Principal Investigator
Michael Talkowski
Director, Center for Genomic Medicine and Institute Member, Broad Institute of MIT and Harvard
Mike received undergraduate degrees in Biology and Psychology and a PhD in Human Genetics with a focus in genetic epidemiology and psychiatric genetics. He joined the Center for Genomic Medicine (CGM) of Massachusetts General Hospital, the Department of Neurology in Harvard Medical School, and the Program in Medical and Population Genetics at the Broad Institute as a Postdoctoral Fellow with Dr. James Gusella in 2008 to study the genetic etiology of neurodevelopmental disorders, particularly autism spectrum disorders. He was appointed to the faculty of the CGM and Harvard Medical School in 2011 and is now the Director of the Genomics and Technology Core at MGH. He also became a Institute Member at the Broad Institute of MIT and Harvard in 2018 and is currently the Director of the Broad Structural Variation Group. He is also a faculty member in the Harvard Biological and Biomedical Sciences (BBS) graduate program as well as the Bioinformatics and Integrative Genomics (BIG) program. In 2015, Mike received the MGH ECOR Scholars award.
Postdoctoral Fellows
Michael holds a BA in Mathematics and Chemistry from Carleton College (Northfield, MN), an MPhil in Computational Biology from the University of Cambridge (Cambridge, UK) where he was a Gates Scholar, and an M.D. and Ph.D. in Genome Sciences (advisor Evan Eichler, PhD) from the University of Washington (Seattle, WA). For his PhD work, he investigated the molecular etiology of autism using genome sequencing, explored genetic modifiers, and used long read sequencing technologies to elucidate difficult to assemble regions of the genome. He pursued his residency in pediatrics at Boston Children’s Hospital and is currently a fellow in Clinical Genetics in the Harvard Genetics Training Program. He joined the Talkowski Group in Winter 2022. He is excited to focus on prenatal diagnostics to provide early diagnosis and enhanced care to the pediatric population and to better understand the genetic architecture of disease.
Jack received his PhD in Biostatistics from Johns Hopkins working with Drs. Ingo Ruczinski, Jeffrey T. Leek, and Robert B. Scharpf. While there, he worked primarily on methods development for an array of genetic sequencing data, including rare deletion detection and association using whole exome sequencing of familial pedigrees, linear modeling of RNA-seq transcript abundances, and de novo copy number variant detection using targeted sequencing trios. With the Talkowski lab, Jack will be investigating the detection of copy number and structural variants, as well as their implications for human health.
Ricardo joined the Talkowski laboratory in 2021 as a research fellow with a Ph.D. in Medical Sciences from the University of Toronto. His research focused on the functional interpretation of the human genome and how it relates to tissue-specific transcriptional changes. Ricardo is interested in using multi-modal datasets to investigate the factors involved in splicing disorders. To gain new biological insights, Ricardo is interested in creating novel algorithms and analysis techniques to interrogate high-dimensional data.
Bimal holds a BS in Chemistry and a MS in Biochemistry from University of Calcutta, India. He received a PhD in Biochemistry studying proteome-wide stress response upon protein aggregation and studied molecular mechanism of protein function at Penn State. Bimal became interested in genome-wide study and employed transposon-sequencing approach to develop therapeutics by identifying the Achilles heel of superbug at University of Copenhagen. To study the functional organization of bacterial genomes, Bimal developed genome-wide tool CRISPRi-TnSeq to construct genetic interaction network in collaboration with Dr. Tim van Opijnen of Boston College. Bimal joined the Talkowski lab in spring of 2022 as a fellow of the Genomics and Technology Core of MGH. He is interested in developing technologies to detect genetic disorder and mapping genome-wide connection of gene or mutation linked to disease.
Nehir got her MSc degree in Molecular Mechanisms of Disease at Radboud University Nijmegen. In 2019, she received her PhD in Genetics, Molecular and Cellular Biology from University of Pavia. By combining whole genome sequencing and cytogenetics data, she studied the nature of constitutional complex chromosomal rearrangements. Her doctoral studies focused on characterization of chromothripsis like events as a formation mechanism of small supernumerary marker chromosomes. With Talkowski lab, she is looking forward to investigating hidden complexity in the human genome and its role in congenital defects. For her future studies, she would like to tackle the ambiguity in genotype-phenotype correlation in cases with numerically and structurally abnormal chromosomes.
Cal received his PhD in Human Genetics from McGill University (Montréal, Canada) as a Vanier Scholar. His research focused on identifying novel genetic and molecular insights for psychiatric and neurological disease. In March 2022, he started as a postdoc jointly co-supervised by Drs. Michael Talkowski and Benjamin Neale. He is excited to investigate the genetics of bipolar disorder, and is also planning to study the functional consequences of structural variation on genome structure. Outside of work, he likes to play piano, and with his two cats PLINK and Chromosome (Chrome).
Chelsea joined the Talkowski laboratory in September 2017 as a postdoctoral fellow, after completing her PhD in Medical Science with Anne Bassett at the University of Toronto in Canada. As a Frederick Banting and Charles Best CIHR funded doctoral student, Chelsea focused on determining the impact of rare copy number variation (CNV) on IQ in schizophrenia and delineating the variable expression and incomplete penetrance of genomic disorders associated with neuropsychiatric disorders. In the Talkowski laboratory Chelsea will be working on the Developmental Genome Anatomy Project (DGAP) using whole-genome sequencing and computational tools to help identify new genetic causes of neurodevelopmental disorders and congenital anomalies.
Xander has long been fascinated by the genetics of disease and human evolution. He is currently a Research Fellow in Mike Talkowski’s lab, having completed his doctoral training with Evan Eichler at the University of Washington. His current focus is understanding genomic disorders, deletions or duplications of particular chromosomal segments that often manifest as neurological disease early in development. By integrating technology development, genome editing, and functional genomics, he hopes to elucidate the mechanistic underpinnings of genomic disorders and their associated phenotypic variability.
