- Principal Investigator : Tuuli Lappalainen
- Senior Staff Scientist in Molecular Biology : Ana Vasileva
- Postdoc : Stephane Castel
- Postdoc : Pejman Mohammadi
- Postdoc : Sarah Kim-Hellmuth
- PhD Student : Margot Brandt
- Associate Scientist I : Aaron Wolman
- Bioinformatics Analyst : Paul Hoffman
- Executive Assistant : Erica Bertisch
- Former members
Tuuli Lappalainen is a Junior Investigator and Core Member at the New York Genome Center. She holds a joint appointment as an Assistant Professor in the Department of Systems Biology at Columbia University.
Her research focuses on functional genetic variation in human populations and its contribution to traits and diseases. She has pioneered the intergration of large-scale genome and transcriptome sequencing data to understand how genetic variation affects gene expression, providing insight to cellular mechanisms underlying genetic risk for disease.
Tuuli received her PhD from University of Helsinki, Finland in 2009, followed by postdoctoral research at University of Geneva, Switzerland with Manolis Dermitzakis and at Stanford University with Carlos Bustamante. She has made an important contribution to several international research consortia in human genomics, including the 1000 Genomes Project and the Genotype Tissue Expression (GTEx) Project, and led the RNA-sequencing work of the Geuvadis Consortium.
In addition to her work in genomics, Tuuli is also interested in scientific journalism, and has written newspaper articles and columns for Finnish newspapers. In her (limited…) free time, she enjoys contemporary art, sports, reading, cooking, and traveling.
Elsewhere in the web
- Q&A at the New York Genome Center webpage
- Columbia Systems Biology News about the new faculty member
- Interview by GenomeWeb for the 8th Annual Young Investigators feature
- Talking about bioinformatics at the ACGT blog
# Corresponding author * Equal contribution
- Rivas MA#*, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T*#, MacArthur DG#* (2015) Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348:666-9
- Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA*#, Lappalainen T*# (2015) The landscape of genomic imprinting across diverse adult human tissues. Genome Research DOI: 10.1101/gr.192278.115
- The GTEx Consortium (2015) The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348: 648-660
- Lappalainen T#, Sammeth M, Friedlander M, ‘t Hoen PAC, Rivas MA, Monlong J, Gonzalez-Porta M, Kurbatova N, Griebel T, Ferreira P, Barann M, Wieland T, Greger L, van Iterson M, Almlof J, Ribeca P, Pulyakhina I, Esser D, Giger T, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans H, Padioleau I, Strom T, Schwartzmayer T, Pirinen M, Karlberg O, Betran Agullo S, Gut M, Amstislavskiy V, Montgomery SB, Donnelly P, McCarthy M, The Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo Alvarez A, Flicek P, Antonarakis S, Hasler R, Syvanen A-C, van Ommen G-J, Brazma A, Meitinger T, Rosenstiel P, Guigo R, Gut I, Estivill X, Dermitzakis ET# (2013) Transcriptome and genome sequencing uncovers human functional variation. Nature 501: 506-511
- ’t Hoen PAC#, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JFJ, Karlberg O, The GEUVADIS Consortium, Syvänen AC, Guigó R, Estivill X, den Dunnen JT, van Ommen GJB, Dermitzakis ET, Lappalainen T# (2013) Reproducible transcriptome sequencing across different laboratories. Nature Biotechnology 31: 1015–1022.
- Lappalainen T#, Montgomery SB, Nica AC, Dermitzakis ET# (2011) Epistatic selection between coding and regulatory variation in human evolution and disease. Am J Hum Genet. 89:459-63
- The 1000 Genomes Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65.
Senior Staff Scientist in Molecular Biology
Ana Vasileva works as a Senior Staff Scientist in the Lappalainen lab. She is now setting up the wetlab of the research group, and she oversees molecular and cell biology research in the Lappalainen lab. She will also participate in project design and grant writing.
Ana got her PhD at ICGEB and Osaka University on strategies for optimization of HBsAg expression in Pichia pastoris under the direction of Dr. Navin Khanna, and she did postdoctoral work woth Prof. Rolf Jessberger at Mount Sinai School of Medicine in New York where she carried out a project aimed at deciphering the mechanisms of gene targeting by recombinant adeno-associated virus in human cells. This effort extended in collaborations with laboratories focusing on correcting mutations in patient-specific iPS cells. It was during this time that she developed her ongoing interest in stem cell biology and began to study the unique niche of germ stem cells. Ana used NGS to compare piRNAs in wild type and Tdrd6-deficient germ cells. She continued to study the germ cell niche under the mentorships of Professor Debra Wolgemuth at Columbia University, specifically utilizing conditional mutant mouse strains to investigate the role of essential cell cycle genes in spermatogenesis.
- Vasileva, A., Linden, R.M. and Jessberger, R. (2006) Homologous recombination is required for AAV-mediated gene targeting. Nucleic Acids Research 34(11), 3345-60.
- Vasileva, A. and Jessberger, R. (2005) Precise Hit: adeno-associated virus in gene targeting. Nat. Rev. Microbiol. 3, 837-47.
Stephane is a genomics based post-doctoral researcher in the Lappalainen Lab. Broadly he is interested in understanding how the genome is interpreted through transcription to produce complex phenotypes, which can be associated with disease. He obtained his PhD from Cold Spring Harbor Laboratory studying the interplay between transcription regulation by RNAi and DNA replication using high-throughput sequencing techniques in Robert Martienssen’s lab. He completed his BSc in Molecular Biology and Genetics at the University of Guelph in Canada, and is a native of Toronto.
