Ecosyste.ms: Papers

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago

10.3390/ijms161226230

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Steffen Sass, Adriana Pitea, Kristian Unger, Julia Heß, Nikola S. Mueller, Fabian J. Theis
Software Mentions: 9
Published: almost 9 years ago

10.1371/journal.pone.0192853

Improving stability of prediction models based on correlated omics data by using network approaches
Cited by: 5
Author(s): Renaud Tissier, Jeanine J. Houwing-Duistermaat, Mar Rodríguez-Girondo
Software Mentions: 8
Published: almost 7 years ago

10.1371/journal.pone.0107957

Simulation Studies as Designed Experiments: The Comparison of Penalized Regression Models in the “Large p, Small n” Setting
Cited by: 13
Author(s): Elias Chaibub Neto, J. Christopher Bare, Adam A. Margolin
Software Mentions: 8
Published: about 10 years ago

10.1016/j.csbj.2021.05.024

Machine learning applied to serum and cerebrospinal fluid metabolomes revealed altered arginine metabolism in neonatal sepsis with meningoencephalitis
Cited by: 12
Author(s): Peng Zhang, Zhangxing Wang, Huixian Qiu, Wenhao Zhou, Mingbang Wang, Guoqiang Cheng
Software Mentions: 8
Published: almost 4 years ago

10.18632/aging.103779

Development and validation of an immune and stromal prognostic signature in uveal melanoma to guide clinical therapy
Cited by: 5
Author(s): Qianwen Gong, Qi Wan, Anqi Li, Yubin Yu, Xiangyu Ding, Lin Leng, Xiao-Liang Qi, Liang Hu
Software Mentions: 7
Published: about 4 years ago

10.1186/s13062-018-0213-x

Predicting survival times for neuroblastoma patients using RNA-seq expression profiles
Cited by: 15
Author(s): Tyler Grimes, Alejandro R. Walker, Susmita Datta
Software Mentions: 6
Published: almost 7 years ago

10.1002/sim.6782

Review and evaluation of penalised regression methods for risk prediction in low‐dimensional data with few events
Cited by: 208
Author(s): Menelaos Pavlou, Gareth Ambler, Shaun Seaman, Maria De Iorio, Rumana Omar
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-015-0574-4

Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease
Cited by: 42
Author(s): Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-12-S13-S17

Stability of building gene regulatory networks with sparse autoregressive models
Cited by: 20
Author(s): Jagath C. Rajapakse, Piyushkumar A. Mundra
Software Mentions: 5
Published: almost 13 years ago

10.3389/fgene.2019.01196

High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering
Cited by: 13
Author(s): Lingfei Wang, Pieter Audenaert, Tom Michoel
Software Mentions: 4
Published: almost 5 years ago

10.26508/lsa.202000944

In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
Cited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2021.701500

Development and Validation of a Radiosensitivity Prediction Model for Lower Grade Glioma Based on Spike-and-Slab Lasso
Cited by: 3
Author(s): Zixuan Du, Shang Cai, Derui Yan, Huijun Li, Xinyan Zhang, Wei Yang, Jianping Cao, Nengjun Yi, Zaixiang Tang
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-92725-8

Lung adenocarcinoma and lung squamous cell carcinoma cancer classification, biomarker identification, and gene expression analysis using overlapping feature selection methods
Cited by: 43
Author(s): Joe W. Chen, Joseph M. Dhahbi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12940-019-0482-6

Two-step approach for assessing the health effects of environmental chemical mixtures: application to simulated datasets and real data from the Navajo Birth Cohort Study
Cited by: 4
Author(s): Li Luo, Laurie G. Hudson, Johnnye Lewis, Ji‐Hyun Lee
Software Mentions: 4
Published: over 5 years ago

10.1186/s13072-019-0276-7

Ovarian dysfunction following prenatal exposure to an insecticide, chlordecone, associates with altered epigenetic features
Cited by: 16
Author(s): Louis Legoff, Ouzna Dali, Shereen Cynthia D’Cruz, Antonio Suglia, Aurore Gély-Pernot, Chloé Hémery, Pierre-Yves Kernanec, Abbassia Demmouche, Christine Kervarrec, Sergei G. Tevosian, Luc Multigner, Fátima Smagulova
Software Mentions: 3
Published: over 5 years ago