Alba joined the Talkowski laboratory as Postdoctoral Fellow in 2020 after completing her PhD in Biotechnology at the Polytechnic University of Valencia, in collaboration with the University of Cambridge. Her research focused on the discovery of unknown etiological genes and variants in coding and non-coding regions of the genome of patients with rare diseases. Fascinated by the complexity of the human genome, she worked on identifying and characterizing causal structural variants using multiple sequencing technologies, including short- and long-read whole-genome sequencing. In the Talkowski group Alba will be working on large-scale population and clinical genomics projects to systematically explore a variety of genomic variation and its implication for human disease.
Gabriela joined Talkowski lab in October 2021. She had her bachelor at Biomedical Science in Universidade Federal de São Paulo, in Brazil. During her undergraduate she joined the psychiatric genetics lab, were she had a three-year internship working specially with gene expression in schizophrenia. During her PhD, at the same lab, she investigated miRNA expression profiles in extracellular vesicles from patients in first episode psychosis. Gabriela had one year research internship in Martin-Luther Universität Halle-Wittenberg in Germany. Now in Talkowski Lab as a Postdoctoral fellow, she will work on genomic studies of human neurodevelopmental disorders (NDDs) and will contribute to a series of molecular and functional genomic studies of individual genes that have been associated with NDDs.
Xuefang joined the Talkowski lab in June 2017 as a postdoc fellow, with a Ph.D in Bioinformatics and Masters’ in Statistics from the University of Michigan at Ann Arbor. Her Ph.D research mainly focused on discovering and understanding structural genomic variants(SVs) through multiple sequencing technologies including the short read next generation sequencing (NGS) and the single molecule real time long sequences (SMRT). Xuefang has gathered rich experience in discovering and understanding genomic SVs, especially those in complex formats, during her graduate training when two independent software were developed to discover and validate genomic SVs. Xuefang has also participated the Human Genomic Structural Variation Consortium (HGSVC) and contributed great effort to integrate genomic variants detected by multiple algorithms and compare multiple sequencing platforms.
Graduate Students
Daniel is a PhD student in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School. He joined the Talkowski lab in 2022, and his thesis work will integrate long and short read sequencing data to characterize structural variation and its role in human disease. Daniel previously graduated from Brown University with a bachelor’s degree in computational biology. At Brown, Daniel worked in Dr. Sorin Istrail’s lab to develop algorithms for associating genetic variation with polygenic disease.
Elise is a PhD candidate in the Biological and Biomedical Sciences program at Harvard Medical School and is supported by an F31 predoctoral fellowship. Her thesis work focuses on genetic diagnostic testing and mosaic variation. Elise graduated from St. Mary’s College of Maryland with a bachelor’s degree in Biology and before attending graduate school, she spent two years as a post-bac at the NIH Undiagnosed Diseases Program followed by two years as an associate computational biologist at the Broad Institute in the lab of Dr. Daniel MacArthur. This research gave her exposure to bioinformatics and Mendelian disease genetics, work she will expand upon during her graduate studies.
Lily is a PhD student in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School. She joined the Talkowski lab in 2021, and is an NSF graduate research fellow as well as an NIH F31 predoctoral fellow. She is interested in investigating the heritable bases of human disease to advance human health. Her thesis work focuses on identifying evolutionarily important regions of the human genome based on selection signatures and exploring the biological functions and disease implications of these elements, particularly in early development. Lily graduated from Cornell University in 2020 with a bachelor’s degree in Biological Sciences and Computer Science. At Cornell, she performed research in the lab of Dr. Andrew Clark, examining cross-ethnic differences in the genetic architecture of complex traits.
Alex is a PhD student in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School. He studied Biology at Washington University in St. Louis, where he graduated in 2019. Before graduate school, he worked for two years in Dr. William Buchser’s lab, working in a group to develop imaging-based perturbation screens. Alex joined the Talkowski Lab in the fall of 2022, where he will focus his thesis work on mobile element insertions and their functional effects in the human genome.
Instructors
Philip holds a B.S. in Biological Sciences from Stanford University and an M.D. and Ph.D. in Molecular and Human Genetics from Baylor College of Medicine. Philip pursued combined residency training in Pediatrics and Medical Genetics at Boston Children’s Hospital (BCH) and the Harvard Genetics Training Program. He is now a K08-funded Instructor, pursuing research in the Talkowski laboratory at Mass General and seeing genetics and metabolism patients at BCH. In the lab, he is using in vitro CRISPR genome engineering to understand how disruption of genomic architecture leads to neurological phenotypes.
Aloy (he/him) focuses his research on the genetic and molecular mechanisms surrounding dystonia, including of X-linked dystonia-parkinsonism (XDP), a unique neurodegenerative disease found mainly in his home country, the Philippines. He obtained his medical degree and residency in clinical neurology from the University of the Philippines. He then pursued a neurogenetics PhD at the University of Lübeck in Germany. Aloy’s studies combine genome editing in stem cell models with functional genomic methods to identify altered signatures in THAP1-dystonia, XDP, and other dystonias.
Dadi joined the Talkowski Laboratory in 2016 as a postdoc fellow with a PhD in Bioinformatics from the University of Sydney. His research focuses on the functional interpretation of human genome. Working on deep sequencing data from iPSC-derived neural cell lines, he investigates transcriptomic abnormality to reveal the molecular mechanisms in multiple neurological disorders and seeks for potential treatment development. Dadi is also interested in developing high-performance pipelines that integrate edge-cutting algorithms to facilitate biological findings.
