Timo Lassmann

Professor

  • The University of Western Australia (M560), 35 Stirling Highway,

    6009 Crawley

    Australia

  • 1405 Citations
  • 10 h-Index
20092020
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Research Output 2009 2018

  • 1405 Citations
  • 10 h-Index
  • 38 Article
  • 1 Abstract/Meeting Abstract
2018

A phenotype centric benchmark of variant prioritisation tools

Anderson, D. & Lassmann, T. 1 Dec 2018 In : npj Genomic Medicine. 3, 1, 5

Research output: Contribution to journalArticle

Open Access
Benchmarking
Phenotype
Inborn Genetic Diseases
Rare Diseases

Arylsulphatase A Pseudodeficiency (ARSA-PD), hypertension and chronic renal disease in Aboriginal Australians

Tang, D., Fakiola, M., Syn, G., Anderson, D., Cordell, H. J., Scaman, E. S. H., Davis, E., Miles, S. J., McLeay, T., Jamieson, S. E., Lassmann, T. & Blackwell, J. M. 1 Dec 2018 In : Scientific Reports. 8, 1, 10912

Research output: Contribution to journalArticle

Open Access
Cerebroside-Sulfatase
Chronic Renal Insufficiency
Type 2 Diabetes Mellitus
Chylomicrons
Hypertension

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Zhang, P. G. Y., Yeung, J., Gupta, I., Ramirez, M., Ha, T., Swanson, D. J., Nagao-Sato, S., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., de Hoon, M., The FANTOM Consortium, Carninci, P., Forrest, A. R. R., Hayashizaki, Y. & Goldowitz, D. 6 Jan 2018 In : Cerebellum. p. 1-18 18 p.

Research output: Contribution to journalArticle

Laser Capture Microdissection
Transcription Factors
Gene Expression Profiling
Transcriptome
Genes
Open Access
Genetic Loci
activity pattern
Genetic Predisposition to Disease
human diseases
Susceptibility

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

Roy, S., Schmeier, S., Kaczkowski, B., Arner, E., Alam, T., Ozturk, M., Tamgue, O., Parihar, S. P., Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Guler, R., Bajic, V. B., Brombacher, F. & Suzuki, H. 1 Dec 2018 In : Scientific Reports. 8, 1, 6758

Research output: Contribution to journalArticle

Open Access
Mycobacterium Infections
Mycobacterium tuberculosis
Macrophages
Host-Pathogen Interactions
Interleukin-13
2017
6 Citations

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

Baillie, J. K., Arner, E., Daub, C. O., De Hoon, M. J. L., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Consortium, F., Faulkner, G. J., Wells, C. A., Rehli, M., Pavli, P., Summers, K. M. & Hume, D. A. 6 Mar 2017 In : PLoS Genetics. 13, 3, 36 p., 1006641

Research output: Contribution to journalArticle

107 Citations

An atlas of human long non-coding RNAs with accurate 5′ ends

Hon, C. C. , Ramilowski, J. A. , Harshbarger, J. , Bertin, N. , Rackham, O. J. L. , Gough, J. , Denisenko, E. , Schmeier, S. , Poulsen, T. M. , Severin, J. , Lizio, M. , Kawaji, H. , Kasukawa, T. , Itoh, M. , Burroughs, A. M. , Noma, S. , Djebali, S. , Alam, T. , Medvedeva, Y. A. , Testa, A. C. & 19 others Lipovich, L., Yip, C. W., Abugessaisa, I., Mendez, M., Hasegawa, A., Tang, D., Lassmann, T., Heutink, P., Babina, M., Wells, C. A., Kojima, S., Nakamura, Y., Suzuki, H., Daub, C. O., De Hoon, M. J. L., Arner, E., Hayashizaki, Y., Carninci, P. & Forrest, A. R. R. 9 Mar 2017 In : Nature. 543, 7644, p. 199-204 6 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Atlases
RNA
Nucleotides
Polymorphism
14 Citations

