Dr Timo Lassmann

Dr Timo Lassmann

BSc (Hons) MSc PhD
Academic Head of Computational Biology

Areas of expertise: Data Integration, Transcriptomics, Sequence Analysis. 

Timo Lassmann became interested in bioinformatics while completing a bachelor degree in biotechnology at King's College London. He then obtained a Master degree in bioinformatics in Sheffield and his PhD in functional genomics at the Karolinska Institute, Sweden. During this time he developed multiple sequence alignment tools to analyse protein and DNA sequences.

In 2006 he moved to the RIKEN Institute Japan, where he established data analysis frameworks to deal with next generation sequencing (NGS) data. The latter include the large-scale transcriptome datasets generated as part of the ENCyclopedia Of DNA Elements (ENCODE) and the Functional ANnotation of The Mammalian Genome (FANTOM) projects.

His main research interests include sequence analysis, probabilistic modelling and large scale data integration using machine learning approaches.



Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Roberto Verardo, Silvano Piazza, Enio Klaric, Yari Ciani, Giulio Bussadori ... (2014) Stem Cells accepted 13th out of 18, DOI: 10.1002/stem.1791.

Digital expression profiling of the compartmentalized translatome of Purkinje neurons. Anton Kratz, Pascal Beguin, Megumi Kaneko, Takahiko Chimura, Ana Maria Suzuki ...(2014) Genome Research doi: 10.1101/gr.164095.113

MOIRAI: A Compact Workflow System for CAGE Analysis. Akira Hasegawa, Carsten Daub, Piero Carninci, Yoshihide Hayashizaki and Timo Lassmann (2014) BMC Bioinformatics 15:144,DOI: 10.1186/1471-2105-15-144.

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). Hiroko Ohmiya, Morana Vitezic, Martin Frith, Masayoshi Itoh, Piero Carninci, Timo Lassmann (2014) BMC Genomics 15:269, DOI: 10.1186/1471-2164-15-269

A promoter-level mammalian expression atlas. Alistair R.R. Forrest, Hideya Kawaji, Michael Rehli, J.Kenneth Baillie, Michiel J.L. de Hoon, Vanja Haberle, Timo Lassmann ...(2014) Nature 507, 462-470.

Ceruloplasmin is a Novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. E Arner, ARR Forrest, A Ehrlund, N Mejhert, M Itoh, H Kawaji, T Lassmann, ...(2014) PloS one 9 (3), e80274

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation H Morikawa, N Ohkura, A Vandenbon, M Itoh, S Nagao-Sato, H Kawaji, ...(2014) Proceedings of the National Academy of Sciences, 201312717

An atlas of active enhancers across human cell types and tissues. R Andersson, C Gebhard, I Miguel-Escalada, I Hoof, J Bornholdt,M Boyd, ...(2014) Nature 507 (7493), 455-461.

Effects of cytosine methylation on transcription factor binding sites. YA Medvedeva, AM Khamis, IV Kulakovskiy, W Ba-Alawi, MSI Bhuyan, ...(2014) BMC genomics 15 (1), 119.

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. E Motakis, S Guhl, Y Ishizu, M Itoh, H Kawaji, M deHoon, T Lassmann, ...(2014) Blood, blood-2013-02-483792

Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation. M Rönnerblad, R Andersson, T Olofsson, I Douagi, M Karimi, S Lehmann, ...(2014) Blood, blood-2013-02-482893

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. P Prasad, M Rönnerblad, E Arner, M Itoh, H Kawaji, T Lassmann, ...(2014) Blood, blood-2013-02-483537

Transcription and enhancer profiling in human monocyte subsets. C Schmidl, K Renner, K Peter, R Eder, T Lassmann, PJ Balwierz, M Itoh, ...(2014) Blood, blood-2013-02-484188

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. C Schmidl, L Hansmann, T Lassmann, PJ Balwierz, H Kawaji, M Itoh, ...(2014) Blood, blood-2013-02-486944

Off-Target Effect of Endogenous siRNA Derived from RMRP in Human Cells. Maida Y, Kyo S, Lassmann T, Hayashizaki Y, Masutomi K (2013). Int J Mol Sci. 2013 Apr 29;14(5):9305-18.

Landscape of transcription in human cells. S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J ...(2012). Nature 489 (7414), 101-108.

An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium (2012). Nature 489 (7414), 57-74.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data. C Cheng, R Alexander, R Min, J Leng, KY Yip, J Rozowsky, KK Yan, X Dong, S ...(2012). Genome Research 22 (9), 1658-1667.

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. T Derrien, R Johnson, G Bussotti, A Tanzer, S Djebali, H Tilgner, G Guernec ...(2012). Genome Research 22 (9), 1775-1789.

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. H Takahashi, T Lass- mann, M Murata, P Carninci (2012). Nature Protocols 7 (3), 542-561.