Derek joined Dr. Gusella and Dr. Talkowski’s laboratory at the Center for Genomic Medicine in October 2013 as a postdoctoral fellow. During his postdoctoral work, he developed a CRISPR/Cas9 genome engineering approach, SCORE, to model reciprocal genomic disorders (RGDs) by mimicking the in vivo non-allelic homologous recombination (NAHR) mechanism. His current research focuses on the RGDs including 16p11.2, 15q13.3, and 15q11.2-13.1 which are associated with ASD, schizophrenia, intellectual disability, PWS, obesity, Dup15q syndrome and AS. We have successfully established the human isogenic iPSC and derivative neuron models for these RGDs in the lab. We aim to identify the critical components of the RGDs by evaluating the molecular, cellular, and functional alterations from global and individual gene deletion models.
Rachita got her training in bioinformatics in India and completed her PhD at Denmark Technical University, Denmark focusing on understanding the effect of genetic, epigenetic and clinical variations on the molecular mechanisms in complex phenotypes. Her current research focus is the integration of multi-dimensional genomics datasets associated with the genetic etiology of neurological disorders. She is developing integrated methods for reference-based and reference–free genome analyses to identify known and novel genomic variation of predicted functional relevance. The pathogenesis of neurological disorders often involves multiple genes, complex interactions thus, the functional genomics aspect of hey project employs genome-wide and targeted transcriptomics analysis of neural cell lines and post-mortem brains from different neurological disorders to investigate pathological mechanisms.
Affiliated Faculty
Harrison is an Assistant Professor in the Department of Neurology at MGH and Harvard Medical School with a secondary affiliation in the MGH Pediatric Surgery group. Upon completion of his PhD in Human Genetics from the University of Pittsburgh he joined the Talkowski lab as a postdoctoral fellow focusing on the statistical and computational aspects of the genetic analysis of structural variation (SV) in complex disease. After his postdoc, Harrison received a NIH K99/R00 pathway to independence grant seeking to understanding the genetic underpinnings of common craniofacial disorders and has started a lab focused on investigating the genetic etiology of congenital birth defects and other developmental anomalies. He still collaborates closely with the Talkowski lab given his shared research interest in the development and application of novel methods for improved detection of pathogenic SV.
Research Support Staff
Jennifer previously worked at MGH for approximately 18 years in the Department of Pediatric Orthopaedics, first as an administrative assistant and then Practice Manager. She received a bachelor’s in psychology from Central Ct State University and pursued a Master’s in Marriage and Family Therapy there as well. She has joined the CGM as a Program Manager working to support Michael Talkowski, PhD and the Fetal Genomic Consortium.
Laura joined the Talkowski lab in January 2017. She has a master’s degree in Human Genetics from the University of Pittsburgh and a Bachelor’s degree in Biochemistry. Before joining the lab she worked briefly as a technologist for LabCorp. She has also taught biology courses at Eastern Nazarene College and Quincy College.
Laura currently works on administration, finances, grants, scheduling, and lab management.
Monica holds a Ph.D. in Cell Biology and a B.S. in Biology from the University “La Sapienza” in Rome, Italy. Monica did her postdoctoral research at the University of Massachusetts Medical School in Worcester, where she studied the molecular mechanism underlying Facioscapulohumeral Muscular Dystrophy (FSHD), a human disease caused by a complex intertwined interaction between genetic and epigenetic factors. After her post-doc, Monica joined the laboratory of Dr. Susan Slaugenhaupt here at the Center for Genomic Medicine. At MGH, both as a research scientist and lab manager, she contributed to the success of several collaborative research projects aimed to develop a therapeutic approach for the ultra-rare disease Familial Dysautonomia (FD). FD is a sensory and autonomic neuropathy caused by an mRNA splicing defect. This work culminated successfully with the identification of a splicing modulator compound that is in clinical development. Monica joined the Talkoski laboratory in March 2020 as Project Manager, to oversee projects, milestones, and collaborations, as well as helping with strategic planning, funding decisions, budgets, and funding portfolio.
Research Staff
Riya joined the Talkowski lab in January 2020 as a research technician. She comes to the lab after having received her Bachelor of Science degree in Pharmacy from India and a Master of Science degree in Pharmacology/Toxicology from Long Island University, New York. During her masters, she participated in the research mainly focused on cardiopulmonary diseases by studying the effects of various receptors and agents in an allergic mouse model of asthma. At the CGM, Riya works closely with PhD student Kiana Mohajeri focusing on using genome editing methods in human cellular models to study the effects of chromosomal structure variation and alterations to 3D genome folding in neurodevelopmental disorders.
Nicole joined the Talkowski lab in August 2022 and is working as a Bioinformatics Specialist. She received a B.S. in Biology with a concentration in bioinformatics from Boston College in May 2022. Her past experiences include summer internships through Hofstra University and the Institute of Cancer Research and Education at SUNY Old Westbury where she contributed to research discovering targeted therapies for cancer treatment. More recently, during her undergrad she participated in research studying the effect of Youth FORWARD, a mental health intervention for violence-exposed youth via youth employment programming, on intimate partner violence in Sierra Leone.
Celine de Esch is a research scientist in Mike Talkowsi’s laboratory at Massachusetts General Hospital in Boston. She received her PhD from the Erasmus University Rotterdam, the Netherlands in 2014 and joined the lab as a postdoc early 2015. Her work focuses on the cellular modeling of neurodevelopmental disorders such as Fragile X syndrome, ASD and Prader-Willi syndrome.
