Current lab members:
Scarlet Shell, Ph.D.
Principal Investigator
Scarlet leads the Shell lab in our quest to understand how mycobacteria regulate their transcriptomes to tolerate stress. She received a B.A. in Biological Sciences from Smith College in 2001 and a Ph.D. in Biomedical Sciences from the University of California, San Diego in 2008. She received postdoctoral training in Sarah Fortune’s lab at the Harvard T.H. Chan School of Public Health were she investigated the role of DNA methylation in M. tuberculosis and developed methodology to map mycobacterial transcription start sites and RNA cleavage sites transcriptome-wide. Scarlet joined the department of Biology and Biotechnology at WPI as an assistant professor in 2014.
More on Scarlet’s background
Juan Hilario Cafiero, Ph.D.
Postdoctoral Fellow
Hilario received a degree in Biotechnology and Molecular Biology and a Ph.D. from the School of Exact Sciences, National University of La Plata (UNLP) in Argentina. In his doctoral thesis (at CINDEFI, UNLP), he studied the intracellular persistence of Bordetella pertussis, the causative agent of whooping cough. He then received postdoctoral training in Florencia Del Papa’s lab at the Biotechnology and Molecular Biology Institute (IBBM, UNLP), where he explored the role of a two-component system in the adaptation of the nitrogen-fixing bacterium Sinorhizobium meliloti to stress by transition metals and characterized a novel metallo-β-lactamase from a Pseudomonas sp. environmental isolate. He joined the Shell lab as a postdoc in December 2021 and is investigating the RNA degradation pathways of Mycobacterium tuberculosis and its link with antibiotic resistance.
Huaming Sun, M.S.
Ph.D. Candidate
Huaming received a Bachelor of Science in Information and Computational Science from Qingdao Agricultural University, followed by a Master of Science in Applied Statistics from WPI. He is now pursuing a Ph.D. in Bioinformatics and Computational Biology under the joint mentorship of Scarlet Shell and Dmitry Korkin. He is harnessing his background in statistics and computer science to address questions relating to gene regulation and mRNA metabolism in mycobacteria with focus on refined understanding of mRNA degradation mechanism.
Julia Ryan, M.S.
Ph.D. Candidate
Julia studied Biology, Biochemistry, and English at Brandeis University, graduating in 2019 after studying x-ray crystallography and protein biochemistry. Looking for more experience in molecular and microbiology, she joined the Shell Lab in spring 2020 to pursue a Ph.D. in Biology & Biotechnology. She is now investigating the roles of putative RNA-binding proteins in the M. smegmatis stress response. Beyond the lab, Julia enjoys roller skating, poetry, plants, and spending time with friends.
Junpei Xiao, M.S.
Ph.D. student
Junpei received a Bachelor of Science in Biology from Arizona State University with experience on utilizing microbes to produce renewable industrial grade bio-based products. He then received a Master of Science in Bioinformatics from Boston University with experience on scRNA-seq and scATAC-seq analysis. He is now pursuing his Ph.D. in Bioinformatics and Computational Biology. He joined the Shell lab in Spring 2021 and is investigating the mechanism of resistance for certain drug of mycobacteria. Beyond the lab, Junpei enjoys fishing.
Abby Rapiejko, B.S.
Ph.D. Candidate
Abby received a Bachelor of Science in Biochemistry and a Certification in Education from Siena College with experience in physical biochemistry and teaching high school chemistry. She is now pursuing a Ph.D. in Biology and Biotechnology and joined the Shell lab in Spring 2022. She’s taking a biochemical approach to investigate post-transcriptional regulation of mycobacteria by RNases. Outside the lab, Abby enjoys spending time with her horse and her favorite activities are jumping, trail riding, games on horseback, and swimming.
Opeyemi Isaac Ibitoye, M.S.
Ph.D. student
Opeyemi received a Bachelor of Science degree in Biochemistry from Kwara State University in Nigeria where he was working on a project on molecular docking analysis to identify novel antimalarial compounds from an indigenous plant. He then received a Master of Science in Life Sciences from Skolkovo Institute of Science and Technology (Skoltech) in Moscow, Russia with experience in using the Molecular Biotechnology approach for identification and screening for new antibiotics that affect the bacterial ribosome. He is now pursuing his Ph.D. in Biology and Biotechnology and joined the Shell Lab in Spring 2022 and is now investigating the regulation of mRNA degradation and stress response in Mycobacterium. Outside the lab, Opeyemi has a sound interest in Bioinformatics, and he enjoys long drives with friends and seeing soccer matches.
Vanesa Lopa, B.S.
