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Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

Nature methods, 2019-05, Vol.16 (5), p.409-412

2019

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ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Proceedings of the National Academy of Sciences - PNAS, 2009-12, Vol.106 (51), p.21521-21526

2009

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Landscape and variation of RNA secondary structure across the human transcriptome

Nature (London), 2014-01, Vol.505 (7485), p.706-709

2014

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Deciphering the role of RNA structure in translation efficiency

BMC bioinformatics, 2022-12, Vol.23 (Suppl 3), p.559-559, Article 559

2022

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Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

Nature biotechnology, 2021-02, Vol.39 (2), p.225-235

2021

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SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

Genome research, 2013-02, Vol.23 (2), p.377-387

2013

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Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins

Quantitative biology, 2020-06, Vol.8 (2), p.119-129

2020

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PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

PLoS computational biology, 2019-08, Vol.15 (8), p.e1007227-e1007227

2019

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LISA2: Learning Complex Single-Cell Trajectory and Expression Trends

Frontiers in genetics, 2021-08, Vol.12, p.681206-681206

2021

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Rapamycin-Induced Feedback Activation of eIF4E-EIF4A Dependent mRNA Translation in Pancreatic Cancer

Cancers, 2023-02, Vol.15 (5), p.1444

2023

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Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis

Proceedings of the National Academy of Sciences - PNAS, 2010-05, Vol.107 (21), p.9736-9741

2010

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Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

Viruses, 2022-06, Vol.14 (7), p.1418

2022

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A new FACS approach isolates hESC derived endoderm using transcription factors

PloS one, 2011-03, Vol.6 (3), p.e17536

2011

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Joint model-based distance embedding of multi-track Hi-C data for chromosomal conformation learning

Statistics and its interface, 2024, Vol.17 (3), p.565-571

2024

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HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure

Genome Biology, 2016-03, Vol.17 (1), p.40-40, Article 40

2016

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Joint Principal Trend Analysis for Longitudinal High-Dimensional Data

Biometrics, 2018-06, Vol.74 (2), p.430-438

2018

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Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure

Nucleic acids research, 2015-10, Vol.43 (19), p.9187-9197

2015

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Translocation detection from Hi‐C data via scan statistics

Biometrics, 2023-06, Vol.79 (2), p.1306-1317

2023

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Model-based distance embedding with applications to chromosomal conformation biology

The annals of applied statistics, 2022-09, Vol.16 (3)

2022

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Differential RNA methylation using multivariate statistical methods

Briefings in bioinformatics, 2022-01, Vol.23 (1)

2022

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Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes

Statistical applications in genetics and molecular biology, 2024-01, Vol.23 (1)

2024

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LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2019, Vol.24, p.338

2019

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A STATISTICAL FRAMEWORK FOR DATA INTEGRATION THROUGH GRAPHICAL MODELS WITH APPLICATION TO CANCER GENOMICS

The annals of applied statistics, 2017-03, Vol.11 (1), p.161-184

2017

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Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

Nature protocols, 2013-05, Vol.8 (5), p.849-869

2013

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Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Landscape and variation of RNA secondary structure across the human transcriptome

Deciphering the role of RNA structure in translation efficiency

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

LISA2: Learning Complex Single-Cell Trajectory and Expression Trends

Rapamycin-Induced Feedback Activation of eIF4E-EIF4A Dependent mRNA Translation in Pancreatic Cancer

Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis

Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

A new FACS approach isolates hESC derived endoderm using transcription factors

Joint model-based distance embedding of multi-track Hi-C data for chromosomal conformation learning

HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure

Joint Principal Trend Analysis for Longitudinal High-Dimensional Data

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure

Translocation detection from Hi‐C data via scan statistics

Model-based distance embedding with applications to chromosomal conformation biology

Differential RNA methylation using multivariate statistical methods

Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes

LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data

A STATISTICAL FRAMEWORK FOR DATA INTEGRATION THROUGH GRAPHICAL MODELS WITH APPLICATION TO CANCER GENOMICS

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

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