Serkan is director of bioinformatics, responsible for bioinformatics activities in the Talkowski Lab and Genomics & Technology Core. His research interests lie in the areas of computational biology, functional genomics and neuroscience. He is primarily involved in computational functional genomic analyses in the context of neuro-degenerative and neuro-developmental disorder. In this respect, he has been working on functional genomic characterization of autism-associated genes and copy number variations in human neural lineage lines and mouse models. He also contributed to several other genetic and functional genomic studies on other neurological disorders including Huntington’s disease and neurofibromatosis types I and II. He was recruited to the lab as a staff scientist following a postdoctoral fellowship at the Computational and Integrative Biomedical Research Center and the Department of Molecular and Human Genetics at Baylor College of Medicine where he worked on protein function-structure relationships and chromatin function. Before he switched his research focus to biology, he conducted research in computational and physical chemistry at the University of Minnesota and Argonne National Laboratory. Serkan holds a B.S. degree in physics from Bogazici University and a Ph.D. degree in theoretical physics from Texas A&M University. During his training, he was awarded competitive fellowships from the Supercomputing Institute of the University of Minnesota, the National Institute of Health and the National Library of Medicine.
Luther joined the lab in July 2022 and is working with Harrison Brand, Ph.D, in the Structural Variation group. H received a B.S. in Computer Science from Framingham State University in 2022. During undergrad, through the CURE Scholars Program, he interned at the Dana-Farber Cancer Institute and Massachusetts General Hospital Martinos Center in Dr. Leo Cheng’s lab to examine metabolites in tissue to develop different cancer diagnostic methods. He also participated in the year-long Congress-Bundestag Youth Exchange (CBYX) for Young Professionals fellowship, funded by the United States Department of State and the German Bundestag. His last internship was in research operations at MGH in Orthopaedics & Department of Anesthesia, Critical Care, and Pain Medicine.
Stephanie joined the Talkowski lab in March 2020 as a Bioinformatic Specialist. She received her Master of Science in Bioinformatics from Johns Hopkins University with a concentration in genomic analysis. Previously, she received her B.S. in Cell and Developmental Biology and her B.A. in Psychology from the University of Rochester. Stephanie comes from a diverse research background having worked in various research areas ranging from cancer biology and osteoimmunology to evolutionary genomics. At the Center for Genomic Medicine, her research focuses on the detection of disease relevant structural variants.
Vahid was awarded his Ph.D. degree in Information Technology in 2016 at the Politecnico di Milano with cum laude (highest recognition). His Ph.D. dissertation focused on systematic solutions for efficient retrieval and inference from a large collection of the next-generation sequencing data. He has been a team member of the Galaxy project since 2016, a Web-based framework for data-driven biomedical analysis. His research within the Galaxy project context has been focused on facilitating cancer informatics. Specifically, enabling users to study large cohorts of in-house data using protected-access commons such as National Cancer Institute’s Cancer Research Data Commons (NCI CRDC). Accordingly, he led a development to extend the Galaxy framework in user authentication and authorization, co-led cloud-based storage and compute resource federation, and Cloud deployment of Galaxy instances. His research interest spans artificial intelligence and computational biology topics, such as applying deep learning to single-cell imaging and sequencing data for cancer therapeutics.
Jack received his Bachelor of Science from Loyola University of Maryland in May of 2020. After graduating he worked as a manufacturing associate at Catalent where he assisted with the production of an adeno associated viral vector for spinal muscular atrophy in the company’s gene therapy division. Jack also spent the summer of 2019 as an intern in the Talkowski lab where he worked with Philip Boone and Kiana Mohajerioptimizing CRISPR and ChIP-seq protocols.
Yating joined the Talkowski Lab in July 2021. She obtained a bachelor’s degree in Biology and a master’s degree in Computer Science with a focus in bioinformatics. After graduation, she joined the Elgin lab at Washington University in St. Louis in 2016 and worked as a bioinformatics application developer focusing on the development of G-OnRamp – an integrated, web-based, scalable environment for interactive gene annotation of eukaryotic genomes. From 2018 to present, she has been working as a bioinformatics scientist in the Dougherty lab in Washington University School of Medicine in St. Louis and has contributed to multiple research projects in the fields of genomics and psychiatric disease research by conducting a variety of bioinformatics analyses, creating a microRNA database, and developing scientific pipelines.
Yulia joined the Talkowski lab as a staff scientist in February 2021 after completing postdoctoral work in Pui Kwok’s lab at UCSF. Her postdoctoral research focused on developing methods for using optical mapping to determine the structure of highly complex areas of the human genome. She has also worked on causal variant analysis and genome assembly. She holds a B.A. from Princeton University in Evolutionary Biology and Applications of Computing and received her PhD in Molecular and Cell Biology from UC Berkeley, where she studied antisense transcription and gene regulation in yeast.
Emma joined the Talkowski lab in June 2020 with a joint appointment to the Broad Data Sciences Platform (DSP). Her work focuses on structural variation methods and research, including contributing to the GATK-SV pipeline. Emma holds a B.S. in Statistics & Data Science from Yale University. Her past experiences include summer internships in Dr. Daniel MacArthur’s lab at the Broad Institute, where she contributed to ExAC and gnomAD; a software development internship at IBM; and undergraduate machine learning research in the lab of Dr. Smita Krishnaswamy.
Sid joined the Talkowski lab in June 2922. He graduated from Carnegie Mellon with an MSc. in Computational Biology. His work focuses on charaterizing the regulatory genomics of XDP and Prader-Willi Syndrome, specifically SNORDs. Previously he has worked on analyzing pan-cancer transcriptomics and how CRISPR systems affect horizontal gene transfer in bacteria. His research interests include multi-omics, integrative analyses and graph-based analyses of biological data. His hobbies include coding and cooking.
Mark joined the lab in 2018 with a joint appointment in the Methods Group of the Data Sciences Platform (DSP) at the Broad Institute, where he has been a computational biologist since 2016. He brings expertise in developing scalable, production-ready genomics analysis tools and pipelines using cloud-enabled data processing technologies developed in DSP. Mark leads development of the GATK-SV pipeline and supports computational operations across large-scale studies in the lab, including gnomAD. He is also a developer on the GATK team, where he has worked on structural variant and pathogen detection tools. He holds a Ph.D. in Biomedical Engineering from Johns Hopkins University and a B.S. in Chemical Engineering from Tufts University.