10.1002/ctm2.11

The distribution of immune cells within combined hepatocellular carcinoma and cholangiocarcinoma predicts clinical outcome
Cited by: 21
Author(s): Bohao Zheng, Jiaqiang Ma, Lingyu Tian, Liangqing Dong, Guohe Song, Jinfeng Pan, Yuming Liu, Shenghong Yang, Xiaoying Wang, Xiaoming Zhang, Jian Zhou, Jia Fan, Jing Shi, Qiang Gao
Software Mentions: 3
Published: over 4 years ago

10.1194/jlr.M057562

Plasma diacylglycerol composition is a biomarker of metabolic syndrome onset in rhesus monkeys
Cited by: 18
Author(s): Michael A. Polewski, Maggie S. Burhans, Minghui Zhao, Ricki J. Colman, Dhanansayan Shanmuganayagam, Mary J. Lindstrom, James M. Ntambi, Rozalyn M. Anderson
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-019-3054-4

Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection
Cited by: 21
Author(s): Jinhong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael C. Horsch, Anthony Kusalik
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13072-021-00413-8

Histone deacetylase inhibition leads to regulatory histone mark alterations and impairs meiosis in oocytes
Cited by: 4
Author(s): Louis Legoff, Ouzna Dali, Elena De La Mata Santaella, Christian Jaulin, Shereen Cynthia D’Cruz, Fátima Smagulova
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-41581-8

Relationship of the orange tissue morphotype with shell and pearl colouration in the mollusc Pinctada margaritifera
Cited by: 7
Author(s): Chin‐Long Ky, Carole Blay, Floriane Broustal, Manaarii Sham Koua, Serge Planes
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2021.691060

Epigenetic Effects Promoted by Neonicotinoid Thiacloprid Exposure
Cited by: 8
Author(s): Colin Hartman, Louis Legoff, Martina Capriati, Gwendoline Lecuyer, Pierre-Yves Kernanec, Sergei G. Tevosian, Shereen Cynthia D’Cruz, Fátima Smagulova
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.112.003822

A Fast and Efficient Approach for Genomic Selection with High-Density Markers
Cited by: 3
Author(s): Vitara Pungpapong, William M. Muir, Xianran Li, Dabao Zhang, Min Zhang
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pcbi.1006838

Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats
Cited by: 10
Author(s): Lucas L. Dwiel, Jibran Y. Khokhar, Michael Connerney, Alan I. Green, Wilder T. Doucette
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1005234

Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series
Cited by: 18
Author(s): Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Software Mentions: 1
Published: almost 8 years ago

10.3389/fpsyt.2018.00336

Machine Learning Based Classification of Deep Brain Stimulation Outcomes in a Rat Model of Binge Eating Using Ventral Striatal Oscillations
Cited by: 14
Author(s): Wilder T. Doucette, Lucas L. Dwiel, Jared E. Boyce, Amanda A. Simon, Jibran Y. Khokhar, Alan I. Green
Software Mentions: 1
Published: over 6 years ago

10.1002/gepi.22159

Prediction of treatment response in rheumatoid arthritis patients using genome‐wide SNP data
Cited by: 14
Author(s): Svetlana Cherlin, Darren Plant, John Taylor, Marco Colombo, Athina Spiliopoulou, Evan Tzanis, Ann W Morgan, Michael R. Barnes, Paul McKeigue, Jennifer H. Barrett, Costantino Pitzalis, Anne Barton, Heather J. Cordell
Software Mentions: 1
Published: about 6 years ago

10.3390/md18050238

Identification, Cloning and Heterologous Expression of the Gene Cluster Directing RES-701-3, -4 Lasso Peptides Biosynthesis from a Marine Streptomyces Strain
Cited by: 7
Author(s): Daniel Oves‐Costales, Marina Sánchez‐Hidalgo, Jesús Martín, Olga Genilloud
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-019-43166-x

A novel data fusion method for the effective analysis of multiple panels of flow cytometry data
Cited by: 9
Author(s): Gerjen H. Tinnevelt, Selma van Staveren, Kristiaan Wouters, Erwin Wijnands, Kenneth Verboven, Rita Folcarelli, Leo Koenderman, L.M.C. Buydens
Software Mentions: 1
Published: over 5 years ago

