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Authors: Timo Lassmann
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Journal Article

SampleExplorer: using language models to discover relevant transcriptome data Open Access

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Wee Loong Chin and Timo Lassmann
Bioinformatics, Volume 41, Issue 1, January 2025, btae759, https://doi.org/10.1093/bioinformatics/btae759
Published: 30 December 2024
Journal Article

Mining single-cell data for cell type–disease associations Open Access

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Kevin G Chen and others
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae180, https://doi.org/10.1093/nargab/lqae180
Published: 18 December 2024
Journal Article

SAMStat 2: quality control for next generation sequencing data Open Access

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Timo Lassmann
Bioinformatics, Volume 39, Issue 1, January 2023, btad019, https://doi.org/10.1093/bioinformatics/btad019
Published: 13 January 2023
Journal Article

Common and Rare Genetic Variants That Could Contribute to Severe Otitis Media in an Australian Aboriginal Population Open Access

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Sarra E Jamieson and others
Clinical Infectious Diseases, Volume 73, Issue 10, 15 November 2021, Pages 1860–1870, https://doi.org/10.1093/cid/ciab216
Published: 09 March 2021
Journal Article

Zika Virus Changes Methylation of Genes Involved in Immune Response and Neural Development in Brazilian Babies Born With Congenital Microcephaly Free

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Denise Anderson and others
The Journal of Infectious Diseases, Volume 223, Issue 3, 1 February 2021, Pages 435–440, https://doi.org/10.1093/infdis/jiaa383
Published: 02 July 2020
Journal Article

Kalign 3: multiple sequence alignment of large datasets Open Access

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Timo Lassmann
Bioinformatics, Volume 36, Issue 6, March 2020, Pages 1928–1929, https://doi.org/10.1093/bioinformatics/btz795
Published: 26 October 2019
Journal Article

Integration of genetics and miRNA–target gene network identified disease biology implicated in tissue specificity Open Access

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Saori Sakaue and others
Nucleic Acids Research, Volume 46, Issue 22, 14 December 2018, Pages 11898–11909, https://doi.org/10.1093/nar/gky1066
Published: 08 November 2018
Journal Article

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

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Hans Ienasescu and others
Database, Volume 2016, 2016, baw144, https://doi.org/10.1093/database/baw144
Published: 26 December 2016
Journal Article

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs Open Access

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David J. Arenillas and others
Bioinformatics, Volume 32, Issue 18, September 2016, Pages 2858–2860, https://doi.org/10.1093/bioinformatics/btw337
Published: 09 June 2016
Journal Article

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

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Georges St. Laurent and others
Nucleic Acids Research, Volume 44, Issue 7, 20 April 2016, Pages 3233–3252, https://doi.org/10.1093/nar/gkw162
Published: 21 March 2016
Journal Article

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics Open Access

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Sugata Roy and others
Nucleic Acids Research, Volume 43, Issue 14, 18 August 2015, Pages 6969–6982, https://doi.org/10.1093/nar/gkv646
Published: 27 June 2015
Journal Article

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells Open Access

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Anagha Joshi and others
Journal of Leukocyte Biology, Volume 97, Issue 5, May 2015, Pages 985–995, https://doi.org/10.1189/jlb.6TA1014-477RR
Published: 25 February 2015
Journal Article

Specific Mesothelial Signature Marks the Heterogeneity of Mesenchymal Stem Cells From High-Grade Serous Ovarian Cancer Get access

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Roberto Verardo and others
Stem Cells, Volume 32, Issue 11, November 2014, Pages 2998–3011, https://doi.org/10.1002/stem.1791
Published: 14 October 2014
Journal Article

SAMStat: monitoring biases in next generation sequencing data Open Access

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Timo Lassmann and others
Bioinformatics, Volume 27, Issue 1, January 2011, Pages 130–131, https://doi.org/10.1093/bioinformatics/btq614
Published: 18 November 2010
Journal Article

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE Open Access

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Morana Vitezic and others
Nucleic Acids Research, Volume 38, Issue 22, 1 December 2010, Pages 8141–8148, https://doi.org/10.1093/nar/gkq729
Published: 19 August 2010
Journal Article

TagDust—a program to eliminate artifacts from next generation sequencing data Open Access

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Timo Lassmann and others
Bioinformatics, Volume 25, Issue 21, November 2009, Pages 2839–2840, https://doi.org/10.1093/bioinformatics/btp527
Published: 07 September 2009
Journal Article

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features Open Access

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Timo Lassmann and others
Nucleic Acids Research, Volume 37, Issue 3, 1 February 2009, Pages 858–865, https://doi.org/10.1093/nar/gkn1006
Published: 22 December 2008
Journal Article

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment Open Access

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Timo Lassmann and Erik L. L. Sonnhammer
Nucleic Acids Research, Volume 34, Issue suppl_2, 1 July 2006, Pages W596–W599, https://doi.org/10.1093/nar/gkl191
Published: 01 July 2006
Journal Article

Pfam: clans, web tools and services Open Access

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Robert D. Finn and others
Nucleic Acids Research, Volume 34, Issue suppl_1, 1 January 2006, Pages D247–D251, https://doi.org/10.1093/nar/gkj149
Published: 01 January 2006
Journal Article

Automatic assessment of alignment quality Open Access

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Timo Lassmann and Erik L. L. Sonnhammer
Nucleic Acids Research, Volume 33, Issue 22, 1 December 2005, Pages 7120–7128, https://doi.org/10.1093/nar/gki1020
Published: 01 January 2005