Ning Yang, Ruiwei Jiang, Bin Zhu, Ling Yang, Yu Fan, Hui Xu, Chun Yang, Ailin Luo
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2019.01335

Enrichments/Derichments of Root-Associated Bacteria Related to Plant Growth and Nutrition Caused by the Growth of an EPSPS-Transgenic Maize Line in the Field
Cited by: 18
Author(s): Zhongling Wen, Minkai Yang, Mei-Hang Du, Zhao-Zhao Zhong, Yun-Ting Lu, Gu-Hao Wang, Xiao-Mei Hua, Aliya Fazal, Chunhua Mu, Shufeng Yan, Yan Zhen, Rongwu Yang, Jinliang Qi, Zhi Hong, Guihua Lü, Yonghua Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/1751-0473-8-10

The non-negative matrix factorization toolbox for biological data mining
Cited by: 147
Author(s): Yifeng Li, Alioune Ngom
Software Mentions: 2
Published: over 11 years ago

10.1186/s12881-018-0528-6

Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India
Cited by: 61
Author(s): Viswanathan Mohan, Venkatesan Radha, Thong Tien Nguyen, Eric Stawiski, Kanika Bajaj Pahuja, Leonard D. Goldstein, Jennifer Tom, Ranjit Mohan Anjana, Monica Kong-Beltran, Tushar Bhangale, Suresh Joghee, Chandni Radhakrishnan, Vijay Gayathri, Paul‐Louis George, Na Zhang, Sakthivel Murugan, Sameer Phalke, Subhra Chaudhuri, Ravi Gupta, Jingli Zhang, Sam Santhosh, Jeremy Stinson, Zora Modrušan, Vedam Ramprasad, Somasekar Seshagiri, Andrew S. Peterson
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0207903

Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton
Cited by: 12
Author(s): Qin Qiao, Jingxia Zhang, Changle Ma, Furong Wang, Yu Chen, Chuanyun Zhang, Hui Zhang, Jun Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-11-367

A flexible R package for nonnegative matrix factorization
Cited by: 976
Author(s): Renaud Gaujoux, Cathal Seoighe
Software Mentions: 2
Published: over 14 years ago

10.3390/molecules25081818

Volatile Profile of Mead Fermenting Blossom Honey and Honeydew Honey with or without Ribes nigrum
Cited by: 13
Author(s): Giulia Chitarrini, Luca Debiasi, Mary Stuffer, Eva Ueberegger, Egon Zehetner, Henry Jaeger, Peter Robatscher, Lorenza Conterno
Software Mentions: 2
Published: over 4 years ago

10.1016/j.ccell.2019.02.002

Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways
Cited by: 72
Author(s): Christopher D. Steele, Maxime Tarabichi, Dahmane Oukrif, A. D. B. Webster, Hongtao Ye, Matthew Fittall, Patrick Lombard, Iñigo Martincorena, Patrick Tarpey, Grace Collord, Kerstin Haase, Sandra J. Strauss, Fitim Berisha, Heli Vaikkinen, Pawan Dhami, Marnix Jansen, Sam Behjati, Maria Fernanda Amary, Roberto Tirabosco, Andrew Feber, Peter J. Campbell, Ludmil B. Alexandrov, Peter Van Loo, Adrienne M. Flanagan, Nischalan Pillay
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40529-021-00322-9

Agricultural management and cultivation period alter soil enzymatic activity and bacterial diversity in litchi (Litchi chinensis Sonn.) orchards
Cited by: 2
Author(s): Yu-Pei Chen, Chia-Fang Tsai, Asif Hameed, Yu-Jen Chang, Chiu-Chung Young
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.11047

Crosstalk between the mitochondrial fission protein, Drp1, and the cell cycle is identified across various cancer types and can impact survival of epithelial ovarian cancer patients
Cited by: 57
Author(s): Deepak K Tanwar, Danitra Parker, Priyanka Gupta, Brian Spurlock, Ronald D. Alvarez, Malay Kumar Basu, Kasturi Mitra
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2019.01055

Clinicopathologic Significance and Immunogenomic Analysis of Programmed Death-Ligand 1 (PD-L1) and Programmed Death 1 (PD-1) Expression in Thymic Epithelial Tumors
Cited by: 16
Author(s): Joon Seon Song, Deokhoon Kim, Ji Hyun Kwon, Hyeong Ryul Kim, Chang‐Min Choi, Se Jin Jang
Software Mentions: 2
Published: about 5 years ago

10.3390/genes11121493

Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data
Cited by: 2
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 2
Published: about 4 years ago

10.3390/genes12020214

Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia
Cited by: 6
Author(s): Željko Antić, Stefan H. Lelieveld, Cédric G. van der Ham, Edwin Sonneveld, Peter M. Hoogerbrugge, Roland P. Kuiper
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13073-015-0169-8

