People

Aloy’s research focuses on the molecular genetic mechanisms surrounding dystonia, including of  X-linked dystonia-parkinsonism (XDP), a unique neurogenetic degenerative 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 where he worked on elucidating the genetic basis of XDP. Aloy’s training in the Talkowski lab involves cell/molecular biology and functional genomics approaches, as his experiments apply genome editing and RNAseq to identify altered signatures in cell models of THAP1-dystonia, XDP, and other dystonic disorders.

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.

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.

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.

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.

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.

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.

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.

Paulina joined the Talkowski lab in June 2021 as a Research Technician in the Genomics and Technology Core. She received her B.S. in Chemistry and Neuroscience with a minor in Biology from University of North Carolina at Chapel Hill in 2021. During her undergraduate degree Paulina has done research focused on oncologic drug testing and on genes implicated in Autism Spectrum Disorder.  At the Center for Genomic Medicine, she performs various molecular genomic based experiments.

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.

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.

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.

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.

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.

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”.

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.

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.

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.

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.

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.

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.

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.

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.