Search filters

List of works by Timo Lassmann

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing

scientific article

A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers

scientific article published on 01 March 2019

A flexible computational pipeline for research analyses of unsolved clinical exome cases

scientific article published on 10 December 2020

A phenotype centric benchmark of variant prioritisation tools

scientific article published on 5 February 2018

A promoter-level mammalian expression atlas

scientific article

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

article

Abstract 2897: Recurrent transcriptome alterations across multiple cancer types

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA

scientific article

An atlas of active enhancers across human cell types and tissues

scientific article

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

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

scientific article

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

scientific article

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

scientific article published on 26 March 2014

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

scientific article

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

scientific article published on 04 January 2019

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

scientific article published on 14 December 2015

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

scientific article published in Scientific Reports

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

scholarly article published in Scientific Data

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

scientific article

Automatic assessment of alignment quality

scientific article

Automatic extraction of reliable regions from multiple sequence alignments.

scientific article

Bilateral murine tumor models for characterizing the response to immune checkpoint blockade

scientific article published on 01 April 2020

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

scientific article

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

scientific article published in Nature Communications

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

scientific article published on 24 December 2014

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

scientific article published on 9 June 2016

CRISPR single base editing, neuronal disease modelling and functional genomics for genetic variant analysis: pipeline validation using Kleefstra syndrome EHMT1 haploinsufficiency

scientific article published on 09 February 2022

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

scientific article

Comparative transcriptomics of primary cells in vertebrates

scientific article published on 27 July 2020

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

scientific article published on 01 August 2018

Corrigendum: Tiny RNAs associated with transcription start sites in animals

scholarly article published in Nature Genetics

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

scientific article

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

scientific article published on 4 November 2015

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

scientific article published on 19 May 2016

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

scientific article published on 27 March 2014

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

scientific article

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

scientific article published on 6 January 2018

Effects of cytosine methylation on transcription factor binding sites

scientific article

Elucidating the Interaction of CF Airway Epithelial Cells and Rhinovirus: Using the Host-Pathogen Relationship to Identify Future Therapeutic Strategies

scientific article published on 07 November 2018

Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics

scientific article published on 29 August 2019

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

scientific article published on 19 April 2009

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

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

scientific article published on 21 March 2016

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

scientific article

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

scientific article published on 26 March 2014

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

scientific article published on 18 September 2019

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation

scientific article

Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity

article

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC.

scientific article published on 11 July 2017

Kalign 3: multiple sequence alignment of large data sets

scientific article published on 26 October 2019

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

scientific article published on July 2006

Kalign--an accurate and fast multiple sequence alignment algorithm

scientific article

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

scientific article

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

scientific article published on 3 October 2017

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

scientific article

MOIRAI: a compact workflow system for CAGE analysis

scientific article

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

scientific article

Monitoring transcription initiation activities in rat and dog.

scientific article

Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages.

scholarly article

Off-target effect of endogenous siRNA derived from RMRP in human cells

scientific article published on 29 April 2013

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

scientific article published on 26 December 2016

Personalised analytics for rare disease diagnostics

scientific article published on 21 November 2019

Pfam: clans, web tools and services

scientific article

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

scientific article published on 16 July 2015

Quality assessment of multiple alignment programs

scientific article published in October 2002

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

scientific article

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

scientific article

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing

scientific article

Reference exome data for Australian Aboriginal populations to support health-based research

scientific article published on 29 April 2020

Reference exome data for a Northern Brazilian population

scientific article published on 21 October 2020

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

scientific article

SAMStat: monitoring biases in next generation sequencing data

scientific article

Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment

scientific article published on 01 July 2019

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

scientific article published in March 2018

Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

Small RNAs derived from snoRNAs

scientific article (publication date: July 2009)

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer.

scientific article

Systematic analysis of transcription start sites in avian development

scientific article published on 5 September 2017

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

scientific article published on 02 June 2020

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

scientific article (publication date: 2017)

TagDust--a program to eliminate artifacts from next generation sequencing data

scientific article

TagDust2: a generic method to extract reads from sequencing data

scientific article published on 28 January 2015

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

scientific article published on 25 February 2015

Telomerase reverse transcriptase regulates microRNAs

scientific article

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

scientific article

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

scientific article published on 26 March 2014

The frequent evolutionary birth and death of functional promoters in mouse and human

scientific article published on 30 July 2015

The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function

scientific article

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

scientific article published on 11 June 2016

The regulated retrotransposon transcriptome of mammalian cells

scientific article (publication date: May 2009)

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

scientific article

Tiny RNAs associated with transcription start sites in animals

scientific article published on 19 April 2009

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcription and enhancer profiling in human monocyte subsets

scientific article published on 26 March 2014

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

scientific article

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

scientific article

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response

scientific article

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

scientific article

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

scientific article

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

scientific article published on 9 November 2015

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

scientific article published on 20 September 2016

Unamplified cap analysis of gene expression on a single-molecule sequencer.

scientific article

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

scientific article

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

scientific article

Paulina is supported by:

About Paulina

Help