Yözen Anthony Hernández

Yözen Anthony Hernández
Rockefeller University | Rockefeller · Laboratory of Genetically Encoded Small Molecules

PhD Bioinformatics

About

25
Publications
4,239
Reads
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441
Citations
Introduction
Bioinformatics scientist and software developer with over 10 years experience and a PhD in Bioinformatics. Research interests include evolutionary biology, genetic variation, algorithm design, and science education. I am currently searching for a job in Bioinformatics/Computational biology in New York City.
Additional affiliations
January 2020 - present
Rockefeller University
Position
  • Bioinformatician
June 2011 - May 2019
Boston University
Position
  • PhD Student
April 2009 - July 2011
City University of New York - Hunter College
Position
  • Research Assistant
Education
July 2011 - May 2013
Boston University
Field of study
  • Bioinformatics
July 2011 - May 2019
Boston University
Field of study
  • Bioinformatics
August 2004 - January 2009
City University of New York - Hunter College
Field of study
  • Computer Science/Quantitative Biology

Publications

Publications (25)
Preprint
Gonorrhea, which is caused by Neisseria gonorrhoeae , is the second most reported sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibioti...
Preprint
Gonorrhea, which is caused by Neisseria gonorrhoeae , is the second most prevalent sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibiot...
Preprint
Gonorrhea, which is caused by Neisseria gonorrhoeae , is the second most prevalent sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibiot...
Preprint
Full-text available
Gonorrhea, which is caused by Neisseria gonorrhoeae, is the second most prevalent sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibioti...
Article
Full-text available
DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportun...
Article
DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportun...
Article
Cationic nonribosomal lipopeptides (CNRLPs) from Paenibacillus spp. have been a rewarding source of Gram-negative-active antibiotics. Here we systematically screened sequenced bacterial genomes for CNRLP biosynthetic gene clusters (BGCs) that we predicted might encode additional Gram-negative-active antibiotics. Total chemical synthesis of the bioi...
Article
Full-text available
In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this p...
Article
Full-text available
The emergence of multidrug-resistant bacteria poses a threat to global health and necessitates the development of additional in vivo active antibiotics with diverse modes of action. Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth o...
Article
Full-text available
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commo...
Article
Full-text available
Tuberculosis (TB) remains one of the deadliest infectious diseases. Unfortunately, the development of antibiotic resistance threatens our current therapeutic arsenal, which has necessitated the discovery and development of novel antibiotics against drug-resistant Mycobacterium tuberculosis (Mtb). Cyclomarin A and rufomycin I are structurally relate...
Preprint
Full-text available
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2,770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ranging from 7 bp to 126 bp, and with array lengths up to 230 b...
Article
This paper presents updated analyses on the genetic associations of sleep disruption in individuals with Alzheimer’s disease (AD). We published previously a study of the association between single nucleotide polymorphisms (SNPs) found in eight genes related to circadian rhythms and objective measures of sleep-wake disturbances in 124 individuals wi...
Article
Full-text available
Background Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There...
Article
Full-text available
Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic o...
Article
Full-text available
DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we describe VNTRseek, our software fo...
Article
Full-text available
Lyme disease is caused by spirochete bacteria from the Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) species complex. To reconstruct the evolution of B. burgdorferi s.l. and identify the genomic basis of its human virulence, we compared the genomes of 23 B. burgdorferi s.l. isolates from Europe and the United States, including B. burgdorfer...
Conference Paper
Cells suffer damage to their DNA from environmental agents including ionizing radiation and DNA-binding chemicals, causing mutations and ultimately cancer. Unrepaired DNA damage typically blocks replicative DNA polymerases (DNAPs). Living systems have evolved lesion-bypass DNAPs, which are mostly in the Y-Family. The IV/κ -class of Y-Family DNAPs,...
Article
Full-text available
How genomic diversity within bacterial populations originates and is maintained in the presence of frequent recombination is a central problem in understanding bacterial evolution. Natural populations of Borrelia burgdorferi, the bacterial agent of Lyme disease, consist of diverse genomic groups co-infecting single individual vertebrate hosts and t...
Article
Full-text available
Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping. In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithm...
Article
Microbial pathogens have evolved sophisticated mechanisms for evasion of host innate and adaptive immunities. PFam54 is the largest paralogous gene family in the genomes of Borrelia burgdorferi, the Lyme disease bacterium. One member of PFam54, the complement-regulator acquiring surface proteins 1 (BbCrasp-1), is able to abort the alternative pathw...
Article
Diplotype Genome Reconstruction Problem: Reconstruct the two haplotype sequences from HTS shotgun sequencing reads. The sensitivity of detecting heterozygous loci from shotgun sequencing reads is severely limited by coverage depth. Wendl and Wilson (9) estimate that a coverage as high as 21! may be required to achieve a genotype calling accuracy co...

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