Michael TalkowskiAssociate Professor of Neurology (Genetics), Psychiatry, and Pathology. Associate Member, Broad Institute of MIT and Harvard
The Talkowski laboratory explores the impact of genomic alterations on human neurodevelopment and neuropsychiatric disorders, and the application of innovations in sequencing technology to genetic diagnostics. Mike received undergraduate degrees in Biology and Psychology and a Ph.D. in Human Genetics with a focus in genetic epidemiology and psychiatric genetics. He joined the Center for Human Genetic Research (CHGR) 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, Director of the CHGR, in 2008 to study the genetic etiology of neurodevelopmental disorders, particularly autism spectrum disorders. He was appointed to the faculty of the CHGR and Harvard Medical School in 2011. Mike’s laboratory is funded by the National Institutes of Health, the Simons Foundation for Autism Research, the Nancy Lurie Marks Family Foundation, the March of Dimes, the Charles Hood Foundation, the CHARGE Syndrome foundation, and NARSAD.

Postdoctoral Fellows

Tatsiana Aneichyk
Tatsiana AneichykPostdoctoral Fellow

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.

Harrison Brand
Harrison BrandPostdoctoral Fellow
Harrison Brand is a postdoc in the Talkowski Laboratory with a PhD in Human Genetics from the University of Pittsburgh, an MPH in Epidemiology from the University of Pittsburgh, and a B.S. in Molecular, Cellular, and Developmental Biology from the University of Michigan. His research focuses on the statistical and computational aspects of genetic analysis of complex disease. Harrison is interested in determining the genetic etiology of autism spectrum disorder through the investigation of all forms of genetic variation. Over the past year he has helped characterize the landscape of karyotypically blind structural variation in the genome of subjects with a variety of psychiatric disorders. Currently, he is working on implementing these findings into a novel diagnostic screening method.
Ben CurrallPostdoctoral Fellow
Celine de Esch
Celine de EschPostdoctoral Fellow
As a postdoctoral fellow in Jim Gusella’s lab, Celine de Esch works closely together with the Talkowski lab to characterize the effects of heterozygous strong-effect ASD gene mutations on RNA expression patterns, chromatin modifications and relevant functional measures in isogenic induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs) and differentiating neurons. Celine’s interest in neurodevelopmental disorders and her graduate work on fragile X syndrome at the University Medical Centre of Rotterdam has led her to join the lab early 2015. Previous publications include papers on mGluR5-dependent alterations of social behavior of fragile X mice as well as the epigenetic characterization of the FMR1 promoter in iPS cells and NPCs.
Aloy Domingo
Aloy DomingoPostdoctoral Fellow
Aloysius Domingo is a clinician-scientist (MD, PhD) with a research focus on the molecular genetic mechanisms surrounding primary dystonia in general, and in particular, of X-linked dystonia-parkinsonism (XDP), a unique neurogenetic degenerative disorder that is endemic to his home country, the Philippines. Aloysius obtained his medical degree from the University of the Philippines College of Medicine and his training in Clinical Neurology at the Philippine General Hospital. He then pursued PhD studies in Molecular Life Sciences at the University of Lübeck, Germany (thesis lab: Klein Lab/Institute of Neurogenetics). At MGH, Aloysius aims to clarify the full genetic architecture of XDP using available genomic technologies. Furthermore, his project involves a combined cell/molecular biology and computational approach, i.e., using CRISPR/Cas9-based genome editing technology on stem cells, and then identifying altered expression, networks and pathways in dystonia via bioinformatic analyses of high-throughput data.
Dadi Gao
Dadi GaoPostdoctoral Fellow
Dadi joined the Talkowski Laboratory in 2016 with a PhD in Bioinformatics from the University of Sydney (2015) and a B.S. in Biology from the Chinese University of Hong Kong (2008). His work focuses on in silico analysis of transcriptomic data and is interested in exploring the molecular machinery of alternative splicing. His graduate work and previous publications include miRNA prediction, the identification and measurement of intron retention and epigenetic regulations of intron retention. Dadi is currently working closely with the Slaugenhaupt Lab to investigate splicing defects in familial dysautonomia, a genetic disorder caused by exon skipping that affects the development and survival of certain nerve cells.
Joseph Glessner
Joseph GlessnerPostdoctoral Fellow
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.
Xander Nuttle
Xander NuttlePostdoctoral Fellow
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.
Parisa Razaz
Parisa RazazPostdoctoral Fellow
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.
Derek Jui-Cheng Tai
Derek Jui-Cheng TaiPostdoctoral Fellow
Derek completed his bachelor’s degree in Life Science and master’s degree in Biochemistry at National Yang-Ming University, Taiwan. He received Ph.D degree in Physiology and Neuroscience at National Defense Medical Center, Taiwan. In addition, he was a postdoc in the Institute of Biomedical Sciences, Academia Sinica, Taiwan. He joined the laboratories of Michael Talkowski and James Gusella in October, 2013 as a visiting Postdoctoral Scholar. Previously, he focused on the molecular signaling of learning and memory in neurons and its implications in neuronal function as well as animal behavior. Currently, his studies focus on developing genome-editing technologies (CRISPR/Cas9) to investigate the functional impact of genomic alterations in autism spectrum disorder.
Rachita Yadav
Rachita YadavPostdoctoral Fellow
Rachita obtained her bachelors and masters degrees in Bioinformatics from India. She did her PhD from Denmark Technical University in the field of systems biology, followed by a postdoc at University of Copenhagen. The main theme of her research during her PhD and postdoc being the integrative analysis of different omics data types to reveal new mechanistic details about the multifactorial phenotypes, like cancer, obesity and asthma. As a postdoctoral fellow in Talkowski lab, her research interests include understanding the genetic etiology of neurological disorders, with particular focus on dystonia and neurodevelopmental disorders. Rachita intends to use functional genomics methods on genetic variations along with transcriptome data to investigate the pathophysiology of different neurological disorders.