Chris joined the lab in 2021 and has worked at the Broad Institute since 2014 in the Broad’s Data Sciences Platform and Stanley Center for Psychiatric Research. Chris focuses on the development of methods for genomic structural variation and copy number variation detection and is a Technical Lead for the development of structural variation methods within the Genome Analysis Toolkit (GATK). He has contributed to and led methods development and analysis projects aimed at understanding patterns of structural variation in human populations, structural variation mutation rates, and the association of copy number variation with human disease. Prior to joining the Talkowski lab he was a member of Steven McCarroll’s lab at the Stanley Center and Harvard Medical School. He holds a Ph.D. in Computer Science, with a focus on computational biology, from Oregon Health & Science University, and an A.B. in Computer Science from Harvard University.
Heather joined the Talkowski lab in May 2021. She is a recent graduate of the Johns Hopkins University School of Medicine’s Human Genetics program. Her work focused on the role of TOP2B in mediating AR-induced transcriptional programs and chromosomal rearrangements in prostate cancer. Before that, she graduated from Tufts University with a BSc in Biology and worked as a Research Coordinator for the Tufts University Bioinformatics and Computational Biology group in collaboration with the Tufts Medical Mother Infant Research Institute where she studied maternal/fetal genetics and curated fetal GO annotation. Heather’s research interests include genetics, epigenetics, genome folding, and the application of integrative analysis to complex biological questions. Outside of work, Heather’s current hobbies include knitting, gardening, games, and disc golf.
Isaac joined the Talkowski laboratory in July 2019 as a bioinformatics specialist. He received a B.S. in Computational Biology and a B.A. in Computer Science from the University of Rochester. While in university, he participated in research studying the evolution of bioluminescence in fireflies and the evolution of satellite DNA in fruit flies. At the Center for Genomic Medicine, he researches the relationship between genomic structural variants and disease.
Shadi joined Talkowski’s lab in May 2022 as a computational scientist, where she works on the GATK-SV pipeline as well as computational studies on large-scale databases, such as the All of Us Research Program and gnomAD.
Shadi received her Ph.D. from the University of Texas at Dallas, school of engineering and computer science, in May 2022. During her Ph.D., she developed an open-source computational and mathematical framework for modeling membrane transporters and ion channels across the cell membrane. While pursuing her Ph.D., she collaborated with the Bleris Lab to apply machine learning approaches for identifying human blood cells harboring CRISPR-mediated fetal chromatin domain ablations.
In addition, during her Ph.D., she did an NSF-funded internship with the Broad Institute’s Methods Group (DSP), where she worked on gCNV (a tool for copy-number variation detection in genomics), under the supervision of Samuel Lee. In the summer of 2017, Shadi interned at the National Energy Laboratory on software development and big data analysis while pursuing her Master’s degree in Mechanical Engineering at the University of California, Merced. Additionally, she holds a B.S. in Chemical Engineering from the Amirkabir University of Technology (Tehran Polytechnic).
Alumni
Dr. Yu An is an Associate Research Fellow in the Birth Defect Center of Fudan University in Shanghai of China. She received her Ph.D degree in Human Genetics from Fudan University. Her research interests include understanding the molecular genetic mechanisms of pediatric genetic diseases and genomic disorders such as autism, unexplained developmental delay and intellectual disability, and translational research for these conditions. She joined the Gusella and Talkowski lab as a Postdoc Fellow in the summer of 2015. Her current research focuses on delineating the functional effects of autism risk genes using CRISPR/Cas9 gene editing technology and the induced pluripotent stem cells (iPSCs) system for genetic and genomic analysis including RNAseq and ChIPseq.
Tatsiana received her bachelor degree in Applied Mathematics and Informatics with focus on Theory of Probabilities and Statistics from Belarusian State University in 2007. She continued her education in Norway, applying her knowledge of mathematical modeling to the field of logistics and production planning, and further worked for several years in traffic flows optimization and software development in academia and in industry. In 2012 Tatsiana joined a PhD program in Molecular Oncology, working on application of bioinformatics and statistics for transcriptional profiling (microarrays and RNA-seq). During her PhD she has worked on discovering molecular mechanisms of anti-leukemic effects of glucocorticoids in pediatric acute lymphoblastic leukemia.
Tatsiana finds it highly fascinating how the data can provide us with answers of pathophysiology of complex genetic diseases, and therefore she is looking forward to continue her work at Talkowski lab, discovering molecular mechanisms underlying neurodevelopmental disorders through statistical analyses of genomics data produced by NGS technology.
Caroline is a research technician in the Talkowski laboratory. She has a BS in Biology from Eckerd College and an MSc from the University of Otago in Dunedin, New Zealand, where her project focused on the detection of mitochondrial DNA heteroplasmy. She has extensive wet lab experience and a background in population and evolutionary genetics. Previous projects have included the conservation genetics of sea turtles, population genetics of endangered marine mammals, and most recently, work studying the human microbiome. She joined the Talkowski laboratory in September 2015 and will focus on using jumping library techniques to sequence prenatal samples and detect chromosome structural variation.
Ian Blumenthal is a molecular and computational biologist in the Talkowski laboratory and member of the G&T Core with a background in biological engineering. He received a B.A. and a B.E. from Dartmouth College in 2010 and 2011, respectively, before joining the laboratory as a research technician. In addition to playing an ongoing support role on the various DNA sequencing projects going on in the lab, Ian’s research has focused on transcriptomic studies, particularly studies of the impact of genomic variation in autism. His primary project has been investigating the transcriptional consequences of 16p11.2 microdeletion in human families and mouse brain.
