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.

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.

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.

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.

Nick joined the Talkowski laboratory 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 is focused on the engineering of cellular models of neurodevelopmental disorders and directly supports the development of high-throughput CRISPR genome editing methods, as well as studies characterizing iPSC-derived neural lineages via single-cell RNA sequencing.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.