An integrated expression atlas of miRNAs and their promoters in human and mouse

de Rie, D. , Abugessaisa, I. , Alam, T. , Arner, E. , Arner, P. , Ashoor, H. , Astrom, G. , Babina, M. , Bertin, N. , Burroughs, A. M. , Carlisle, A. J. , Daub, C. O. , Detmar, M. , Deviatiiarov, R. , Fort, A. , Gebhard, C. , Goldowitz, D. , Guhl, S. , Ha, T. J. , Harshbarger, J. & 50 others Hasegawa, A., Hashimoto, K., Herlyn, M., Heutink, P., Hitchens, K. J., Hon, C. C., Huang, E., Ishizu, Y., Kai, C., Kasukawa, T., Klinken, P., Lassmann, T., Lecellier, C-H., Lee, W., Lizio, M., Makeev, V., Mathelier, A., Medvedeva, Y. A., Mejhert, N., Mungall, C. J., Noma, S., Ohshima, M., Okada-Hatakeyama, M., Persson, H., Rizzu, P., Roudnicky, F., Saetrom, P., Sato, H., Severin, J., Shin, J. W., Swoboda, R. K., Tarui, H., Toyoda, H., Vitting-Seerup, K., Winteringham, L., Yamaguchi, Y., Yasuzawa, K., Yoneda, M., Yumoto, N., Zabierowski, S., Zhang, P. G., Wells, C. A., Summers, K. M., Kawaji, H., Sandelin, A., Rehli, M., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & de Hoon, M. J. L. Sep 2017 In : Nature Biotechnology. 35, 9, p. 872–878

Research output: Contribution to journalArticle

Open Access
1 Citations

Data Descriptor: Monitoring transcription initiation activities in rat and dog

Lizio, M., Mukarram, A. K., Ohno, M., Watanabe, S., Itoh, M., Hasegawa, A., Lassmann, T., Severin, J., Harshbarger, J., Abugessaisa, I., Kasukawa, T., Hon, C. C., Carninci, P., Hayashizaki, Y., Forrest, A. R. R. & Kawaji, H. 28 Nov 2017 In : Scientific Data. 4, 170173

Research output: Contribution to journalArticle

Open Access
Transcription
Descriptors
Rats
Genes
Gene expression
3 Citations

FANTOM5 CAGE profiles of human and mouse samples

Noguchi, S. , Arakawa, T. , Fukuda, S. , Furuno, M. , Hasegawa, A. , Hori, F. , Ishikawa-Kato, S. , Kaida, K. , Kaiho, A. , Kanamori-Katayama, M. , Kawashima, T. , Kojima, M. , Kubosaki, A. , Manabe, R. I. , Murata, M. , Nagao-Sato, S. , Nakazato, K. , Ninomiya, N. , Nishiyori-Sueki, H. , Noma, S. & 158 others Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Kenneth Baillie, J., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, B. A. S., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J. I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Peter Klinken, S., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., MacKay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H., Mummery, C. L., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nozaki, T., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Passier, R., Patrikakis, M., Pombo, A., Pradhan-Bhatt, S., Qin, X. Y., Rehli, M., Rizzu, P., Roy, S., Sajantila, A., Sakaguchi, S., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schmidl, C., Schneider, C., Schulze-Tanzil, G. G., Schwegmann, A., Sheng, G., Shin, J. W., Sugiyama, D., Sugiyama, T., Summers, K. M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tomoiu, A., Toyoda, H., Wetering, M., Berg, L. M. V. D., Verardo, R., Vijayan, D. I., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yamaguchi, Y., Yamamoto, M., Yanagi-Mizuochi, C., Yoneda, M., Yonekura, Y., Zhang, P. G., Zucchelli, S., Abugessaisa, I., Arner, E., Harshbarger, J., Kondo, A., Lassmann, T., Lizio, M., Sahin, S., Sengstag, T., Severin, J., Shimoji, H., Suzuki, M., Suzuki, H., Kawai, J., Kondo, N., Itoh, M., Daub, C. O., Kasukawa, T., Kawaji, H., Carninci, P., Forrest, A. R. R. & Hayashizaki, Y. 29 Aug 2017 In : Scientific Data. 4, 170112

Research output: Contribution to journalArticle

Open Access
Gene Expression Profile
Gene expression
Mouse
Transcription
Cell
1 Citations

Integrative CAGE and DNA methylation profiling identify epigenetically regulated genes in NSCLC

Horie, M., Kaczkowski, B., Ohshima, M., Matsuzaki, H., Noguchi, S., Mikami, Y., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Takai, D., Yamaguchi, Y., Micke, P., Saito, A. & Nagase, T. 1 Oct 2017 In : Molecular Cancer Research. 15, 10, p. 1354-1365 12 p.

