For inquiries about a PhD in evolutionary genomics:
Info on PhD program in Applied Biology at UMass Lowell and email: frederic_chain[at]uml.edu
Info on PhD program in Applied Biology at UMass Lowell and email: frederic_chain[at]uml.edu
current lab members
PHD APPLIED BIOLOGY Evolutionary genomics of duplicated genes Michael is applying bioinformatics techniques to analyze genome evolution and regulation. His primary goal is to apply computational techniques and develop tools that facilitate addressing biological problems. *B.S Parasitology, University of Lagos (First Class) BIO Major Alternative splicing in stickleback Hi I’m Dang Nguyen, an undergrad sophomore majoring in biology. I’m a member of the honors college and I’ll be studying alternative splicing in stickleback populations. I plan to dedicate myself to the field of medical genetics in the future. *Immersive Scholar (2022) *Honors Fellowship (2024) Bio-ChemInformatics Major *Data Analyst *Working on genomics of stickleback fishes using R to find associations between DNA methylation and gene duplications *Moloney Student Scholar (2024) |
Single-cell RNA-seq analysis -duplicate gene expression divergence in ape brains *B.S. in Cell and Molecular Biology (2021) *Interests in Genomics, Transcriptomics, Spatial Transcriptomics *Specializes in R, Python and Machine Learning Computer science major Developing 3D visualization tools for genomic data using Vulkan Sophomore experienced in C/Java/Python with an interest in bioinformatics as well as artificial intelligence *Immersive Scholar (2023) Bio MAJOR Single-cell RNA-seq analysis *Interests in genetics, cellular biology, and biochemistry *Concentration in Biotechnology |
PhD Applied Biology Epigenomics and duplicate gene evolution *B.S. in biology from UML (2021) Summa Cum Laude *Senior Research on single cell methylation and expression *Teaching Assistant * Goal is to develop/apply bioinformatic tools that can aid in biology and health research. *2022 Research Symposium Award Bio Major eDNA metabarcoding bioinformatic analysis *Designing Bioinformatics Education for High Schoolers *Investigating structural variation genotypes across stickleback populations *Honors Student in Biology *KCS Scholar (2022) Principal investigator genome evolution duplicate genes epigenetic regulation mutation rates eDNA biodiversity monitoring microbial profiling alternative splicing |
lab alumni
2023-2024
Gene co-expression networks *B.S. in Computer Science at UML (2022) *Experience with R, Python, C/C++ *Interested in applying bioinformatics tools to research in genetics and evolutionary biology BIO Major I am a sophomore, with interests in bioinformatics, and I will be employing R programming to explore stickleback genome divergence. *Immersive Scholar (2023) |
Master's student eDNA metabarcoding to monitor aquatic biodiversity during Alewife migration *Senior research on molecular approaches in metabarcoding *Conducted in silico analysis of metabarcoding primer pairs to evaluate the extent of taxonomic diversity and resolution |
Computer science Major I am an undergraduate and a first generation RHSA student. I will be employing my programming skills to analyse data sets to find new genes in fish. *Roads to Research Intern (2023) |
Master's biology Single cell RNA-sequencing analysis of immune cells *Interests in Systems Biology |
2022-2023
master's Biotechnology '22 Regulation of Iron in Huntingtin Null Cells *B.S. at UML (2021) *Research on iron and magnesium dependence of huntingtin deficient Dictyostelium cells *Concentration in Biotechnology *2022 Research Symposium Award BIO Major Single-cell RNA-seq analysis of primate brains *MS student Northeastern *Honors college fellowship (2021) *Completed co-op internship at Genomic Expression *Concentration in Bioinformatics Computer Science Major Developing RShiny Packages I'm an undergrad computer science major concentrating in bio-cheminformatics. I am excited to see how my programming knowledge could be used to interprate biological data. *Immersive Scholar (2023) |