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer. M Itoh, M Kojima, S Nagao-Sato, E Saijo, T Lassmann ...(2012). PloS one 7 (1), e30809

Unamplified cap analysis of gene expression on a single-molecule sequencer. M Kanamori-Katayama, M Itoh, H Kawaji, T Lassmann ...(2011). Genome Research 21 (7), 1150-1159.

A user's guide to the encyclopedia of DNA elements(ENCODE). RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, BE ...(2011). PLoS Biology 9 (4), e1001046

Genome-wide analysis of promoterarchitectureinDrosophilamelanogaster. RAHoskins,JMLandolin,JBBrown,JESandler,HTaka- hashi, T Lassmann ...(2011). Genome Research 21 (2), 182-192.

SAMStat: monitoring biases in next generation sequencing data. T Lassmann, Y Hayashizaki, CO Daub (2011). Bioinformatics 27 (1), 130.

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. M Vitezic, T Lassmann, ARR Forrest, M Suzuki, Y Tomaru, J Kawai, P Carninci ...(2010). Nucleic Acids Research 38 (22), 8141.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. C Plessy, N Bertin, H Takahashi, R Simone, M Salimullah, T Lassmann ...(2010). Nature Methods 7 (7), 528-534.

An atlas of combinatorial transcriptional regulation in mouse and man. T Ravasi, H Suzuki, CV Cannistraci, S Katayama, VB Bajic, K Tan, A Akalin, S ...(2010). Cell 140 (5), 744-752.

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. MJL deHoon,RJ Taft, T Hashimoto, M Kanamori-Katayama, H Kawaji, M Kawano ...(2010). Genome Research 20 (2), 257-264.

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503,promotes monocytic differentiation through combinatorial regulation. ARR Forrest, M Kanamori-Katayama, Y Tomaru, T Lassmann ...(2009). Leukemia 24 (2), 460-466.

TagDust-a program to eliminate artifacts from next generation sequencing data. T Lassmann, Y Hayashizaki, CO Daub (2009). Bioinformatics 25 (21), 2839.

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Y Maida, M Yasukawa, M Furuuchi, T Lassmann, R Pos- semato, N Okamoto, V Kasim ...(2009). Nature 461 (7261), 230-235.

Small RNAs derived from snoRNAs. RJ Taft, EA Glazov, T Lassmann, Y Hayashizaki, P Carninci, JS Mattick (2009). RNA 15 (7), 1233-1240.

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. J Severin, AM Waterhouse, H Kawaji, T Lassmann ...(2009). Genome Biology 10 (4), R39.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. H Suzuki, ARR Forrest, E van Nimwegen, CO Daub, PJ Balwierz, KM Irvine, T ...(2009). Nature Genetics 41 (5), 553-562.

The regulated retrotransposon transcriptome of mammalian cells. GJ Faulkner, Y Kimura, CO Daub, S Wani, C Plessy, KM Irvine, K Schroder, N ...(2009). Nature Genetics 41 (5), 563-571.

Tiny RNAs associated with transcription start sites in animals. RJ Taft, EA Glazov, N Cloonan, C Simons, S Stephen, GJ Faulkner, T Lassmann ...(2009). Nature Genetics 41 (5), 572-578.

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. T Lassmann, O Frings, ELL Sonnhammer (2009). Nucleic Acids Research 37 (3), 858-865.

Algorithms for building and evaluating multiple sequence alignments. Timo Lassmann(2006) Karolinska Institutet. Dissertation.

Automatic extraction of reliable regions from multiple sequence alignments. T Lassmann, E Sonnhammer (2007). BMC Bioin- formatics 8 (Suppl 5), S9.

The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. C Scheele, N Petrovic, M Faghihi, T Lassmann, K Fredriksson, O Rooyackers, C ...(2007) BMC Genomics 8 (1), 74.

Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages. JA Timmons, K Wennmalm, O Larsson, TB Walden, T Lassmann, N Petrovic, DL ...(2007) Proceedings of the National Academy of Sciences 104 (11), 4401.

Kalign,Kalignvu and Mumsa: webservers for multiple sequence alignment. TLassmann, ELLSonnhammer (2006) Nucleic Acids Research 34 (suppl 2), W596-W599.

Pfam: clans, web tools and services. RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T ...(2006). Nucleic Acids Research 34 (suppl 1), D247-D251.

Kalign-an accurate and fast multiple sequence alignment algorithm. T Lassmann,E Sonnhammer(2005).BMC Bioinformatics 6 (1), 298.

Automatic assessment of alignment quality. T Lassmann, ELL Sonnhammer (2005). Nucleic Acids Research 33 (22), 7120. 1. Quality assessment of multiple alignment programs. T Lassmann, ELL Sonnhammer (2002). FEBS Letters 529 (1), 126-130.

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