Graduate Students

Ryan Collins
Ryan CollinsPhD Student
Ryan is a PhD candidate (G1) in the Bioinformatics and Integrative Genomics (BIG) program at Harvard Medical School (HMS) and an NSF graduate research fellow. Ryan’s research interests fuse genome architecture, structural variation (SV), population genetics, epigenomics, transcriptional regulation, and bioinformatics, with a particular emphasis the applications of these disciplines to understanding human disease and translations to clinical diagnostics. In the Talkowski Laboratory, he heads computational efforts for discovery and annotation of SV from whole-genome sequencing datasets, and leads the wing of the lab specifically interested in characterizing SV across large human populations and their effects on coding and regulatory noncoding loci. Ryan earned his bachelor’s in Computational Genetics from Dartmouth College in 2013, and was a staff analyst in the Talkowski Lab for the intervening three years before joining the BIG PhD program at HMS in the fall of 2016. Read more about Ryan’s research and scientific background at his personal website: http://ryanlcollins.com/
Kiana Mohajeri
Kiana MohajeriPhD Student
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 implications of structural variation. In her thesis work, she aims integrate data from patients and genome edited cell lines to study the effects of chromosomal structural variation on nuclear chromatin compaction 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.
Catarina Seabra
Catarina SeabraPhD Student
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.

Lab Technicians

Caroline Antolik
Caroline AntolikResearch Technician
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.
Carrie Hanscom
Carrie HanscomLaboratory Technician
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.

Bioinformaticians

Matt Stone
Matt StoneBioinformatician
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.
Harold Wang
Harold WangBioinformatician
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.

Staff Scientists

Serkan Erdin
Serkan ErdinStaff Scientist in Computational Biology
Serkan is a staff scientist in the Talkowski laboratory whose research interests lie in bioinformatics/computational biology, functional genomics and genome biology. He currently works on computational and statistical analyses of next generation sequencing data to understand the relationships between genomic changes and phenotype in the context of neuro-degenerative and neuro-developmental disorders. He was recruited to the lab 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.
Alexei Stortchevoi
Alexei StortchevoiStaff Scientist
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.

Visiting Faculty

Yu An
Yu AnVisiting Scientist
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.
Matthew Waterman
Matthew WatermanVisiting Scientist
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.

Alumni

Ian Blumenthal
Ian BlumenthalBioinformatician and G&T Core Project Manager
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.
Colby Chiang
Colby ChiangBioinformatician
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.
Stacey Eggert
Stacey EggertPostdoctoral Fellow
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.
Rebecca Kass
Rebecca KassVisiting Student
Rebecca’s research in the Talkowski lab focused on the role of genetic and epigenetic alterations in determination of potential expression pathways for autism spectrum disorder. As a visiting undergraduate student during the summer of 2014, her project involved manipulation of critical autism genes in HEK cells using the CRISPR/Cas9 gene editing system. Rebecca received her BA in Creative Writing, with a minor in chemistry and music, from Eckerd College. She is interested in pursuing a PhD in neuroscience and eventually intends to become involved in scientific communication.
Emanuela Kerschbamer
Emanuela KerschbamerPostdoctoral Fellow
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 Manavalan
Poornima ManavalanLaboratory Technician
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.
Vamsee Pillalamarri
Vamsee PillalamarriBioinformatician
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 Ragavendran
Ashok RagavendranStaff Scientist in Computational Biology
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.
Claire Redin
Claire RedinPostdoctoral Fellow
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.
Aarathi Sugathan
Aarathi SugathanPostdoctoral Fellow
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.