Nick joined the Talkowski lab in June 2018 as a research technician in the wet lab. He received his B.S. in Biochemistry, with a minor in psychology, from Eastern Nazarene College, where he participated in research ranging from retinal degenerative disorders to perovskite nanoparticle synthesis. At the Center for Genomic Medicine, Nick focused on the engineering of cellular mutational models of neurodevelopmental disorders, as well as the characterization of resultant iPSC-derived neural lineages and the development of high-throughput CRISPR genome editing methods. Nick left the lab in July 2021 to study medicine at the New York Institute of Technology College of Osteopathic Medicine.
Colby Chiang received his B.A. from Dartmouth College in 2010. He worked in the Talkowski lab from 2010 to 2011, where he studied the mechanisms of chromosomal rearrangements in humans and transgenic animals. His work on the Developmental Genome Anatomy Project (DGAP) led to some of the first published cases of germline chromothripsis in humans. He is currently an MD-PhD student at Washington University in St. Louis.
Ryan is a PhD candidate in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School (HMS) and an NSF graduate research fellow. He joined the Talkowski lab as a research technician in 2013 before transitioning to a graduate student with the lab in 2016. Ryan is interested in structure-function dynamics in the human genome and their implications for development, disease, population genetics, and precision medicine. In the Talkowski lab, he leads analyses of genomic structural variants (SVs) across a spectrum of technologies, study designs, and applications. His thesis research focuses on mapping SVs across large human populations and predicting their effects on genes and noncoding regulatory elements. Ryan graduated from Dartmouth College in 2013 with a Bachelor’s degree in genetics. Read more about Ryan’s research and scientific background here and here.
Ben is a staff scientist in the Talkowski laboratory who manages the Genomics and Technology Core (GTC). His work focuses on the development of advanced technologies for the analysis of the human genome, its 3D architecture and its functional consequences. Ben Joined the lab in 2016 after finishing his postdoctoral fellowship in Human Genetics at Brigham and Women’s Hospital where he investigated the phenotypic consequences of balanced chromosomal abnormalities. Ben holds a B.S. degree in biology and B.A. in Philosophy from Santa Clara University and obtained his Ph.D. in Biomedical Sciences from Creighton University where he studied the electrophysiological properties of neurosensory systems.
Stacey Eggert was a Clinical Cytogenetics Fellow in Harvard Medical School’s Genetics Training Program. She received her Ph.D. from Harvard in Genetics and has a B.S. in Cell Biology/Biochemistry from Bucknell University. Stacey’s thesis work focused on identifying genetic variants that predispose women to develop uterine fibroids. She worked in the BWH Clinical Cytogenetics Lab before joining the Talkowski lab and her work here focuses on using next generation sequencing to identify cryptic structural variation in a variety of genetic disorders. Stacey is now a medical writer in the pharmaceutical industry, focusing on product information and clinical trials.
Joseph Glessner is a bioinformatics specialist with focus on copy number variations (CNVs) and structural variations (SVs). He attended University of the Sciences in Philadelphia studying bioinformatics 2003-2007. He worked at the Center for Applied Genomics at the Children’s Hospital of Philadelphia 2006-2014. He earned his PhD from the University of Pennsylvania 2010-2014. He started at the Talkowski laboratory in 2015. He has analyzed large cohorts of SNP microarray and DNA sequencing datasets and has taken statistical results into manuscripts. He has also fulfilled roles of developing quality control methods for SNP genotyping microarrays, provided collaborators with data and analytical support, and have led analyses of genotype and copy number variations from genome-wide association data that have been published in various high-impact journals, including Nature. His major focus has been copy number variation analysis of psychiatric disorders. He has developed CNV association software ParseCNV to characterize the complex overlap of CNV calls. He works to develop new genetic, computational, and statistical methods. He works on methods to improve robustness and reproducibility of signals from different array versions, types, processing centers, and sample sources.
Carrie joined the Talkowski laboratory as a wet lab technician and has led most of the molecular genetic studies on chromosomal rearrangements, particularly the development of jumping library sequencing for structural variation detection. Carrie holds a B.S. in Chemistry, an M.S. in Molecular Biotechnology and has experience in both industry and academic research. Her interests lie in understanding the manners in which chemical and physical dynamics could be applied towards understanding the energy dynamics of living systems (in general, in Biochronometry). She is also interested in cognitive neuroscience, synesthesia, psychology, and various forms of art.
Alex joined the Talkowski lab in March 2020 as a Computational Scientist. He completed his PhD in Biomedical Informatics at Columbia University with Yufeng Shen and Wendy Chung and holds a BS in Bioengineering: Bioinformatics from the University of California San Diego. His doctoral research involved developing computational methods to detect mosaic variation in the context of rare developmental diseases and to characterize the association between patient clinical outcomes and their genetic information. Alex will be working on cell-free fetal technology and pipeline development as part of the non-invasive prenatal testing program, as well as other methods development work related to mosaicism.
Nichole began her research career within the cancer field focusing on the inappropriate activation of the STAT pathway. With a strong desire to gain more experience in bioinformatics and computational biology, Nichole transitioned into a Next Generation Sequencing Research Technologist position here at MGH. Coming into the Talkowski Lab, Nichole plans to apply her extensive knowledge of library construction techniques and sequencing within the Genomics and Technology Core as the lead technologist while pursuing her graduate studies at Northeastern University in Bioinformatics. Nichole’s long term career plan is to obtain her PhD within the sciences.
Emanuela is a molecular biologist who got her PhD in computational biology in March 2015 from Padua University (Italy) and Edmund Mach Foundation (Italy), working on apple comparative and population genomics. Then she started a post-doc in the NeuroEpigenetics Lab at the University of Trento (Italy), working on Autism Spectrum Disorders epigenetics. She is visiting the Talkowski Lab since January 2016 to train in ChIP-seq analysis.