Research output: Contribution to journalArticle

DNA Fingerprinting
DNA Methylation
Non-Small Cell Lung Carcinoma
Lung Neoplasms
Gene Expression

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Bertin, N., Mendez, M., Hasegawa, A., Lizio, M., Abugessaisa, I., Severin, J., Sakai-Ohno, M., Lassmann, T., Kasukawa, T., Kawaji, H., Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Plessy, C. 3 Oct 2017 In : Scientific Data. 4, 8 p., 170147

Research output: Contribution to journalArticle

Open Access
1 Citations

Systematic analysis of transcription start sites in avian development

Lizio, M., Deviatiiarov, R., Nagai, H., Galan, L., Arner, E., Itoh, M., Lassmann, T., Kasukawa, T., Hasegawa, A., Ros, M. A., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Kawaji, H., Gusev, O. & Sheng, G. Sep 2017 In : PLoS Biology. 15, 9, 23 p., 2002887

Research output: Contribution to journalArticle

Open Access
1 Citations

Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

Cruickshank, M. N., Ford, J., Cheung, L. C., Heng, J., Singh, S., Wells, J., Failes, T. W., Arndt, G. M., Smithers, N., Prinjha, R. K., Anderson, D., Carter, K. W., Gout, A. M., Lassmann, T., O'Reilly, J., Cole, C. H., Kotecha, R. S. & Kees, U. R. 1 Jan 2017 In : Leukemia. 31, 1, p. 40-50 11 p.

Research output: Contribution to journalArticle

Open Access
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Leukemia
Histone Deacetylase Inhibitors
Cell Line
Pharmaceutical Preparations
2 Citations

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution

Ehrlund, A., Mejhert, N., Bjork, C., Andersson, R., Kulyte, A., Astrom, G., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Sandelin, A., Ingelsson, E., FANTOM Consortium, Ryden, M., Laurencikiene, J., Arner, P. & Arner, E. Jan 2017 In : Diabetes. 66, 1, p. 218-230 13 p.

Research output: Contribution to journalArticle

1 Citations

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Francescatto, M., Lizio, M., Philippens, I., Bontrop, R., Sakai, M., Watanabe, S., Itoh, M., Hasegawa, A., Lassmann, T., Severin, J., Harshbarger, J., Abugessaisa, I., Kasukawa, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Kawaji, H., Rizzu, P. & Heutink, P. 31 Oct 2017 In : Scientific Data. 4, 170163

Research output: Contribution to journalArticle

Open Access
Neurology
Transcription
Profiling
RNA
Genes
1 Citations

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

Qin, X. Y. , Hara, M. , Arner, E. , Kawaguchi, Y. , Inoue, I. , Tatsukawa, H. , Furutani, Y. , Nagatsuma, K. , Matsuura, T. , Wei, F. , Kikuchi, J. , Sone, H. , Daub, C. , Kawaji, H. , Lassmann, T. , Itoh, M. , Suzuki, H. , Carninci, P. , Hayashizaki, Y. , Kokudo, N. & 3 others Forrest, A. R. R., Kojima, S. & The FANTOM Consortium 1 Oct 2017 In : EBioMedicine. 24, p. 257-266 10 p.

Research output: Contribution to journalArticle

Open Access
Orosomucoid
Gene Expression Profiling
Hepatocytes
Liver
Hepatectomy
2016
3 Citations

CAGEd-oPOSSUM: Motif enrichment analysis from CAGE-derived TSSs

Arenillas, D. J., Forrest, A., Kawaji, H., Lassmann, T., Wasserman, W. W. & Mathelier, A. 2016 In : Bioinformatics. 32, 18, p. 2858-2860

Research output: Contribution to journalArticle

Transcription Initiation Site
Transcription
Gene expression
Gene Expression
Transcription factors
3 Citations

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C

Klein, S., Dieterich, L. C., Mathelier, A., Chong, C., Sliwa-Primorac, A., Hong, Y. K., Shin, J. W., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., Carninci, P., Hayashizaki, Y., Forrest, A., Wasserman, W. W. & Detmar, M. 2016 In : Journal of Cell Science. 129, 13, p. 2573-2585