10.1186/s12891-020-03498-6

Influence of cement-augmented pedicle screws with different volumes of polymethylmethacrylate in osteoporotic lumbar vertebrae over the adjacent segments: a 3D finite element analysis
Cited by: 6
Author(s): Haipeng Guo, Shun-cong Zhang, Dan‐qing Guo, Yuwei Ma, Kai Yuan, Yongxian Li, Jian-cheng Peng, Jinglan Li, De Liang, Yong‐chao Tang
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-95230-0

OCTA reveals remodeling of the peripheral capillary free zones in normal aging
Cited by: 2
Author(s): Edmund Arthur, Jessica Alber, Louisa I. Thompson, Stuart Sinoff, Peter J. Snyder
Software Mentions: 1
Published: over 3 years ago

10.1186/s13287-019-1457-9

Antler stem cell-conditioned medium stimulates regenerative wound healing in rats
Cited by: 29
Author(s): Xiaoli Rong, Wenhui Chu, Haiying Zhang, Yusu Wang, Xiaoyan Qi, Guokun Zhang, Yimin Wang, Chunyi Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s13287-020-01971-6

Epidermal stem cell-derived exosomes promote skin regeneration by downregulating transforming growth factor-β1 in wound healing
Cited by: 51
Author(s): Mengna Duan, Yan Zhang, Haiyang Zhang, Yupeng Meng, Ming Qian, Guokun Zhang
Software Mentions: 1
Published: about 4 years ago

10.1155/2019/9570218

A Data Mining Approach Identified Salivary Biomarkers That Discriminate between Two Obesity Measures
Cited by: 4
Author(s): Peng Shi, J. Max Goodson
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-018-2070-0

Hierarchical structural component modeling of microRNA-mRNA integration analysis
Cited by: 15
Author(s): Yongkang Kim, Sung Young Lee, Sungkyoung Choi, Jin‐Young Jang, Taesung Park
Software Mentions: 1
Published: over 6 years ago

10.1155/2016/3456153

Efficient Regularized Regression with<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:msub><mml:mrow><mml:mi>L</mml:mi></mml:mrow><mml:mrow><mml:mn fontstyle="italic">0</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Penalty for Variable Selection and Network Construction
Cited by: 23
Author(s): Zhenqiu Liu, Gang Li
Software Mentions: 1
Published: almost 9 years ago

10.1155/2017/2747431

Ensembling Variable Selectors by Stability Selection for the Cox Model
Cited by: 7
Author(s): Qingyan Yin, Junli Li, Chunxia Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0092624

Gap43 Transcription Modulation in the Adult Brain Depends on Sensory Activity and Synaptic Cooperation
Cited by: 48
Author(s): Nicole Roßkothen-Kuhl, Robert‐Benjamin Illing
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0068722

The Impact of Bdnf Gene Deficiency to the Memory Impairment and Brain Pathology of APPswe/PS1dE9 Mouse Model of Alzheimer’s Disease
Cited by: 46
Author(s): Tomi Rantamäki, Susanna Kemppainen, Henri Autio, Saara Stavén, Hennariikka Koivisto, Masami Kojima, Hanna Antila, Pasi Miettinen, Elisa Kärkkäinen, Nina N. Karpova, Liisa Vesa, Lothar Lindemann, Marius C. Hoener, Heikki Tanila, Eero Ċastrén
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000587

Statistical Estimation of Correlated Genome Associations to a Quantitative Trait Network
Cited by: 205
Author(s): Seyoung Kim, Eric P. Xing
Software Mentions: 1
Published: over 15 years ago

10.1007/s00421-013-2783-8

Hypoxia refines plasticity of mitochondrial respiration to repeated muscle work
Cited by: 34
Author(s): Dominique Desplanches, Myriam Amami, Sylvie Dupré-Aucouturier, Paola Valdivieso, Silvia Schmutz, Matthias Müeller, Hans Hoppeler, Roland Kreis, Martin Flück
Software Mentions: 1
Published: almost 11 years ago

10.12688/f1000research.8427.1

Survival prognosis and variable selection: A case study for metastatic castrate resistant prostate cancer patients
Cited by: 2
Author(s): Søren Wengel Mogensen, Anne Petersen, Ann-Sophie Buchardt, Niels Richard Hansen
Software Mentions: 1
Published: about 8 years ago