BS Biology (2022) Genome Browsers *Quality Control Analyst @ Charm Sciences Inc *Studied the concentration and effects of E. coli in the Merrimack river on public health Paschal Ugwu Stickleback Comparative Genomics Research interests lie in Bioinformatics and Genomics. He is fluent in R and Python to analyze complex biological data. *Bachelor of Science in Biochemistry, First Class Degree University of Agriculture in Umudike, Nigeria |
Alternative splicing in Sticklebacks *B.S. in Molecular and Cell Biology from UConn (2020) *Currently working in mRNA Manufacturing for Moderna Tx. *Goal is to study traits of evolution using bioinformatic tools. Precious Nworie Phylogenetics I am interested in evolutionary changes in major infectious diseases and how they evade drug interactions. *Master's degree in Molecular Biology and Genomics with a minor in Drug Design BIO Major Epigenetic divergence among young duplicate genes in cichlids *Honors College Fellowship (2023) |
Master's Biotechnology '23 Metagenomic analysis of aquatic microbiome exposed to pollutants *Worked on metagenomic analysis of platispheres using EDGE *B.Tech Biotechnology at SRMIST, Chennai, India Salma Tariq Stickleback Pangenomics Research interests in bioinformatics, pangenomes, and evolution. I am an expert in NGS analysis, Python, R, and bash. *Bachelor of Science in Bioinformatics Comsats University Islamabad *Master of Science in Bioinformatics from the National University of Science and Technology Islamabad |
2021-2022
Phd (2022) IMPROVING TAXONOMIC IDENTIFICATION OF BACTERIAL AMPLICON SEQUENCES AND META-ANALYSIS DEFINING MOSQUITO GUT MICROBIAL DIVERSITY Publications here and here *Previously clinical field application specialist for Roche Diagnostics *Now at Dovetail Biopartners immersive scholar Tardigrade gene family evolution (see publication here) *Now at UConn School of Dental Medicine *Dean's Medal for Outstanding Academic Achievement *Major in Biomedical Engineering '23 |
MS Biology (2022) Thesis: A Bioinformatic Survey of Tardigrade Viruses and Antiviral Genes *B.S. at UML (2020) Magna Cum Laude *Phlebotomist *Part-time assistant - laboratory animal care and maintenance *Now PhD Candidate immersive scholar RNA-seq of huntingtin mutant cells *Tardigrade culturing *Concentration in Biotechnology * Now Research Assistant/Technical Associate @ MIT immersive scholar 16S and 18S profiling and macroinvertebrate diversity *Concentration in Biotechnology |
bS Biology (2022) Copy Number Variation mutation rates (see publication here) *Co-op at uniQure gene therapy *UML Learning in Retirement Association Student Scholarship *2022 Outstanding Graduating Scholar in Biology *2022 Outstanding Service in Biology *Honors college fellowship (2020) *Immersive Scholar (2019) immersive scholar Hoang Truc Kim Michael Campos Disha Patel Sequence data visualization using genome browsers |
Master's student Investigation into the role of Huntingtin protein as a scaffolding protein in the autophagy pathway *B.S. Biotechnology UML (2020) Magna Cum Laude *Lab Technician at Lahey Hospital and Medical Center, COVID testing with RT-PCR *2022 Outstanding Graduate Student in Biology *Now Research Associate at Mercy BioAnalytics, Inc. IMMERSIVE SCHOLAR 16S and 18S profiling and macroinvertebrate diversity *Majoring in Env. Engineering IMMERSIVE SCHOLAR Alternative splicing in sticklebacks *Data Coder @ Brigham and Women's |
2020-2021
