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Funding (2)

Surveillance of drug-resistant bacteria in resource-limited settings: a focus on cost-effective long-read sequencing of eyedrop-associated P. aeruginosa and locally sourced metagenomic samples

2024-09-01 to 2028-08-31 | Grant
National Institute of Allergy and Infectious Diseases (Bethesda, US)
URL: https://app.dimensions.ai/details/grant/grant.14351549
GRANT_NUMBER: R16AI184350
Source: Self-asserted source
H. Shim via DimensionsWizard

Simulation-based inference of complex population genetic models for experimental evolution

2017-01-01 to 2017-08-31 | Grant
Swiss National Science Foundation (Bern, CH)
URL: https://app.dimensions.ai/details/grant/grant.6662606
GRANT_NUMBER: 168490
Source: Self-asserted source
H. Shim via DimensionsWizard

Works (23)

Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals

Computational and Structural Biotechnology Journal
2025 | Journal article
DOI: 10.1016/j.csbj.2025.01.002
Contributors: Branden Hunter; Timothy Cromwell; Hyunjin Shim
Source: check_circle
Crossref

Nanopore sequencing from protozoa to phages: decoding biological information on a string of biochemical molecules into human-readable signals

2024-08-07 | Preprint
DOI: 10.1101/2024.08.04.606558
Contributors: Branden Hunter; Timothy Cromwell; Hyunjin Shim
Source: check_circle
Crossref

A pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models

Frontiers in Molecular Biosciences
2024-06-21 | Journal article
DOI: 10.3389/fmolb.2024.1395450
Part of ISSN: 2296-889X
Contributors: Jeesu Lee; Branden Hunter; Hyunjin Shim
Source: Self-asserted source
H. Shim

NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling

2023-12-15 | Preprint
DOI: 10.1101/2023.12.14.571721
Contributors: Hyunjin Shim
Source: check_circle
Crossref

Sequencing, Fast and Slow: Profiling Microbiomes in Human Samples with Nanopore Sequencing

Applied Biosciences
2023-08-17 | Journal article
DOI: 10.3390/applbiosci2030028
Part of ISSN: 2813-0464
Contributors: Yunseol Park; Jeesu Lee; Hyunjin Shim
Source: Self-asserted source
H. Shim

CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins

BMC Bioinformatics
2023-04-25 | Journal article
DOI: 10.1186/s12859-023-05296-y
Contributors: Ho-min Park; Jongbum Won; Yunseol Park; Esla Timothy Anzaku; Joris Vankerschaver; Arnout Van Messem; Wesley De Neve; Hyunjin Shim
Source: check_circle
Crossref

Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity

Antibiotics
2023-01-18 | Journal article
DOI: 10.3390/antibiotics12020204
Part of ISSN: 2079-6382
Contributors: Hyunjin Shim
Source: Self-asserted source
H. Shim

In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials

Biology Direct
2022-10-07 | Journal article | Author
DOI: 10.1186/s13062-022-00339-5
Part of ISSN: 1745-6150
Contributors: Ho-min Park; Yunseol Park; Urta Berani; Eunkyu Bang; Joris Vankerschaver; Arnout Van Messem; Wesley De Neve; H. Shim
Source: Self-asserted source
H. Shim

Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins

Pharmaceuticals
2022-03-04 | Journal article
DOI: 10.3390/ph15030310
Part of ISSN: 1424-8247
Contributors: Ho-min Park; Yunseol Park; Joris Vankerschaver; Arnout Van Messem; Wesley De Neve; Hyunjin Shim
Source: Self-asserted source
H. Shim

Investigating the Genomic Background of CRISPR-Cas Genomes for CRISPR-Based Antimicrobials

Evolutionary Bioinformatics
2022-01 | Journal article
DOI: 10.1177/11769343221103887
Contributors: Hyunjin Shim
Source: check_circle
Crossref

Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP

Frontiers in Microbiology
2021-07-08 | Journal article
DOI: 10.3389/fmicb.2021.691847
Part of ISSN: 1664-302X
Contributors: Hyunjin Shim; Haridha Shivram; Shufei Lei; Jennifer A. Doudna; Jillian F. Banfield
Source: Self-asserted source
H. Shim

The NIH Somatic Cell Genome Editing program

Nature
2021-04-08 | Journal article
DOI: 10.1038/s41586-021-03191-1
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Contributors: Krishanu Saha; The SCGE Consortium; Erik Sontheimer; P. J. Brooks; Melinda R. Dwinell; Charles Gersbach; David Liu; Stephen A. Murray; Shengdar Q. Tsai; Ross C. Wilson et al.
Source: Self-asserted source
H. Shim

