Selected Publications

  1. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. A Abyzov, J Mariani, D Palejev, Y Zhang, MS Haney, L Tomasini, AF Ferrandino, LA Rosenberg Belmaker, A Szekely, M Wilson, A Kocabas, NE Calixto, EL Grigorenko, A Huttner, K Chawarska, S Weissman, AE Urban, M Gerstein, FM Vaccarino (2012). Nature 492: 438-42.
  2. Modeling human cortical development in vitro using induced pluripotent stem cells. J Mariani, MV Simonini, D Palejev, L Tomasini, G Coppola, AM Szekely, TL Horvath, FM Vaccarino (2012). Proc Natl Acad Sci U S A 109: 12770-5.
  3. Induced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders. FM Vaccarino, HE Stevens, A Kocabas, D Palejev, A Szekely, EL Grigorenko, S Weissman (2011). Neuropharmacology 60: 1355-63.
  4. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. FM Vaccarino, AE Urban, HE Stevens, A Szekely, A Abyzov, EL Grigorenko, M Gerstein, S Weissman (2011). J Child Psychol Psychiatry 52: 504-16.
  5. CNVnator: An approach to discover, genotype and characterize typical and atypical CNVs from family and population genome sequencing.  A Abyzov, AE Urban, M Snyder, M Gerstein (2011) Genome Res.
  6. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.   L Habegger, A Sboner, TA Gianoulis, J Rozowsky, A Agarwal, M Snyder, M Gerstein (2011) Bioinformatics  27: 281-3.2.
  7. ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks.  J Jee, J Rozowsky, KY Yip, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein (2011) Bioinformatics.
  8. Mapping copy number variation by population-scale genome sequencing.  RE Mills, K Walter, C Stewart, RE Handsaker, K Chen, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham, A Chinwalla, DF Conrad, Y Fu, F Grubert, I Hajirasouliha, F Hormozdiari, LM Iakoucheva, Z Iqbal, S Kang, JM Kidd, MK Konkel, J Korn, E Khurana, D Kural, HY Lam, J Leng, R Li, Y Li, CY Lin, R Luo, XJ Mu, J Nemesh, HE Peckham, T Rausch, A Scally, X Shi, MP Stromberg, AM Stütz, AE Urban, JA Walker, J Wu, Y Zhang, ZD Zhang, MA Batzer, L Ding, GT Marth, G McVean, J Sebat, M Snyder, J Wang, K Ye, EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, JO Korbel, 1000 Genomes Project (2011) Nature  470: 59-65.
  9. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.  A Abyzov, M Gerstein (2011) Bioinformatics  27: 595-603.
  10. Neural stem cell regulation, fibroblast growth factors, and the developmental origins of neuropsychiatric disorders. HE Stevens, KM Smith, BG Rash, FM Vaccarino (2010). Front Neurosci 4.
  11. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.  A Sboner, L Habegger, D Pflueger, S Terry, DZ Chen, JS Rozowsky, AK Tewari, N Kitabayashi, BJ Moss, MS Chee, F Demichelis, MA Rubin, MB Gerstein (2010) Genome Biol  11: R104.
  12. Astroglial cells in the external granular layer are precursors of cerebellar granule neurons in neonates. J Silbereis, T Heintz, MM Taylor, Y Ganat, LR Ment, A Bordey, F Vaccarino (2010). Mol Cell Neurosci 44: 362-73.
  13. Fgfr2 is required for the development of the medial prefrontal cortex and its connections with limbic circuits. HE Stevens, KM Smith, ME Maragnoli, D Fagel, E Borok, M Shanabrough, TL Horvath, FM Vaccarino (2010). J Neurosci 30: 5590-602.
  14. Decreased number of parvalbumin and cholinergic interneurons in the striatum of individuals with Tourette syndrome. Y Kataoka, PS Kalanithi, H Grantz, ML Schwartz, C Saper, JF Leckman, FM Vaccarino (2010). J Comp Neurol 518: 277-91.
  15. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.  A Agarwal, D Koppstein, J Rozowsky, A Sboner, L Habegger, LW Hillier, R Sasidharan, V Reinke, RH Waterston, M Gerstein (2010) BMC Genomics  11: 383.
  16. Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.  ZD Zhang, MB Gerstein (2010) BMC Bioinformatics  11: 539.
  17. A map of human genome variation from population-scale sequencing.  1000 Genomes Project Consortium, RM Durbin, GR Abecasis, DL Altshuler, A Auton, LD Brooks, RM Durbin, RA Gibbs, ME Hurles, GA McVean (2010) Nature  467: 1061-73.
  18. Personal genome sequencing: current approaches and challenges.  M Snyder, J Du, M Gerstein (2010) Genes Dev  24: 423-31.
  19. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.  HY Lam, XJ Mu, AM Stütz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010) Nat Biotechnol  28: 47-55.
  20. Increased brain size in autism--what it will take to solve a mystery. FM Vaccarino, KM Smith (2009). Biol Psychiatry 66: 313-5.
  21. Precursors with glial fibrillary acidic protein promoter activity transiently generate GABA interneurons in the postnatal cerebellum. J Silbereis, E Cheng, YM Ganat, LR Ment, FM Vaccarino (2009). Stem Cells 27: 1152-63.
  22. Fgfr1 is required for cortical regeneration and repair after perinatal hypoxia. DM Fagel, Y Ganat, E Cheng, J Silbereis, Y Ohkubo, LR Ment, FM Vaccarino (2009). J Neurosci 29: 1202-11.
  23. Regulation of cerebral cortical size and neuron number by fibroblast growth factors: implications for autism. FM Vaccarino, EL Grigorenko, KM Smith, HE Stevens (2009). J Autism Dev Disord 39: 511-20.
  24. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.  J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009) PLoS Comput Biol  5: e1000432.
  25. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.  JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009) Genome Biol  10: R23.
  26. MSB: a mean-shift-based approach for the analysis of structural variation in the genome.  LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009) Genome Res  19: 106-17.
  27. Decrease in excitatory neurons, astrocytes and proliferating progenitors in the cerebral cortex of mice lacking exon 3 from the Fgf2 gene. K Chen, Y Ohkubo, D Shin, T Doetschman, LP Sanford, H Li, FM Vaccarino (2008). BMC Neurosci 9: 94.
  28. Deficiency in inhibitory cortical interneurons associates with hyperactivity in fibroblast growth factor receptor 1 mutant mice. K Müller Smith, DM Fagel, HE Stevens, RL Rabenstein, ME Maragnoli, Y Ohkubo, MR Picciotto, ML Schwartz, FM Vaccarino (2008). Biol Psychiatry 63: 953-62.
  29. The current excitement about copy-number variation: how it relates to gene duplications and protein families.  JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008) Curr Opin Struct Biol  18: 366-74.
  30. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.  JS Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel, U Nagalakshmi, J Yang, D Zheng, R Guigó, TR Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein (2007) Genome Res  17: 732-45.
  31. Paired-end mapping reveals extensive structural variation in the human genome.  JO Korbel, AE Urban, JP Affourtit, B Godwin, F Grubert, JF Simons, PM Kim, D Palejev, NJ Carriero, L Du, BE Taillon, Z Chen, A Tanzer, AC Saunders, J Chi, F Yang, NP Carter, ME Hurles, SM Weissman, TT Harkins, MB Gerstein, M Egholm, M Snyder (2007) Science  318: 420-6.
  32. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007) Proc Natl Acad Sci U S A  104: 10110-5.