Research output: Contribution to journalArticle

Vascular Endothelial Growth Factor Receptor-3
Vascular Endothelial Growth Factor C
Transcription Factors
Lymphangiogenesis
Endothelial Cells
9 Citations

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

Laurent, G. S., Vyatkin, Y., Antonets, D., Ri, M., Qi, Y., Saik, O., Shtokalo, D., De Hoon, M. J. L., Kawaji, H., Itoh, M., Lassmann, T., Arner, E., Forrest, A. R. R., Nicolas, E., Mccaffrey, T. A., Carninci, P., Hayashizaki, Y., Wahlestedt, C. & Kapranov, P. 2016 In : Nucleic Acids Research. 44, 7, p. 3233-3252

Research output: Contribution to journalArticle

Open Access
Untranslated RNA
Systems Biology
Genes
Genomics
Long Noncoding RNA
2 Citations

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

lenasescu, H., Li, K., Andersson, R., Vitezic, M., Rennie, S., Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Bornholdt, J., Kawaji, H., Lassmann, T., The FANTOM Consortium, Forrest, A. & Carninci, P. 2016 In : Database-The Journal of Biological Databases and Curation. p. 1-10 10 p., baw144

Research output: Contribution to journalArticle

Open Access
File

Recurrent transcriptome alterations across multiple cancer types

Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itot, M., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & FANTOM5 Consortium Jul 2016 In : Cancer Research. 76, 3 p.

Research output: Contribution to journalAbstract/Meeting Abstract

7 Citations

Reference genotype and exome data from an Australian Aboriginal population for health-based research

Tang, D., Anderson, D., Francis, R., Syn, G., Jamieson, S., Lassmann, T. & Blackwell, J. 12 Apr 2016 In : Scientific Data. 3, p. 1-7 7 p., 160023

Research output: Contribution to journalArticle

Open Access
Nucleotides
Genotype
Sequencing
Health
Genomics
17 Citations

The rare and undiagnosed diseases diagnostic service - application of massively parallel sequencing in a state-wide clinical service

Baynam, G. , Pachter, N. , McKenzie, F. , Townshend, S. , Slee, J. , Kiraly-Borri, C. , Vasudevan, A. , Hawkins, A. , Broley, S. , Schofield, L. , Verhoef, H. , Walker, C. E. E. , Molster, C. , Blackwell, J. M. , Jamieson, S. , Tang, D. , Lassmann, T. , Mina, K. , Beilby, J. , Davis, M. & 5 others Laing, N., Murphy, L., Weeramanthri, T., Dawkins, H. & Goldblatt, J. 2016 In : Orphanet Journal of Rare Diseases. 11, 7 p., 77

Research output: Contribution to journalArticle

Genetic Services
Diagnostic Services
High-Throughput Nucleotide Sequencing
Rare Diseases
Western Australia
16 Citations

Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers

Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itoh, M., Lassmann, T., Hayashizaki, Y., Carninci, P. & Forrest, A. 2016 In : Cancer Research. 76, 2, p. 216-226

Research output: Contribution to journalArticle

Gene Expression Profiling
Tumor Biomarkers
Genes
Neoplasms
Short Interspersed Nucleotide Elements
4 Citations

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Chen, C. Y., Shi, W., Balaton, B. P., Matthews, A. M., Li, Y., Arenillas, D. J., Mathelier, A., Itoh, M., Kawaji, H., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Brown, C. J. & Wasserman, W. W. 18 Nov 2016 In : Scientific Reports. 6, 37324

Research output: Contribution to journalArticle

Open Access
Sex Characteristics
YY1 Transcription Factor
Long Noncoding RNA
X Chromosome Inactivation
Transcription Initiation Site
2015

Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage

Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A., Carninci, P., Hayashizaki, Y., Daub, C. O., Okada-Hatakeyama, M. & Mar, J. C. 2015 In : PLoS One. 10, 12, p. 1-22

Research output: Contribution to journalArticle

Open Access
Gene expression
trajectories
Genes
Chemical activation
promoter regions
8 Citations