Futuristic Methods in Virus Genome Evolution Using the Third-Generation DNA Sequencing and Artificial Neural Networks

Global Virology III: Virology in the 21st Century
2019 | Book chapter
DOI: 10.1007/978-3-030-29022-1_17
Part of ISBN: 9783030290214
Part of ISBN: 9783030290221
Contributors: Hyunjin Shim
Source: Self-asserted source
H. Shim

Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Evolutionary Bioinformatics
2019-01 | Journal article
DOI: 10.1177/1176934318821072
Part of ISSN: 1176-9343
Part of ISSN: 1176-9343
Contributors: Hyunjin Shim
Source: Self-asserted source
H. Shim

Likelihood-free Inference of Population Genetic Parameters from Time-Sampled Genetic Data

Lausanne, EPFL
2018 | Journal article
DOI: 10.5075/EPFL-THESIS-7605
Contributors: H. Shim
Source: Self-asserted source
H. Shim

Resistance of Echovirus 11 to ClO2 Is Associated with Enhanced Host Receptor Use, Altered Entry Routes, and High Fitness

Environmental Science & Technology
2017-09-19 | Journal article
DOI: 10.1021/acs.est.7b03288
Part of ISSN: 0013-936X
Part of ISSN: 1520-5851
Contributors: Qingxia Zhong; Anna Carratalà; Hyunjin Shim; Virginie Bachmann; Jeffrey D. Jensen; Tamar Kohn
Source: Self-asserted source
H. Shim

Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin

Virus Evolution
2017-07-01 | Journal article
DOI: 10.1093/ve/vex035
Part of ISSN: 2057-1577
Contributors: Anna Carratalà; Hyunjin Shim; Qingxia Zhong; Virginie Bachmann; Jeffrey D Jensen; Tamar Kohn
Source: Self-asserted source
H. Shim

On the importance of skewed offspring distributions and background selection in virus population genetics

Heredity
2016-12 | Journal article
DOI: 10.1038/hdy.2016.58
Part of ISSN: 0018-067X
Part of ISSN: 1365-2540
Contributors: K K Irwin; S Laurent; S Matuszewski; S Vuilleumier; L Ormond; H Shim; C Bank; J D Jensen
Source: Self-asserted source
H. Shim

An experimental evaluation of drug‐induced mutational meltdown as an antiviral treatment strategy

Evolution
2016-11 | Journal article
DOI: 10.1111/evo.13041
Part of ISSN: 0014-3820
Part of ISSN: 1558-5646
Contributors: Claudia Bank; Nicholas Renzette; Ping Liu; Sebastian Matuszewski; Hyunjin Shim; Matthieu Foll; Daniel N. A. Bolon; Konstantin B. Zeldovich; Timothy F. Kowalik; Robert W. Finberg et al.
Source: Self-asserted source
H. Shim

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

G3 Genes|Genomes|Genetics
2016-04-01 | Journal article
DOI: 10.1534/g3.115.023200
Part of ISSN: 2160-1836
Contributors: Hyunjin Shim; Stefan Laurent; Sebastian Matuszewski; Matthieu Foll; Jeffrey D Jensen
Source: Self-asserted source
H. Shim

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1310
PMID: 26615188
PMC: PMC4702916
Contributors: SIB Swiss Institute of Bioinformatics Members
Source: Self-asserted source
H. Shim via Europe PubMed Central

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Molecular Ecology Resources
2015-01 | Journal article
DOI: 10.1111/1755-0998.12280
Part of ISSN: 1755-098X
Contributors: Matthieu Foll; Hyunjin Shim; Jeffrey D. Jensen
Source: Self-asserted source
H. Shim

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

PLoS Genetics
2014-02-27 | Journal article
DOI: 10.1371/journal.pgen.1004185
Part of ISSN: 1553-7404
Contributors: Matthieu Foll; Yu-Ping Poh; Nicholas Renzette; Anna Ferrer-Admetlla; Claudia Bank; Hyunjin Shim; Anna-Sapfo Malaspinas; Gregory Ewing; Ping Liu; Daniel Wegmann et al.
Source: Self-asserted source
H. Shim

Peer review (3 reviews for 3 publications/grants)

Review activity for Heliyon. (1)
Review activity for Microbiological research. (1)
Review activity for Nature communications (1)
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