Ph.D. Candidate
Vane received a Bachelor degree in Biotechnological Engineering from the Santa Maria Catholic University in Arequipa, Peru. After working in research for Environmental and Plant Biotechnology, she decided to pursue a Ph.D. in Biology and Biotechnology joining the Shell Lab in spring 2022. She is focusing her research in identifying and characterizing potential RNA binding proteins in M. smegmatis. Outside the lab, Vane loves to dance.
Alana Lue Chee Lip
Undergraduate
Alana is an international student from Trinidad and Tobago currently pursuing a B.S. in Biology and Biotechnology. She joined the Shell lab in the summer of 2022 and is working to investigate the roles of RNA degradation proteins in mycobacteria. She also works as a Peer Learning Assistant (PLA) and Biology Ambassador for the Biology department. Outside of work, she enjoys knitting, watching reality TV, and spending time with friends.
Madelaine Freitas
Undergraduate
Maddie is currently pursuing a B.S. in Biology and Biotechnology. She joined the Shell lab in June 2022 and began work to investigate the role of RNA degradation proteins in M. smegmatis. She hopes to pursue a career in Microbiology following her graduation in 2024. Outside of lab, she enjoys crocheting, music, and participating in campus activities such as a comedy group, Guerilla Improv.
Shell lab alumni:
Olivia Atkins, B.S.
Livvie received a B.S. in Biology and Biotechnology in 2023. She joined the Shell Lab in spring 2021 and works on determining the effects of certain codons on translation efficiency and mRNA stability in Mycobacterium smegmatis. Outside of the lab, Livvie enjoys running, hiking, and spending time with friends and family.
Position after graduation: M.S. student in Biotechnology (drug design and discovery concentration) at Georgetown University
Amelia Sadlon
Undergraduate
Amelia joined the Shell Lab in January 2021 and began work to observe the effects that certain codons can have on mRNA stability and translation efficiency in Mycobacterium smegmatis. Outside of the lab, Amelia finds joy in baking, as well as hiking and collecting plants. She hopes to combine these passions for nature and molecular biology in the future.
Natalia Alonso, Ph.D.
Postdoctoral Fellow
Natalia received a bachelor´s degree in Molecular Biology from the School of Exact and Natural Sciencies, University of Mar del Plata, Argentina. Then, she obtained her PhD degree from the School of Pharmacy and Biochemistry of the University of Buenos Aires, Argentina. She received postdoctoral training in Maria Isabel Romano´s lab at the Institute of Agrobiotechnology and Molecular Biology (IABiMo, INTA-CONICET), Argentina where she investigated genes potentially related to virulence in Mycobacterium avium subsp paratuberculosis (MAP) and developed methodology to detect MAP and Mycobacterium bovis in bovine serum samples. Natalia joined Shell lab as a posdoc in May 2021 and worked on investigating the relationship between RNA metabolism and antibiotic resistance using a combination of biochemistry, genetics, genomics, transcriptomics, and phenotypic profiling.
Position after leaving the lab: Assistant Researcher at Bovine Paratuberculosis Laboratory. Institute of Agrobiotechnology and Molecular Biology
Sarah Bibeau, B.S.
Post-baccalaureate
Sarah graduated in 2021 from Clark University with a BA in Biology. In Shell lab, she worked on understanding the mechanisms of ESX-1 secretion system in Mycobacterium smegmatis. Outside of the lab, she enjoys spending time with friends and family and going to the beach.
Position after leaving the lab: Technician at BWH. Later PhD student in Biology at Boston College
Hannah Allen
Undergraduate
Hannah joined the Shell Lab the summer of 2021 and worked on understanding the possible connection between a mutation in the enzyme RNase E in Mycobacterium tuberculosis and resistance to the drug cycloserine. Outside of the lab she enjoys baking, exploring nature, and drawing.
Catherine Masiello, B.S.
Catherine received a B.S. in Biology and Biotechnology in 2022. She joined the Shell Lab in the Summer of 2020 and began examining the ribosomal binding sites of Mycobacterium smegmatis and Mycobacterium tuberculosis. She was looking to identify site characteristics, such as sequence motifs and spacing, and their relation to the translation efficiency of mycobacteria genes. Outside of the lab, Catherine enjoys theatre, reading, and podcasts.
Position after graduation: Research Associate II for the Metagenomics Discovery Team at Arbor Biotechnologies
Adrian Orszulak, B.S.
Adrian got his B.S. in Biology and Biotechnology and B.S. in Bioinformatics and Computational Biology in 2022. He was in awe of microbiology and the mechanisms of molecular biology, especially those involving regulatory roles for transcription and translation. Beginning in the winter of 2020 and together with Van Le, Arian began to work on examining mRNA half-life and protein degradation rate through an inducible system using Mycobacterium smegmatis. Outside of the lab, Adrian enjoys board games, hiking, and swimming.
