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Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas

Breast cancer research : BCR, 2022-07, Vol.24 (1), p.1-54, Article 54

2022

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Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers

Nucleic acids research, 2022-10, Vol.50 (19), p.10869-10881

2022

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SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

Nucleic acids research, 2021-09, Vol.49 (17), p.9633-9647

2021

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COVID‐19db linkage maps of cell surface proteins and transcription factors in immune cells

Journal of medical virology, 2023-06, Vol.95 (6), p.e28887-n/a

2023

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Genomic and transcriptomic analysis of cutaneous squamous cell carcinoma arising in immunocompetent and immunosuppressed patients

Oral oncology, 2024-01, Vol.148, p.106582, Article 106582

2024

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Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort

Nature communications, 2024-02, Vol.15 (1), p.1533-13, Article 1533

2024

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Isolated BAP1 Genomic Alteration in Malignant Pleural Mesothelioma Predicts Distinct Immunogenicity with Implications for Immunotherapeutic Response

Cancers, 2022-11, Vol.14 (22), p.5626

2022

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STGIC: A graph and image convolution-based method for spatial transcriptomic clustering

PLoS computational biology, 2024-02, Vol.20 (2), p.e1011935-e1011935

2024

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Single-cell analysis reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of ovarian cancer

Communications biology, 2024-01, Vol.7 (1), p.20-20, Article 20

2024

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MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011623-e1011623

2023

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Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

PLoS computational biology, 2023-05, Vol.19 (5), p.e1011122-e1011122

2023

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N-gram analysis of 970 microbial organisms reveals presence of biological language models

BMC bioinformatics, 2011-01, Vol.12 (1), p.12-12, Article 12

2011

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PLoS Computational Biology conference postcards from ISMB 2010

PLoS computational biology, 2010-11, Vol.6 (11), p.e1002000-e1002000

2010

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Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2660, p.149

2023

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Thin alumina nanoporous membranes for similar size biomolecule separation

Journal of membrane science, 2009-11, Vol.343 (1), p.1-6

2009

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Isolated IBAP1/I Genomic Alteration in Malignant Pleural Mesothelioma Predicts Distinct Immunogenicity with Implications for Immunotherapeutic Response

Cancers, 2022-11, Vol.14 (22)

2022

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Abstract 3370: Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

Cancer research (Chicago, Ill.), 2019-07, Vol.79 (13_Supplement), p.3370-3370

2019

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Estrogen represses gene expression through reconfiguring chromatin structures

Nucleic acids research, 2013-09, Vol.41 (17), p.8061-8071

2013

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Evaluating the barriers to point-of-care documentation for nursing staff

Computers, informatics, nursing, 2012-03, Vol.30 (3), p.126-133

2012

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PLoS Computational Biology Conference Postcards from ISMB 2010: e1002000

PLoS computational biology, 2010-11, Vol.6 (11)

2010

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Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

BMC genomics, 2012-01, Vol.13 Suppl 1 (Suppl 1), p.S1-S1, Article S1

2012

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Information integration approaches for investigating estrogen receptor mediated transcription

Osmanbeyoglu, Hatice Ulku

2012

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Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas

Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers

SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

COVID‐19db linkage maps of cell surface proteins and transcription factors in immune cells

Genomic and transcriptomic analysis of cutaneous squamous cell carcinoma arising in immunocompetent and immunosuppressed patients

Clinical and biomarker results from a phase II trial of combined cabozantinib and durvalumab in patients with chemotherapy-refractory colorectal cancer (CRC): CAMILLA CRC cohort

Isolated BAP1 Genomic Alteration in Malignant Pleural Mesothelioma Predicts Distinct Immunogenicity with Implications for Immunotherapeutic Response

STGIC: A graph and image convolution-based method for spatial transcriptomic clustering

Single-cell analysis reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of ovarian cancer

MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

N-gram analysis of 970 microbial organisms reveals presence of biological language models

PLoS Computational Biology conference postcards from ISMB 2010

Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

Thin alumina nanoporous membranes for similar size biomolecule separation

Isolated IBAP1/I Genomic Alteration in Malignant Pleural Mesothelioma Predicts Distinct Immunogenicity with Implications for Immunotherapeutic Response

Abstract 3370: Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

Estrogen represses gene expression through reconfiguring chromatin structures

Evaluating the barriers to point-of-care documentation for nursing staff

PLoS Computational Biology Conference Postcards from ISMB 2010: e1002000

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

Information integration approaches for investigating estrogen receptor mediated transcription

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