Centers & Labs

RIKEN Center for Life Science Technologies

Genomics Algorithms Development Unit

Unit Leader: Timo Lassmann (Ph.D.)
Timo Lassmann(Ph.D.)

Data generated by next generation sequencers poses a formidable challenge for the downstream data analysis. This unit will apply and develop machine learning approaches to analyze high throughput sequencing data. We plan to develop algorithms in the following three areas: data processing, computational aspects of data management and functional annotation.

Research Fields

Molecular Biology & Genetics / Computer Science / Multidisciplinary

Research Subjects

  • Algorithms for Sequence Analysis
  • Machine Learning Approaches

Publications

  1. ENCODE Project Consortium
    "An integrated encyclopedia of DNA elements in the human genome"
    Nature, Vol. 489, No. 7414. (2012)
  2. S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J ...
    "Landscape of transcription in human cells."
    Nature 489 (7414), 101-108 (2012)
  3. T Lassmann, Y Hayashizaki, CO Daub
    "SAMStat: monitoring biases in next generation sequencing data"
    Bioinformatics 27 (1), 130 (2011)
  4. Y Maida, M Yasukawa, M Furuuchi, T Lassmann, R Possemato, N Okamoto, V Kasim ...
    "An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA"
    Nature 461 (7261), 230-235 (2009)
  5. H Suzuki, ARR Forrest, E van Nimwegen, CO Daub, PJ Balwierz, KM Irvine, T Lassmann ...
    "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line"
    Nature genetics 41 (5), 553-562 (2009)
  6. *T Lassmann, Y Hayashizaki, CO Daub
    "TagDust—a program to eliminate artifacts from next generation sequencing data"
    Bioinformatics 25 (21), 2839 (2009)
  7. *JA Timmons, K Wennmalm, O Larsson, TB Walden, T Lassmann, N Petrovic, DL ...
    "Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages"
    Proceedings of the National Academy of Sciences 104 (11), 4401 (2007)
  8. *T Lassmann, E Sonnhammer
    "Kalign–an accurate and fast multiple sequence alignment algorithm"
    BMC bioinformatics 6 (1), 298 (2005)
  9. *T Lassmann, ELL Sonnhammer
    "Quality assessment of multiple alignment programs"
    FEBS letters 529 (1), 126-130, 149 (2002)