Position after graduation: PhD student in Biomedical Sciences at UMass Chan Medical School
Van Le, B.S.
Van received her B.S. in Biology and Biotechnology in 2022. She was born and raised in Ho Chi Minh City, Vietnam. When she was in high school, she knew that she wanted to pursue a career in Biology. Moving to the United States at the age of 15, she attended a high school where she was inspired by her biology teacher, who taught her how to run PCR for the first time. She joined Shell Lab at the beginning of 2020 and began working with Adrian Orszulak in understanding mRNA half-life and protein degradation rate at different inducer concentrations in Mycobacterium smegmatis. Outside of the lab, she enjoys cooking Asian dishes, practicing martial arts, watching cat videos, and traveling around the world!
Position after graduation: Research Associate of Preclinical Biomarkers at Caraway Therapeutics
Ying Zhou, Ph.D.
Ying received a bachelor’s degree in Biopharmaceutics from Beijing University of Chinese Medicine and a master’s degree in Biotechnology from the NYU School of Engineering. She joined the Shell lab as a Ph.D. student in 2014 and worked on investigating the roles and regulation of mycobacterial RNases.
Position after graduation: Postdoc at University of California, Davis (Xinbin Chen laboratory)
Carla Martini, Ph.D.
Postdoctoral Fellow
Carla received a bachelor’s degree in Biotechnology and Molecular Biology from the School of Exact Sciences, La Plata National University (Argentina). She then obtained a Doctorate Fellowship from the National Council of Scientific and Technological Research of Argentina (CONICET) and acquired the PhD degree in Exact Sciences from the Institute of Biotechnology and Molecular Biology in 2016. She joined the Shell lab as a postdoc in October 2016 and is investigating the role of RNAse J in the resistance to certain antibiotics and other stresses in mycobacteria.
Position after leaving the lab: Faculty-track position at La Plata National University
Ryan Peters, B.S.
Ryan received a B.S. in Biology & Biotechnology in 2021. He is amazed at the vast complexity of gene regulation and enjoys studying and exploring how so many components work together seamlessly. In Shell lab, he worked on determining the role of 5’ UTRs in ribosomal gene regulation in mycobacteria, especially in the cell response to antibiotic stress. Outside of research he enjoys camping, hiking and technical theatre.
Position after graduation: PhD student in Biological Sciences at Purdue University
Justin Moy, B.S.
Justin Moy got his B.S. in Bioinformatics and Computational Biology in 2022. He volunteered in the lab working on documenting characteristics of the 3′ UTR using Python and R. Outside the lab, Justin enjoys travel and cooking.
Position after graduation: PhD student in Bioinformatics at Boston University
Samantha Joubran, B.S.
Samantha received a bachelor’s and master’s degree in biochemistry in 2021, with a passion for microbiology and infectious diseases. She was working on understanding the role of RNase III in the gene expression of Mycobacterium smegmatis.
Position after graduation: PhD student in Chemical Biology at Harvard University
Diego Vargas Blanco, Ph.D.
Diego’s fascination with understanding how things work, alongside a passion for biological sciences, led him to study biotechnological engineering at Universidad Católica de Santa María (Arequipa, Peru). He joined Shell lab to pursue a Ph.D. with a Fulbright scholarship. He was focused on understanding the regulation of mRNA stability as an adaptive response to deleterious environment changes. Besides research, Diego enjoys oil painting, baking and ballroom dancing.
Diego describes his research and experience at WPI
More on Diego’s path to WPI
Position after graduation: Research fellow at Massachusetts General Hospital (Jatin Vyas laboratory)
Jess Kelly, B.S.
Jess obtained a B.S. in Biology and Biotechnology and a B.S. in Bioinformatics and Computational Biology in 2021. She was fascinated by the mechanisms of gene regulation as well as how computational methods can be applied to study molecular biology. Jess worked in the Shell lab since fall of 2019, doing computational and bench work to explore the effect of secondary structure on mRNA stability in mycobacteria. Her project was to examine the role of stem loops in the 5’UTR on mRNA stability, specifically looking at the virulent esxB gene. Outside of the lab, she enjoys traveling and hiking.
Position after graduation: Research Assistant at the Friedman lab at Beth Israel Deaconess Medical Center
Alexa Davis, B.S.