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

Dieterich, L. C., Klein, S., Mathelier, A., Sliwa-Primorac, A., Ma, Q., Hong, Y. K., Shin, J. W., Hamada, M., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Wasserman, W. W. & Detmar, M. 2015 In : Cell Reports. 13, 7, p. 1493-1504

Research output: Contribution to journalArticle

Open Access
Lymphatic Endothelium
Vascular Endothelial Growth Factor C
Transcription Factors
Vascular Endothelial Growth Factor Receptor-3
Gene expression
134 Citations

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M. , Harshbarger, J. , Shimoji, H. , Severin, J. , Kasukawa, T. , Sahin, S. , Abugessaisa, I. , Fukuda, S. , Hori, F. , Ishikawa-Kato, S. , Mungall, C. J. , Arner, E. , Baillie, J. K. , Bertin, N. , Bono, H. , De Hoon, M. , Diehl, A. D. , Dimont, E. , Freeman, T. C. , Fujieda, K. & 249 others Hide, W., Kaliyaperumal, R., Katayama, T., Lassmann, T., Meehan, T. F., Nishikata, K., Ono, H., Rehli, M., Sandelin, A., Schultes, E. A., T Hoen, P. A. C., Tatum, Z., Thompson, M., Toyoda, T., Wright, D. W., Daub, C. O., Itoh, M., Carninci, P., Hayashizaki, Y., Forrest, A., Kawaji, H., Alam, I., Albanese, D., Altschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, P., Babina, M., Bajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Davis, C., De Lima Morais, D., Detmar, M., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Frith, M., Fujita, R., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Katayama, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okzaki, Y., Orlando, V., Ovchinnokov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Sheng, G., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, M., Suzuki, N., Swoboda, R., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Taylor, M., Toyoda, H., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X. & Zucchelli, S. 2015 In : Genome Biology. 16, p. 1-14

Research output: Contribution to journalArticle

Open Access
Atlases
atlas
Transcription Factors
promoter regions
Cell Line
3 Citations

Mapping mammalian cell-type-specific transcriptional regulatory networks using KD-CAGE and ChIP-seq data in the TC-YIK cell line

Lizio, M., Ishizu, Y., Itoh, M., Lassmann, T., Hasegawa, A., Kubosaki, A., Severin, J., Kawaji, H., Nakamura, Y., Suzuki, H., Hayashizaki, Y., Carninci, P. & Forrest, A. 2015 In : Frontiers in Genetics. 6, p. 1-17

Research output: Contribution to journalArticle

Open Access
Gene Regulatory Networks
Transcription Factors
Gene Expression
Cell Line
Gene Knock-In Techniques
10 Citations

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ERBB receptors in breast cancer cells

Mina, M., Magi, S., Jurman, G., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A., Carninci, P., Hayashizaki, Y., Daub, C. O., Okada-Hatakeyama, M. & Furlanello, C. 2015 In : Scientific Reports. 5, p. 1-13

Research output: Contribution to journalArticle

Open Access
Neuregulin-1
Cluster Analysis
Transcription Factor AP-1
Breast Neoplasms
Gene Expression
9 Citations

TagDust2: A generic method to extract reads from sequencing data

Lassmann, T. 2015 In : BMC Bioinformatics. 16, 1, p. 1-8

Research output: Contribution to journalArticle

Open Access
Sequencing
Libraries
Hidden Markov models
Processing
Artifacts
11 Citations

Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Joshi, A., Pooley, C., Freeman, T. C., Lennartsson, A., Babina, M., Schmidl, C., Geijtenbeek, T., Michoel, T., Severin, J., Itoh, M., Lassmann, T., Kawaji, H., Hayashizaki, Y., Carninci, P., Forrest, A., Rehli, M. & Hume, D. A. 2015 In : Journal of leukocyte biology. 97, 5, p. 985-995

Research output: Contribution to journalArticle

Open Access
Myelopoiesis
Myeloid Cells
Transcription Factors
Myeloid Progenitor Cells
Untranslated RNA
7 Citations

Telomerase reverse transcriptase regulates microRNAs

Lassmann, T., Maida, Y., Tomaru, Y., Yasukawa, M., Ando, Y., Kojima, M., Kasim, V., Simon, C., Daub, C. O., Carninci, P., Hayashizaki, Y. & Masutomi, K. 2015 In : International Journal of Molecular Sciences. 16, 1, p. 1192-1208