Poornima is a research technician and a cell and molecular biologist in the Talkowski and Gusella laboratories since October 2011. She received a B.Tech degree in Biotechnology from India in 2007 and an M.S in Biology from UMass Lowell, MA in 2010 and has a diverse skill set and research experience in both the Industry and academia. Her interests lie in studying the interactions of chromatin regulators in molecular pathways involved in neurodevelopmental and neuropsychiatric disorders, and in therapeutic development for complex genetic disorders. Much of Poornima’s current research has focused on understanding the functional consequences of cell adhesion, chromatin remodeling genes in ASD by means of designing, optimizing and generating a library of gene knockouts in induced pluripotent stem cells (iPSCs) utilizing gene editing technologies such as CRISPR-Cas9 and short-hairpin RNAs (shRNA) in both patient lines and control cohorts.
Kiana is a PhD candidate in the Biological and Biomedical Sciences (BBS) program at Harvard Medical School and an NSF graduate research fellow. Kiana joined the Talkowski Lab in the Fall of 2016 with an interest in understanding the functional impact of structural variation. In her thesis work, Kiana has generated and differentiated various types of genome edited cell lines to study the effects of chromosomal rearrangements on 3D chromatin organization and gene expression in neurodevelopmental disorders. Kiana’s interest in the study of structural variation began in her post-baccalaureate work in the lab of Dr. Evan Eichler, with whom she worked for over three years after completing her undergraduate studies in Cell and Molecular Biology at the University of Washington in 2012. In her post-baccalaureate work, Kiana led efforts to identify and characterize the disease implications and evolutionary history of various structural variant classes, work that has driven her interests in the Talkowski Lab as well. Outside of the lab, Kiana is actively involved in science outreach and mentoring.
Outside of the lab, Kiana is actively involved in science outreach and mentoring.
Mariana joined the Talkowski lab in November 2018, after receiving her PhD in Medical Science at Federal University of São Paulo, in Brazil, and conducting a research internship at University of Lausanne, in Switzerland. As a Postdoctoral Fellow in Talkowski laboratory and Autism Speaks Fellow, Mariana is currently focused on the impact of chromatin remodelers on neurodevelopmental disorders by generating genomic alterations in cellular systems to address the etiology of human neurological phenotypes. She is CRISPR engineering human isogenic pluripotent lines with variants on genes associated with autism, differentiating those models into neuronal lines and addressing the molecular signatures followed by the disruption of these genes.
In April 2022, Mariana started at new position as a Researcher at a non-profit Institution, named Associação Fundo de Incentivo à Pesquisa (AFIP), where she leads a research group focused on functional neurobiology.
Katie joined the Talkowski laboratory in June 2018 as a research technician in the Genomics and Technology Core. She received her Bachelor of Science degree in Neuroscience from the University of Michigan in April 2018. While pursuing her degree, Katie participated in research dedicated to ascertaining the relationship between the microbiome and neurodegenerative diseases through the study of Parkinson’s associated proteins.
At the Center for Genomic Medicine, Katie works closely with Ben Currall performing various molecular genomic based experiments.
Vamsee joined the Talkowski laboratory in 2011 as a computational biologist and has largely focused on bioinformatics methods to delineate structural variation in the human genome. He is also a member of the G&T Core. Vamsee has experience spanning both academic and industrial research. He holds both B.S. and M.S. degrees in Computer Science and Computational Biology from Carnegie Mellon University (Pittsburgh, PA). Following his education at CMU, he worked for the Massachusetts Institute of Technology’s Lincoln Laboratory as an analyst in national biodefense initiatives. His experience in the design of ‘big data’ analysis algorithms at MIT has translated well into analysis of genomics data. His primary efforts have been in analyzing jumping library sequencing for balanced chromosomal abnormalities, as well as cryptic structural variation in patients with neurodevelopmental and neuropsychiatric disorders, and translating these methods into clinical diagnostic applications.
Ashok primarily focuses on statistical and computational approaches towards understanding the genetic basis of traits, at various levels of biological organization within a collaborative framework. His previous work includes data analysis for micro-array gene expression from transcriptional profiling to detect candidate genes for meat quality and assessing environmental determinants of gene expression in Daphnia from an Eco-evolutionary perspective. Ashok has also worked on statistical and computational aspects of Genomic Selection for poultry, an application of genomic information in the context of selective breeding. Additionally, he is also involved in understanding whole genome signatures of selection for domestication in chicken populations, using Next-Gen sequencing data. Currently, Ashok is working on elucidating the role of alternative splicing in relation to CAG repeat expansion in Huntington’s disease from a whole genome perspective.
Parisa is a computational biologist who obtained her MA in Natural Sciences from the University of Cambridge, followed by an MSc in Molecular Medicine from Imperial College London. She received her PhD in Computational Biology and Chemogenomics from the Institute of Cancer Research London. Her PhD research focused on identifying novel drug targets for cancer through multi-parameter druggability assessment of the human proteome, and large-scale bioinformatics analysis of multi-omic clinical profiling data. Her work resulted in the identification of a novel drug target candidate that the institute is now actively pursuing. Upon completion of her PhD, Parisa joined the biotechnology company Exscientia, where she helped develop their cancer drug discovery project portfolio and consulted on potential oncology targets that are amenable to bispecific drugs. As a Postdoctoral Research Fellow in the Talkowski laboratory, Parisa is analyzing neurodevelopmental transcriptomes in order to gain insight into the consequences of large genomic rearrangements such as reciprocal copy-number variation at chromosome 16p11.2—one of the most common genetic causes of autism spectrum disorder. She is integrating data from genetic lesion models into multi-level data-driven frameworks, and evaluating the co-expression of disease relevant gene-sets across neurodevelopmental disorders.
