Publications by authors named "Heewook Lee"

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An AI-Guided Framework Reveals Conserved Features Governing microRNA Strand Selection.
Dalton Meadows, Hailee Hargis, Amanda Ellis, Heewook Lee, Marco Mangone

bioRxiv· November 2025

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Iterative attack-and-defend framework for improving TCR-epitope binding prediction models.
Pengfei Zhang, Hao Mei, Seojin Bang, Heewook Lee

Bioinformatics· July 2025

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Self-Contemplating In-Context Learning Enhances T Cell Receptor Generation for Novel Epitopes.
Pengfei Zhang, Seojin Bang, Heewook Lee

bioRxiv· January 2025

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Encrypted data-sharing for preserving privacy in wastewater-based epidemiology.
Erin M Driver, Manazir Ahsan, Lucas Piske, Heewook Lee, Stephanie Forrest

Sci Total Environ· August 2024

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PiTE: TCR-epitope Binding Affinity Prediction Pipeline using Transformer-based Sequence Encoder.
Pengfei Zhang, Seojin Bang, Heewook Lee

Pac Symp Biocomput· December 2022

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ATM-TCR: TCR-Epitope Binding Affinity Prediction Using a Multi-Head Self-Attention Model.
Michael Cai, Seojin Bang, Pengfei Zhang, Heewook Lee

Front Immunol· July 2022

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Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica.
Jiao Pan, Weiyi Li, Jiahao Ni, Kun Wu, Iain Konigsberg, Heewook Lee

Mol Biol Evol· April 2022

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DNA Replication-Transcription Conflicts Do Not Significantly Contribute to Spontaneous Mutations Due to Replication Errors in Escherichia coli.
Patricia L Foster, Brittany A Niccum, Heewook Lee

mBio· October 2021

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New complexities of SOS-induced "untargeted" mutagenesis in Escherichia coli as revealed by mutation accumulation and whole-genome sequencing.
Brittany A Niccum, Christopher P Coplen, Heewook Lee, Wazim Mohammed Ismail, Haixu Tang

DNA Repair (Amst)· June 2020

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The Symmetrical Wave Pattern of Base-Pair Substitution Rates across the Escherichia coli Chromosome Has Multiple Causes.
Brittany A Niccum, Heewook Lee, Wazim MohammedIsmail, Haixu Tang, Patricia L Foster

mBio· July 2019

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Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami.
Heewook Lee, Carl Kingsford

Methods Mol Biol· March 2019

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Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective .
Patricia L Foster, Brittany A Niccum, Ellen Popodi, Jesse P Townes, Heewook Lee

Genetics· August 2018

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The Spectrum of Replication Errors in the Absence of Error Correction Assayed Across the Whole Genome of .
Brittany A Niccum, Heewook Lee, Wazim MohammedIsmail, Haixu Tang, Patricia L Foster

Genetics· August 2018

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Adaptation of Escherichia coli to long-term batch culture in various rich media.
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee

Res Microbiol· April 2018

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Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.
Heewook Lee, Carl Kingsford

Genome Biol· February 2018

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Adaptation of to Long-Term Serial Passage in Complex Medium: Evidence of Parallel Evolution.
Karin E Kram, Christopher Geiger, Wazim Mohammed Ismail, Heewook Lee, Haixu Tang

mSystems· March 2017

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Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli.
Heewook Lee, Thomas G Doak, Ellen Popodi, Patricia L Foster, Haixu Tang

Nucleic Acids Res· September 2016

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Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola.
Sutichot Nimkulrat, Heewook Lee, Thomas G Doak, Yuzhen Ye

Front Microbiol· July 2016

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Antibiotic treatment enhances the genome-wide mutation rate of target cells.
Hongan Long, Samuel F Miller, Chloe Strauss, Chaoxian Zhao, Lei Cheng, Heewook Lee

Proc Natl Acad Sci U S A· May 2016

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Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli.
Ashok S Bhagwat, Weilong Hao, Jesse P Townes, Heewook Lee, Haixu Tang

Proc Natl Acad Sci U S A· February 2016

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Determinants of spontaneous mutation in the bacterium Escherichia coli as revealed by whole-genome sequencing.
Patricia L Foster, Heewook Lee, Ellen Popodi, Jesse P Townes, Haixu Tang

Proc Natl Acad Sci U S A· November 2015

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Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.
Haruo Suzuki, Amy L Dapper, Craig E Jackson, Heewook Lee, Vikas Pejaver

Genome Announc· November 2015

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Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.
Hongan Long, Sibel Kucukyildirim, Way Sung, Emily Williams, Heewook Lee

Mol Biol Evol· September 2015

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Detection of structural variants involving repetitive regions in the reference genome.
Heewook Lee, Ellen Popodi, Patricia L Foster, Haixu Tang

J Comput Biol· March 2014

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On the mutational topology of the bacterial genome.
Patricia L Foster, Andrew J Hanson, Heewook Lee, Ellen M Popodi, Haixu Tang

G3 (Bethesda)· March 2013

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