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STEM: a tool for the analysis of short time series gene expression data

BMC bioinformatics, 2006-04, Vol.7 (1), p.191-191, Article 191

2006

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Algorithms in nature: the convergence of systems biology and computational thinking

Molecular systems biology, 2011-11, Vol.7 (1), p.546-n/a

2011

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Deep learning for inferring gene relationships from single-cell expression data

Proceedings of the National Academy of Sciences - PNAS, 2019-12, Vol.116 (52), p.27151-27158

2019

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GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Genome Biology, 2020-12, Vol.21 (1), p.300-300, Article 300

2020

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Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer

Genes chromosomes & cancer, 2019-01, Vol.58 (1), p.34-42

2019

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Evaluation of different biological data and computational classification methods for use in protein interaction prediction

Proteins, structure, function, and bioinformatics, 2006-05, Vol.63 (3), p.490-500

2006

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CINS: Cell Interaction Network inference from Single cell expression data

PLoS computational biology, 2022-09, Vol.18 (9), p.e1010468-e1010468

2022

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Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Nature communications, 2020-06, Vol.11 (1), p.3055-3055, Article 3055

2020

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Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments

Cell systems, 2016-07, Vol.3 (1), p.35-42

2016

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Analyzing time series gene expression data

Bioinformatics, 2004-11, Vol.20 (16), p.2493-2503

Bar-Joseph, Ziv

2004

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Iterative point set registration for aligning scRNA-seq data

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007939-e1007939

2020

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scSTEM: clustering pseudotime ordered single-cell data

Genome Biology, 2022-07, Vol.23 (1), p.150-150, Article 150

2022

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SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

Bioinformatics (Oxford, England), 2017-08, Vol.33 (15), p.2314-2321

2017

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A transcription factor hierarchy defines an environmental stress response network

Science (American Association for the Advancement of Science), 2016-11, Vol.354 (6312), p.598-598

2016

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Protein interaction disruption in cancer

BMC cancer, 2019-04, Vol.19 (1), p.370-370, Article 370

2019

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A web server for comparative analysis of single-cell RNA-seq data

Nature communications, 2018-11, Vol.9 (1), p.4768-11, Article 4768

2018

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Inferring TF activation order in time series scRNA-Seq studies

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007644-e1007644

2020

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Membrane marker selection for segmenting single cell spatial proteomics data

Nature communications, 2022-04, Vol.13 (1), p.1999-1999, Article 1999

2022

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Interactive single-cell data analysis using Cellar

Nature communications, 2022-04, Vol.13 (1), p.1998-1998, Article 1998

2022

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Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

Cell stem cell, 2018-10, Vol.23 (4), p.586-598.e8

2018

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RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets

Bioinformatics (Oxford, England), 2017-09, Vol.33 (17), p.2774-2775

2017

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LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering

Bioinformatics (Oxford, England), 2017-03, Vol.33 (5), p.764-766

2017

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Biological Solution to a Fundamental Distributed Computing Problem

Science (American Association for the Advancement of Science), 2011-01, Vol.331 (6014), p.183-185

2011

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STEM: a tool for the analysis of short time series gene expression data

Algorithms in nature: the convergence of systems biology and computational thinking

Deep learning for inferring gene relationships from single-cell expression data

GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

Transcriptional regulatory model of fibrosis progression in the human lung

CINS: Cell Interaction Network inference from Single cell expression data

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments

Analyzing time series gene expression data

Iterative point set registration for aligning scRNA-seq data

scSTEM: clustering pseudotime ordered single-cell data

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

A transcription factor hierarchy defines an environmental stress response network

Protein interaction disruption in cancer

A web server for comparative analysis of single-cell RNA-seq data

Inferring TF activation order in time series scRNA-Seq studies

Membrane marker selection for segmenting single cell spatial proteomics data

Interactive single-cell data analysis using Cellar

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets

LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering

Biological Solution to a Fundamental Distributed Computing Problem

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors

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