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List of works by Jaegil Kim

A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma

scientific article published on 20 December 2019

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer

scientific article

Abstract 2727: The premalignant state captured in the landscape of somatic mutations can reveal the cancer cell-of-origin

scholarly article

Abstract SY05-03: Dissecting genomic correlates of response and resistance to chemotherapy in bladder cancer through clinical computational oncology

scholarly article

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Association of tumour microRNA profiling with outcomes in patients with advanced urothelial carcinoma receiving first-line platinum-based chemotherapy

scientific article published on 23 June 2016

Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

scientific article published in 2022

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables ⬇️

scientific article published on August 14, 2011

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

scientific article published on 2 April 2018

Comprehensive Analyses of Genetic Features Identify Coordinate Signatures in Diffuse Large B-Cell Lymphoma ⬇️

scholarly article

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

scientific article published in April 2018

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive Genomic Analysis of Flow-Sorted Hodgkin Reed Sternberg Cells Reveals Additional Genetic Bases of Immune Evasion ⬇️

scholarly article

Comprehensive Genomic Analysis of Primary Mediastinal B-Cell Lymphoma ⬇️

scholarly article

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

scientific article

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

scientific article published on 01 August 2018

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

scientific article

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

scientific article

Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

scientific article published on 28 April 2015

Exploring the Solid–Liquid Phase Change of an Adapted Dzugutov Model Using Generalized Replica Exchange Method ⬇️

scientific article published on April 10, 2012

Generalized replica exchange method

scientific article

Generalized simulated tempering for exploring strong phase transitions ⬇️

scientific article published on October 21, 2010

Genome-Wide Analysis of a Novel Murine Model of Chronic Lymphocytic Leukemia ⬇️

scholarly article

Genomic Characterization of Biliary Tract Cancers Identifies Driver Genes and Predisposing Mutations.

scientific article published on 19 January 2018

Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma

scientific article published on 16 November 2016

Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade

scientific article published on 01 December 2019

Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion

scientific article published on 01 December 2019

Genomic landscape of micropapillary nonmuscle-invasive bladder cancer.

scientific article published in 2016

Genomic predictors of good outcome, recurrence or progression in High grade T1 non-muscle invasive bladder cancer

scientific article published on 31 August 2020

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.

scientific article published on May 2015

Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation

article

Inherent structure analysis of protein folding

scientific article

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients

scientific article

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

scientific article

KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors

scientific article

Limit of metastability for liquid and vapor phases of water.

scientific article

Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites

scientific article published on 28 December 2018

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

scientific article published on 20 January 2016

Mutational heterogeneity in cancer and the search for new cancer-associated genes

scientific article

Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer.

scientific article

Mutational processes shape the landscape of TP53 mutations in human cancer.

scientific article

Next-generation characterization of the Cancer Cell Line Encyclopedia

scientific article published on 08 May 2019

Optimal replica exchange method combined with Tsallis weight sampling

scientific article published on April 2009

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method

scientific article published in March 2013

Passenger Hotspot Mutations in Cancer

scientific article published on 01 September 2019

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

scientific article published in April 2018

Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

Publisher’s Note: “Generalized simulated tempering for exploring strong phase transitions” [J. Chem. Phys. 133, 154101 (2010)].

scientific article published on 25 October 2010

Quantification of somatic mutation flow across individual cell division events by lineage sequencing

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

scientific article published on 01 June 2019

Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas

scientific article published on 02 March 2017

Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine

scientific article published on 14 June 2018

Recurrent and functional regulatory mutations in breast cancer

scientific article published on 28 June 2017

Regulation of Transient Site-specific Copy Gain by MicroRNA.

scientific article published on 11 January 2016

Relationship between protein folding thermodynamics and the energy landscape

scientific article published on 4 March 2009

Replica Exchange Statistical Temperature Molecular Dynamics Algorithm ⬇️

scientific article published on May 15, 2012

Replica exchange statistical temperature Monte Carlo

scientific article published on March 2009

Reply To Kenneth B. Yatai, Mark J. Dunning, Dennis Wang. Consensus Genomic Subtypes of Muscle-invasive Bladder Cancer: A Step in the Right Direction but Still a Long Way To Go. Eur Urol 2020;77:434-5

scientific article published on 07 February 2020

SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma

scientific article published on 03 May 2018

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

scientific article published on 6 November 2017

Scaling computational genomics to millions of individuals with GPUs

scientific article published on 01 November 2019

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

scientific article published on 25 April 2016

Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma

scientific article

Sporadic Early-Onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations, but Low Frequency of Somatic RHOA Mutations Compared With Late-Onset Cancers.

scientific article published on 15 May 2017

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models

scientific article

Statistical-temperature Monte Carlo and molecular dynamics algorithms

scientific article published in August 2006

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing

scientific article published on 18 July 2007

Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile

scientific article published on 13 October 2020

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Cancer Genome Atlas Expression Subtypes Stratify Response to Checkpoint Inhibition in Advanced Urothelial Cancer and Identify a Subset of Patients with High Survival Probability

scientific article published on 07 March 2019

The Cancer Genome Atlas Project on Muscle-invasive Bladder Cancer

scientific article published on 6 June 2015

The Integrated Genomic Landscape of Thymic Epithelial Tumors

scientific article published in February 2018

The Repertoire of Mutational Signatures in Human Cancer

The genetic landscape of high-risk neuroblastoma

scientific article published on 20 January 2013

The repertoire of mutational signatures in human cancer

scientific article published on 05 February 2020

Tumor mutational landscape is a record of the pre-malignant state

Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development

scientific article

Whole exome sequencing of urachal adenocarcinoma reveals recurrent NF1 mutations

scientific article published on 07 April 2016

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