Research output: Contribution to journalArticle

Open Access
Telomerase
RNA
MicroRNAs
retarding
telomeres
2014
3 Citations

CAGE-defined promoter regions of the genes implicated in Rett Syndrome

Vitezic, M., Bertin, N., Andersson, R., Lipovich, L., Kawaji, H., Lassmann, T., Sandelin, A., Heutink, P., Goldowitz, D., Ha, T., Zhang, P., Patrizi, A., Fagiolini, M., Forrest, A., Carninci, P. & Saxena, A. 2014 In : BMC Genomics. 15, 1, p. 1-16

Research output: Contribution to journalArticle

Open Access
2009
41 Citations

FANTOM4 EdgeExpressDB: An integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Severin, J., Waterhouse, A. M., Kawaji, H., Lassmann, T., Van Nimwegen, E., Balwierz, P. J., De Hoon, M. J. L., Hume, D. A., Carninci, P., Hayashizaki, Y., Suzuki, H., Daub, C. O. & Forrest, A. R. R. 19 Apr 2009 In : Genome Biology. 10, 4, R39

Research output: Contribution to journalArticle

MicroRNAs
microRNA
gene expression
promoter regions
Databases
424 Citations

The regulated retrotransposon transcriptome of mammalian cells

Faulkner, G. J. , Kimura, Y. , Daub, C. O. , Wani, S. , Plessy, C. , Irvine, K. M. , Schroder, K. , Cloonan, N. , Steptoe, A. L. , Lassmann, T. , Waki, K. , Hornig, N. , Arakawa, T. , Takahashi, H. , Kawai, J. , Forrest, A. R. R. , Suzuki, H. , Hayashizaki, Y. , Hume, D. A. , Orlando, V. & 2 others Grimmond, S. M. & Carninci, P. May 2009 In : Nature Genetics. 41, 5, p. 563-571 9 p.

Research output: Contribution to journalArticle

Retroelements
Transcriptome
Genome
Untranslated RNA
Nucleic Acid Regulatory Sequences
297 Citations

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Suzuki, H. , Forrest, A. R. R. , Van Nimwegen, E. , Daub, C. O. , Balwierz, P. J. , Irvine, K. M. , Lassmann, T. , Ravasi, T. , Hasegawa, Y. , De Hoon, M. J. L. , Katayama, S. , Schroder, K. , Carninci, P. , Tomaru, Y. , Kanamori-Katayama, M. , Kubosaki, A. , Akalin, A. , Ando, Y. , Arner, E. , Asada, M. & 140 others Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Björkegren, J. L. M., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hörnquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M. C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., MacPherson, C., Maeda, N., Maher, C. A., Maqungo, M., Mar, J., Matigian, N. A., Matsuda, H., Mattick, J. S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schönbach, C., Schwartz, A. S., Semple, C. A., Sera, M., Severin, J., Shirahige, K., Simons, C., St. Laurent, G., Suzuki, M., Suzuki, T., Sweet, M. J., Taft, R. J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M. S., Teasdale, R. D., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C. A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D. A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J. & Hayashizaki, Y. May 2009 In : Nature Genetics. 41, 5, p. 553-562 10 p.

Research output: Contribution to journalArticle

Myeloid Leukemia
Gene Regulatory Networks
Myeloid Cells
Transcription Factors
Cell Line
259 Citations

Tiny RNAs associated with transcription start sites in animals

Taft, R. J. , Glazov, E. A. , Cloonan, N. , Simons, C. , Stephen, S. , Faulkner, G. J. , Lassmann, T. , Forrest, A. R. R. , Grimmond, S. M. , Schroder, K. , Irvine, K. , Arakawa, T. , Nakamura, M. , Kubosaki, A. , Hayashida, K. , Kawazu, C. , Murata, M. , Nishiyori, H. , Fukuda, S. , Kawai, J. & 7 others Daub, C. O., Hume, D. A., Suzuki, H., Orlando, V., Carninci, P., Hayashizaki, Y. & Mattick, J. S. May 2009 In : Nature Genetics. 41, 5, p. 572-578 7 p.

Research output: Contribution to journalArticle

Transcription Initiation Site
RNA
RNA Polymerase II
Eukaryota
Drosophila