- Castel, S.E., Ren, J., Bhattacharjee, S., Chang, A.-Y., Sánchez, M., Valbuena, A., Antequera, F., and Martienssen, R.A. (2014). Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability. Cell 159, 572–583.
- Castel, S.E., and Martienssen, R.A. (2013). RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14, 100–112.
- Zaratiegui, M., Castel, S.E., Irvine, D.V., Kloc, A., Ren, J., Li, F., de Castro, E., Marín, L., Chang, A.-Y., Goto, D., et al. (2011). RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479, 135–138.
Pejman Mohammadi joined Lappalainen lab at the beginning of 2015. He is a machine learner/computational biologist by training; having developed integrative models for fusing multiple datatypes, he is working on the genomics of complex diseases and primarily Rheumatoid Arthritis here at NYGC.
Pejman was born and raised in Isfahan, and obtained his BSc. degree from the Isfahan University of Technology in Software engineering. In 2008 he joined the Finnish centre of Excellence in Adaptive informatics research where he was baptised as Bayesian Orthodox. He obtained his MSc. in computer science and bioinformatics from Aalto School of Sciences in Helsinki. In 2010 he moved on to Switzerland to join the the Department of Biosystems Science and Engineering at ETH Zurich where he obtained his PhD. in computational biology of HIV in 2014.
- Integrative analysis of biological systems, and regularized inference
- Statistical machine learning and Bayesian data analysis
- Computational immunology and auto-immune disorders
- Computational design of synthetic biological networks
Publications on Google Scholar: http://scholar.google.com/citations?user=PCZVnXYAAAAJ&hl=en
Sarah Kim-Hellmuth is a Postdoctoral Research Scientist in the Lappalainen lab. She is interested in human genetic variation and its effects on cellular functions linked to infectious and autoimmune disease.
Sarah studied Medicine in Munich, Germany and obtained her doctoral degree in Immunology in Veit Hornung’s lab, focusing on the recognition of microbial DNA by pattern recognition receptors. During her residency in Human Genetics at the University of Bonn she pursued her research interest both in immunology and human genetics by investigating expression quantitative trait loci (eQTLs), which underpin innate immune responses, and provide mechanistic insights to complement genome-wide association studies.
- Kim S, Becker J, Bechheim M, et al. Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. Nature Communications 2014;5:5236.
- Kim S, Kaiser V, Beier E, et al. Self-priming determines high type I IFN production by plasmacytoid dendritic cells. Eur J Immunol 2014;44(3):807–18.
- Kim S, Bauernfeind F, Ablasser A, et al. Listeria monocytogenes is sensed by the NLRP3 and AIM2 inflammasome. Eur J Immunol 2010;40(6):1545–51.
- Hornung V, Ellegast J, Kim S, et al. 5′-Triphosphate RNA Is the Ligand for RIG-I. Science 2006;314(5801):994–7.
Margot is a graduate student rotating in the lab from the Integrated Program in Cellular, Molecular and Biomedical Sciences at Columbia University. Before coming to Columbia she worked as a technician in Leonard Zon’s lab at Harvard Medical School using zebrafish as a model for investigating the molecular mechanisms of hematopoietic stem cell differentiation and self renewal. She earned her bachelor’s degree in biology from Wake Forest University where she did research in evolutionary genetics.
Associate Scientist I
Aaron Wolman works in the Lappalainen lab as a molecular biologist where he will conduct, design, and troubleshoot experiments focusing on genome editing by CRISPR/Cas9. Aaron was raised in Pennsylvania, and obtained his Bachelor’s degree in Biology and Master’s degree in Bioengineering from Wilkes University. During his time at Wilkes University he investigated the substrate profile of organic anion transporter 3 as well as studying murine early onset Alzheimer’s disease using adeno-associated virus retrograde labeling.
- Wolman A, Bommareddy A, Gionfriddo M, Witkowski S, Heindel G, Mukhija P, VanWert A. Organic Anion Transporter 3 (OAT3) Interacts Selectively with Lipophilic b-Lactam Antibiotics. Drug Metab Dispos. April 2013; 41:791-800.
Paul is a bioinformatics analyst, shared jointly with Rahul Satija’s lab. Before this position, he was a bioinformatics specialist for Peter Morrell at the University of Minnesota Agronomy Department. While there, he worked on finding the physical location of SNP markers on the barley genome, helped identify mutations that are important in cold tolerance in barley, and started asking how different motifs in genomic DNA influence point mutations in soybean. Paul earned his Bachelor’s degree in Microbiology from the University of Minnesota.
- Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross‐Ibarra J, angsd‐wrapper: utilities for analysing next‐generation sequencing data. Molecular Ecology Resources, August 2016. 16 (6): 1449-1454.
- Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL. The role of deleterious substitutions in crop genomes. Molecular Biology and Evolution. June 2016. 33 (9): 2307-2317.
Executive Assistant for Faculty
Erica Bertisch is the Executive Assistant for Faculty at the New York Genome Center, working for the Lappalainen and Pickrell labs. Previously, she was Executive Assistant to the President and Chief Executive Officer of The Leukemia & Lymphoma Society and assistant to the Executive Vice President, Founders Affiliate of the American Heart Association. Erica is a graduate of Russell Sage College in Troy, New York, and makes her home in Brooklyn Heights.
Nicholas Giangreco, Rotation student (2016)
Alejandra Cervera, Visiting student (2016)
Alexandre Yahi, Rotation student (2016)
Zach Baker, Rotation student (2015)
Ana Pascoini, Research Assistant (2014-2015)