Claire joined the Talkowski laboratory in Fall 2014 as a molecular and computational biologist. She received her Engineering degree in Molecular Biology from the University of Technology of Compiègne (UTC, France) in 2010, and completed her Ph.D. in Human Genetics from the University of Strasbourg. Her thesis work in Prof. Mandel’s lab (IGBMC, Strasbourg, France) focused on developing NGS-based approaches for the diagnosis of intellectual disability and other genetically heterogeneous developmental disorders, and translating them into routine clinical diagnostic practice. Her current research focuses on elucidating the missing genetic etiologies of various neurodevelopmental disorders, primarily looking into the mosaic hypothesis.
As a visiting PhD student of the GABBA Program (University of Porto, Portugal), Catarina’s research in the Gusella and Talkowski labs is focused on neurodevelopmental disorders and the role of genetic and epigenetic alterations underlying these complex diseases. Her project involves using in vitro models (iPSC-derived neuronal cells) as an approach to identify crucial molecular pathways involved in autism spectrum disorder. Catarina will be performing CRISPR/Cas9 technology for precise gene editing and whole transcriptome (RNAseq) and ChIPseq analyses. She received a degree in Biomedical Sciences and a Master’s degree in Molecular Biomedicine, where she investigated the genetics of male infertility. Catarina also appreciates scientific communication, education outreach and is enjoying Boston’s landscapes to practice photography.
Jaeweon joined the Talkowski lab in February 2020 as a bioinformatics specialist. He received a B.A. in Mathematics from Rice University. While pursuing his degree, Jaeweon participated in research studying the evolution of societies in the Holocene and the rare cell subset detection from scRNA data. At the Center for Genomic Medicine, his work focuses on transcriptome analysis.
Jae left the lab in May 2022 to attend graduate school.
Matt joined the lab in the summer of 2012 as an undergraduate intern, and will enter as a full time bioinformatician in early 2015 after he graduates from Dartmouth College. He focuses on computational methods development and his most notable contributions have been to the lab’s supervised learning approaches to SV detection. Currently, Matt is finishing a computer science major at Dartmouth, where he is working on an undergraduate thesis project to probabilistically model SV signals in deep sequencing data.
Alexei is a staff scientist in the Talkowski laboratory and a member of the Genomics and Technology (G&T) Core. Alexei graduated with a B.S. from Moscow State University (Russia) and with Ph.D. in Biochemistry from the University of Sydney (Australia). In the U.S.A., he did research in Hematology/Oncology at BU, tRNA at MIT, Molecular Diagnostics at Yale University and Mass Spectrometry – at Howard University. He joined the Talkowski lab in October 2012. Alexei has broad expertise in biochemistry, molecular biology, molecular immunology, cell biology, and related fields. He leads the molecular aspects of many of the genomics projects in the laboratory and the G&T Core, and is also involved in genomics methods development.
Aarathi Sugathan was a postdoc in the Talkowski Laboratory with a PhD in Bioinformatics from Boston University. She specialized in functional genomics, including analysis of RNA-seq, ChIP-seq, and DNase-seq data. Her research focused on integration of RNA-seq data from knockdown of transcriptional and chromatin regulatory genes that have been associated with autism spectrum disorder, with ChIP-seq of regulatory proteins as well as histone modifications, in order to identify genes and networks affected by different ASD-associated genes. Previously she profiled DNase hypersensitivity and epigenetic modifications genome-wide in mouse liver to determine relationships between transcription factor binding and chromatin state in sex-dependent gene regulation in liver.
Harold Wang joined the Talkowski laboratory in 2016 as a Bioinformatic Specialist with a Master’s in Computation Biology and Quantitative Genetics from Harvard University School of Public Health, and a B.A. in Mathematics from Princeton University. His work focuses on using computational methods to detect disease relevant structural variations from genomics data. Harold left the lab in August 2020 to attend graduate school at UCLA.
Matthew Waterman is a visiting scientist in the Talkowski Laboratory with a PhD in Cellular-Molecular Biology from the University of Pennsylvania. In addition, he was a postdoctoral fellow in the Sukhatme Laboratory at BIDMC/Harvard Medical School. He has a faculty appointment in the Department of Biology and Chemistry at Eastern Nazarene College where he serves as Chair of the Natural Science Division. Matthew started work in the Talkowski Lab in May 2014. His current research focus is to establish 4C-seq and other chromatin interaction methods in the Talkowski Laboratory for use in identifying the functional significance and epigenetic involvement of non-genic translocations and inversions.
Hsin-Lan received her M.S. and Ph.D. at Yang-Ming University in Taiwan. For her M.S. and Ph.D research, she explored the molecular and cellular mechanisms involved in the development of Spinal muscular atrophy. At Academia Sinica, where she worked and studied under the mentorship of Dr. Hung Li who published the first SMA mouse model among the literatures, she had training in molecular and cell biology. She analyzed the role of microtubule destabilizing factor associated with disease severity by using the in vitro and in vivo models and generating in vitro models for compound screening as well. She continued studying the field of neuron degeneration disease in her first postdoc career, and then shortly stayed in Boston Children Hospital as research fellow, where she conducted research about the molecular mechanism of synapse formations by using FGF22 and FGF7 knockout mice. In Li- Huei Tsai’s lab, she utilized iPSC technology to model various cell types involved in neurodegenerative disease. In this context, she utilized CRISPR-Cas9 to generate isogenic lines to help determine gene-specific function on Alzheimer’s disease. Within the Tsai lab, she was also involved in combinatorial cell culture with other projects such as an iPS-derived blood brain barrier and our lab’s development of an iPS “mini-brain”.