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status
Cited by: 146
Author(s): Victor Greiff, Pooja Bhat, Skylar C. Cook, Ulrike Menzel, Wenjing Kang, Sai T. Reddy
Software Mentions: 2
Published: over 9 years ago

10.3389/fonc.2020.591254

Identification of Epithelial–Mesenchymal Transition-Related lncRNA With Prognosis and Molecular Subtypes in Clear Cell Renal Cell Carcinoma
Cited by: 24
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 2
Published: about 4 years ago

10.1242/jcs.245043

Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes
Cited by: 20
Author(s): Björn Eismann, Teresa G Krieger, Jürgen Beneke, Ruben Bulkescher, Lukas Adam, Holger Erfle, Carl Herrmann, Roland Eils, Christian Conrad
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep28990

High Fat Diets Induce Colonic Epithelial Cell Stress and Inflammation that is Reversed by IL-22
Cited by: 232
Author(s): Max Gulhane, Lydia S. Murray, Rohan Lourie, Hui Tong, Yonghua Sheng, Ran Wang, Alicia Kang, Veronika Schreiber, Kuan Yau Wong, Graham Magor, Stuart E. Denman, Jakob Begun, Timothy H. Florin, Andrew C. Perkins, Páraic Ó Cuív, Michael A. McGuckin, Sumaira Z. Hasnain
Software Mentions: 2
Published: over 8 years ago

10.1186/s12967-018-1589-1

Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles
Cited by: 15
Author(s): Angelina Boccarelli, Flavia Esposito, Mauro Coluccia, Maria Antonia Frassanito, Angelo Vacca, Nicoletta Del Buono
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-78624-4

Deregulation of extracellular matrix modeling with molecular prognostic markers revealed by transcriptome sequencing and validations in Oral Tongue squamous cell carcinoma
Cited by: 10
Author(s): Soundara Viveka Thangaraj, Vidyarani Shyamsundar, Arvind Krishnamurthy, Vijayalakshmi Ramshankar
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0040996

Constructing Endophenotypes of Complex Diseases Using Non-Negative Matrix Factorization and Adjusted Rand Index
Cited by: 8
Author(s): Huimin Wang, Ching‐Lin Hsiao, Ai-Ru Hsieh, Yi‐Hao Lin, Cathy S.J. Fann
Software Mentions: 2
Published: over 12 years ago

10.3389/fgene.2020.595242

Mechanistic Modeling of Gene Regulation and Metabolism Identifies Potential Targets for Hepatocellular Carcinoma
Cited by: 4
Author(s): Ruiyan Sun, XU Yi-zhou, Hang Zhang, Qiangzhen Yang, Ke Wang, Yongyong Shi, Zhuo Wang
Software Mentions: 1
Published: about 4 years ago

10.3389/fgene.2021.639246

Glycolysis-Related Gene Expression Profiling Screen for Prognostic Risk Signature of Pancreatic Ductal Adenocarcinoma
Cited by: 9
Author(s): Wenjing Song, Xin He, Peng Gong, Yan Yang, Shu‐Chun Huang, Yifan Zeng, Lei Wei, Jingwei Zhang
Software Mentions: 1
Published: over 3 years ago

10.1038/srep26001

Molecular Subtyping of Serous Ovarian Cancer Based on Multi-omics Data
Cited by: 34
Author(s): Zhe Zhang, Ke Huang, Chenglei Gu, Lei Zhao, Nan Wang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang, Yiming Lu, Yuanguang Meng
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.0030148

Automated Discovery of Functional Generality of Human Gene Expression Programs
Cited by: 37
Author(s): Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford
Software Mentions: 1
Published: over 17 years ago

10.1186/s12918-018-0532-7

Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization
Cited by: 48
Author(s): Hui Yu, Kui-Tao Mao, Jian-Yu Shi, Huang Hua, Zhi Chen, Kai Dong, Siu-Ming Yiu
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2020.587284

Gut Microbiotic Features Aiding the Diagnosis of Acute Ischemic Stroke
Cited by: 20
Author(s): Lei Xiang, Yanfeng Lou, Lingyu Liu, Yuanling Liu, Weizheng Zhang, Jianxin Deng, Yubin Guan, Miaoqin She, Xinchao You, Minqi Liu, Hongwei Li, Xiaosong Xu, Fang Liu, Xiangsheng Cai
Software Mentions: 1
Published: about 4 years ago

10.3390/biomedicines9030257

MicroRNA Signatures Associated with Bronchopulmonary Dysplasia Severity in Tracheal Aspirates of Preterm Infants
Cited by: 10
Author(s): Roopa Siddaiah, Christiana N. Oji‐Mmuo, Deborah T. Montes, Nathalie Fuentes, Debra Spear, Ann Donnelly, Patricia Silveyra
Software Mentions: 1
Published: almost 4 years ago

Projects: cran: NMF

Papers Mentioning NMF 108