As a highly curious and detail oriented person with a love for life sciences, Alexa quickly found a passion in molecular biology and genetics. In 2020, Alexa obtained a B.S. in Biology and Biotechnology and a B.S. in Biochemistry. On Summer of 2019 Alexa began exploring the role of 5’ UTRs of mRNA transcripts that encode ribosomal proteins in mycobacteria. Her Major Qualifying Project was about learning how these 5’ UTRs may be regulating mRNA stability or protein expression under stress conditions.
Position after graduation: Research Associate at Custom Solutions at Abcam
Karina Franca, B.S.
Karina graduated from WPI in 2020 with a B.S. in Biology and Biotechnology. Karina joined the Shell lab during summer of 2018 where she began exploring the regulatory function of the rne 5’ UTR. This project continued as her Major Qualifying Project, where it evolved to exploring specifically the autoregulatory ability of the rne 5’ UTR in mycobacteria.
Position after graduation: M.S. student at Boston University
Tien Nguyen, B.S.
Tien graduated from WPI in 2019 with a B.S. in Biology and Biotechnology. His work focused on the effect of 5′ UTRs on mRNA stability in mycobacteria, specifically for the sigma factor sigA.
Position after graduation: Research Associate at Broad Institute of MIT and Harvard
Sam Randall, B.S.
Sam graduated from WPI in 2019 with a B.S. in Biology and Biotechnology. Her work in the Shell lab focused on understanding the role of DNA methylation in mycobacteria.
Position after graduation: Research Associate at PAI Life Sciences
Oscar Lee, B.S.
Oscar graduated from WPI in 2019 with a dual B.S. in Biology & Biotechnology and in Biochemistry. While at the Shell lab, he performed structure-function analysis of the mycobacterial RNase E.
Position after graduation: Doctor of Dental Surgery student at New York University
David Morgan, B.S.
David received his B.S. in Biology and Biotechnology from WPI in 2017. He spent 2.5 years in the Shell lab as an undergraduate investigating the regulation of heat-shock proteins in mycobacteria.
Position after graduation: Ph.D. student at Brown University
Charlotte Reames, B.S.
Charlotte received her B.S. in Biology and Biotechnology from WPI in 2017. Her senior research project in the Shell lab focused on tagging and quantifying RNA degradation proteins to understand how their abundance is regulated in stress conditions.
Position after graduation: Laboratory technician at UMass Chan Medical School
Paula de Camargo Bertuso, M.S.
Paula received her M.S. in Biology and Biotechnology from WPI in 2016. Her thesis work in the Shell lab focused on understanding the role of RNase J in mycobacterial mRNA metabolism as well as understanding the mechanistic basis of the mycobacterial response to oxidative stress. Her studies at WPI were funded by a Science Without Borders scholarship from the Brazilian government. Prior to coming to WPI, Paula received a bachelor’s degree in biotechnology from the Federal University of Sao Carlos in Brazil.
Position after graduation: Ph.D. student at Universidade de São Paulo, Brazil
Izzy Garver, B.S.
Izzy received her B.S. degree in Biology and Biotechnology, with a focus on the pre-health track,from WPI in 2017. She received a fellowship from the WPI’s Arts & Sciences Advisory Board and the WPI Life Sciences Advisory Board to spend the Summer of 2016 in the Shell lab, where she worked on understanding the relationship between RNase J, mutation rate, and acquisition of drug resistance in M. smegmatis.
Position after graduation: Research Associate at Cell Signaling Technology (CST)
Daniel Santos, B.S.
Daniel is a Biotechnology major at the Federal University of Paraiba in Brazil and spent his junior year at WPI through a fellowship from the Brazilian government sponsored by the International Institute of Education. He spend a summer with the Shell trying to find new antibiotics against M. tuberculosis from soil strains, which were isolated and screened for antibiotic production.
Brianna Courteau, B.S.
Brianna was pursuing a B.S. in Biology and Biotechnology at WPI on a pre-health track. She received a WPI Summer Undergraduate Research Fellowship to spend the summer of 2017 in the Shell lab investigating the antimicrobial properties of the medicinal plant Artemisia Annua.
John de Rivera, B.S.
John received his B.S. in Biochemistry from WPI in 2016. His senior research project focused on investigating the determinants of transcript stability for the mycobacterial esxB transcript. He is currently a firefighter and paramedic at West Boylston Fire Department.
Nicholas Lemere, B.S.
Nick received his B.S. is Biology and Biotechnology from WPI in 2016. His senior research project aimed to investigate the role of DNA methylation in promoting survival of hypoxia in mycobacteria.
Kristen Behrakis, B.S.
Kristen investigated the effects of colloidal silver on mycobacterial growth and survival while attending high school at the Massachusetts Academy of Math and Science at WPI.