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Big data in basic and translational cancer research

Nature reviews. Cancer, 2022-11, Vol.22 (11), p.625-639

2022

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A transcription-centric model of SNP-age interaction

PLoS genetics, 2021-03, Vol.17 (3), p.e1009427-e1009427

2021

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Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis

Cell, 2021-04, Vol.184 (8), p.2033-2052.e21

2021

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Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing

PloS one, 2010-08, Vol.5 (8), p.e12029

2010

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Prioritizing and characterizing functionally relevant genes across human tissues

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009194

2021

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Predicting tissue-specific gene expression from whole blood transcriptome

Science advances, 2021-04, Vol.7 (14)

2021

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A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Frontiers in immunology, 2022-07, Vol.13, p.918817-918817

2022

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Automated network analysis identifies core pathways in glioblastoma

PloS one, 2010-02, Vol.5 (2), p.e8918-e8918

2010

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Why transcription factor binding sites are ten nucleotides long

Genetics (Austin), 2012-11, Vol.192 (3), p.973-985

2012

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Analysis and correction of compositional bias in sparse sequencing count data

BMC genomics, 2018-11, Vol.19 (1), p.799-799, Article 799

2018

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A novel hypergraph model for identifying and prioritizing personalized drivers in cancer

PLoS computational biology, 2024-04, Vol.20 (4), p.e1012068-e1012068

2024

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ChIPulate: A comprehensive ChIP-seq simulation pipeline

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006921-e1006921

2019

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Broad misappropriation of developmental splicing profile by cancer in multiple organs

Nature communications, 2022-12, Vol.13 (1), p.7664-18, Article 7664

2022

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Harnessing synthetic lethality to predict the response to cancer treatment

Nature communications, 2018-06, Vol.9 (1), p.2546-12, Article 2546

2018

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A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005793-e1005793

2017

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Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

Cell reports (Cambridge), 2019-12, Vol.29 (10), p.3019-3032.e6

2019

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High nucleosome occupancy is encoded at human regulatory sequences

PloS one, 2010-02, Vol.5 (2), p.e9129-e9129

2010

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Evolutionarily conserved network properties of intrinsically disordered proteins

PloS one, 2015-05, Vol.10 (5), p.e0126729-e0126729

2015

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Ligand dependent gene regulation by transient ERα clustered enhancers

PLoS genetics, 2020-01, Vol.16 (1), p.e1008516

2020

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Transcription factors organize into functional groups on the linear genome and in 3D chromatin

Heliyon, 2023-08, Vol.9 (8), p.e18211-e18211, Article e18211

2023

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miRSCAPE - inferring miRNA expression from scRNA-seq data

iScience, 2022-09, Vol.25 (9), p.104962, Article 104962

2022

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Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes

PloS one, 2008-08, Vol.3 (8), p.e2955-e2955

2008

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Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Journal of translational medicine, 2023-03, Vol.21 (1), p.209-209, Article 209

2023

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Selection of target sites for mobile DNA integration in the human genome

PLoS computational biology, 2006-11, Vol.2 (11), p.e157-e157

2006

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Regulation of lung endoderm progenitor cell behavior by miR302/367

Development (Cambridge), 2011-04, Vol.138 (7), p.1235-1245

2011

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Big data in basic and translational cancer research

A transcription-centric model of SNP-age interaction

Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis

Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing

Prioritizing and characterizing functionally relevant genes across human tissues

Predicting tissue-specific gene expression from whole blood transcriptome

A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2

Automated network analysis identifies core pathways in glioblastoma

Why transcription factor binding sites are ten nucleotides long

Analysis and correction of compositional bias in sparse sequencing count data

A novel hypergraph model for identifying and prioritizing personalized drivers in cancer

ChIPulate: A comprehensive ChIP-seq simulation pipeline

Broad misappropriation of developmental splicing profile by cancer in multiple organs

Harnessing synthetic lethality to predict the response to cancer treatment

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

High nucleosome occupancy is encoded at human regulatory sequences

Evolutionarily conserved network properties of intrinsically disordered proteins

Ligand dependent gene regulation by transient ERα clustered enhancers

Transcription factors organize into functional groups on the linear genome and in 3D chromatin

miRSCAPE - inferring miRNA expression from scRNA-seq data

Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients

Selection of target sites for mobile DNA integration in the human genome

Regulation of lung endoderm progenitor cell behavior by miR302/367

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