honors project Huntingtin deficiency in Dictyostelium development & expression *KCS Scholar (2019) *2021 UMass Lowell Trustees’ Key and Chancellor’s Distinguished Academic Achievement Medal *2021 Biology Department Academic Achievement Award (Top GPA) *Medical ophthalmology assistant Master's student Duplicate gene expression variation in single-cell RNA-seq *Bsc in Bioinformatics *Programming in R, python and C/C++ *Goal is to apply bioinformatics tools to study gene functions |
senior thesis Microbial metagenomics & Dictyostelium mutagenesis *UMLSAMP Scholar (2020) *Graduated in Biology with a Minor in Public Health (Cum Laude) *College of Science Dean's List *Intern at the Smithsonian Astrophysical Observatory 2020 *Pharmacy School @ University of Wisconsin Madison |
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immersive scholar |
2019-2020
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volunteer Differential Gene Splicing *Research Associate @ Cystic Fibrosis Foundation Therapeutics Lab |
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2018-2019
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2017-2018
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Dylan Beeber Honors thesis Developed and published an R program to design guide RNA for CRISPR applications Software found here * Hired @ SQZ biotech *MS in Bioinformatics *Now Bioinformatics Research Associate at Edigene Inc. |
Mapping pollutants and biodiversity in canals & DNA Methylation between populations Max Kalinowski Monitoring urban waterways for pollutants and biodiversity |
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lab guests
Donghyun Lee (2020-2021) - Structural variation calling using long read technologies
Guy Moore (2018-2019) - Comparing metagenomics analysis and taxonomic assignment pipelines
Louis Astorg (2018) - PhD Candidate at UQAM studying eco-evolutionary dynamics in ionic gradients
Gillian Martin (2017) - PhD Candidate at UQAM studying the impact of dispersal and genetic diversity on metacommunity dynamics
Guy Moore (2018-2019) - Comparing metagenomics analysis and taxonomic assignment pipelines
Louis Astorg (2018) - PhD Candidate at UQAM studying eco-evolutionary dynamics in ionic gradients
Gillian Martin (2017) - PhD Candidate at UQAM studying the impact of dispersal and genetic diversity on metacommunity dynamics
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some collaborators
Stress and Transcriptomics
Natalie Steinel @ UMass Lowell
Jennifer Fish @ UMass Lowell
Stickleback Genomics
Philine Feulner @ eawag
Britta Meyer @ Max Planck Institute for Evolutionary Biology
Erich Bornberg-Bauer @ University of Münster
Anne Dalziel @ Saint Mary's University
Christophe Eizaguirre @ Queen Mary University of London
Thorsten Reusch @ GEOMAR Kiel
Jason Goldstein @ Wells National Estuarine Research Reserve
Daphnia Genomics and Biodiversity
Melania Cristescu @ McGill University
Teri Crease @ Guelph University
Xenopus Genomics
Ben Evans @ McMaster University
Environmental Monitoring in Lowell
Sheree Pagsuyoin @ UMass Lowell
Grace Chen @ UMass Lowell
Daniel Obrist @ UMass Lowell
Richard Gaschnig @ UMass Lowell
Jane Calvin @ Lowell Parks & Conservation Trust
Sheila Kirschbaum @ UMass Lowell & Tsongas Industrial History Center
Natalie Steinel @ UMass Lowell
Jennifer Fish @ UMass Lowell
Stickleback Genomics
Philine Feulner @ eawag
Britta Meyer @ Max Planck Institute for Evolutionary Biology
Erich Bornberg-Bauer @ University of Münster
Anne Dalziel @ Saint Mary's University
Christophe Eizaguirre @ Queen Mary University of London
Thorsten Reusch @ GEOMAR Kiel
Jason Goldstein @ Wells National Estuarine Research Reserve
Daphnia Genomics and Biodiversity
Melania Cristescu @ McGill University
Teri Crease @ Guelph University
Xenopus Genomics
Ben Evans @ McMaster University
Environmental Monitoring in Lowell
Sheree Pagsuyoin @ UMass Lowell
Grace Chen @ UMass Lowell
Daniel Obrist @ UMass Lowell
Richard Gaschnig @ UMass Lowell
Jane Calvin @ Lowell Parks & Conservation Trust
Sheila Kirschbaum @ UMass Lowell & Tsongas Industrial History Center