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List of works by Ulf Leser

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature

scientific article

A detailed error analysis of 13 kernel methods for protein-protein interaction extraction

scientific article

A fast and effective dependency graph kernel for PPI relation extraction.

scientific article

A query language for biological networks

scientific article published in September 2005

A survey on annotation tools for the biomedical literature

scientific article published on 18 December 2012

Adaptive efficient compression of genomes

scientific article published on 12 November 2012

Algorithms for differential splicing detection using exon arrays: a comparative assessment

scientific article

AliBaba: PubMed as a graph

scientific article

Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach

scientific article published on 6 May 2015

Basal subtype is predictive for response to cetuximab treatment in patient-derived xenografts of squamous cell head and neck cancer

scientific article published on 30 May 2017

BioCreative III interactive task: an overview

scientific article

CELDA -- an ontology for the comprehensive representation of cells in complex systems

scientific article

CellFinder: a cell data repository

scientific article (publication date: 2014)

Classical Hodgkin's lymphoma shows epigenetic features of abortive plasma cell differentiation ⬇️

scientific article published on March 10, 2011

Columba: an integrated database of proteins, structures, and annotations

scientific article

Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction ⬇️

scientific article published on December 20, 2010

Comparative Analysis of Public Knowledge Bases for Precision Oncology

scientific article published on 24 July 2019

Comparative assessment of differential network analysis methods

scientific article published on 29 July 2016

Computer-assisted curation of a human regulatory core network from the biological literature.

scientific article published on 29 November 2014

Convolutional event embeddings for fast probabilistic earthquake assessment

scholarly article published 18 December 2019

Cross talk between Wnt/β-catenin and Irf8 in leukemia progression and drug resistance.

scientific article published on 7 October 2013

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer.

scientific article

Deep learning with word embeddings improves biomedical named entity recognition

scientific article published on July 2017

Deregulation of the endogenous C/EBPβ LIP isoform predisposes to tumorigenesis

scientific article published on 18 November 2014

Discovery and Validation of Novel Biomarkers for Detection of Epithelial Ovarian Cancer

scientific article published on 12 July 2019

End-to-end PGA estimation for earthquake early warning using transformer networks

scholarly article published 23 March 2020

Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization.

scientific article

Estimation of Transcription Factor Activity in Knockdown Studies

scientific article published on 03 July 2019

FRESCO: Referential compression of highly similar sequences

scientific article published on September 2013

Fast Sampling-Based Whole-Genome Haplotype Block Recognition

scientific article published in March 2016

Finding kinetic parameters using text mining

scientific article published in January 2004

GandrKB--ontological microarray annotation and visualization

scientific article published on 31 March 2005

Gene mention normalization and interaction extraction with context models and sentence motifs.

scientific article published on September 2008

GeneView: a comprehensive semantic search engine for PubMed ⬇️

scientific article published on June 12, 2012

Graph-Based Ontology Construction from Heterogenous Evidences

scientific article published in ISWC 2009

H3K9me3-mediated epigenetic regulation of senescence in mice predicts outcome of lymphoma patients

scientific article published on 20 July 2020

HUNER: improving biomedical NER with pretraining

scientific article published on 01 January 2020

Histone acetylation and DNA demethylation of T cells result in an anaplastic large cell lymphoma-like phenotype ⬇️

scientific article published on August 16, 2012

How well are protein structures annotated in secondary databases?

scientific article published in September 2005

HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition ⬇️

scholarly article published 18 August 2020

Implications for molecular mechanisms of glycoprotein hormone receptors using a new sequence-structure-function analysis resource

scientific article

Inference of surface membrane factors of HIV-1 infection through functional interaction networks

scientific article

Integrating protein-protein interactions and text mining for protein function prediction

scientific article

Large-scale Entity Representation Learning for Biomedical Relationship Extraction

scientific article published on 29 July 2020

Low uncertainty multifeature magnitude estimation with 3-D corrections and boosting tree regression: application to North Chile

scholarly article

Mining phenotypes for gene function prediction

scientific article

Novel Approaches Toward Scalable Composable Workflows in Hyper-Heterogeneous Computing Environments

scientific article published on 10 November 2023

On-Demand Indexing for Referential Compression of DNA Sequences.

scientific article published on 6 July 2015

PEDL: extracting protein-protein associations using deep language models and distant supervision

scientific article published on 01 July 2020

PIEJoin

Phenoclustering: online mining of cross-species phenotypes

scientific article

Phenotype mining for functional genomics and gene discovery

scientific article published on January 2011

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

scientific article published on 18 April 2013

Question answering for biology

scientific article

Ras-mediated deregulation of the circadian clock in cancer

scientific article

Recognizing chemicals in patents: a comparative analysis

scientific article (publication date: 2016)

Reflection of successful anticancer drug development processes in the literature.

scientific article published on 18 July 2016

Robust in-silico identification of Cancer Cell Lines based on RNA and targeted DNA sequencing data

scientific article published in Scientific Reports

Robust in-silico identification of cancer cell lines based on next generation sequencing

scientific article published on 10 March 2017

SETH detects and normalizes genetic variants in text

scientific article published on 2 June 2016

Sequence Factorization with Multiple References

scientific article published on 30 September 2015

Simple tricks for improving pattern-based information extraction from the biomedical literature ⬇️

scientific article published on September 24, 2010

SoFIA: a data integration framework for annotating high-throughput datasets

scientific article

Species identification for gene name normalization.

scientific article published on 6 October 2010

Subspace Clustering Techniques

Systematic feature evaluation for gene name recognition

scientific article published on 24 May 2005

The Stratosphere platform for big data analytics

Tools for managing and analyzing microarray data ⬇️

scientific article published on March 21, 2011

Using ontologies to study cell transitions

scientific article

VIST - a Variant-Information Search Tool for precision oncology

scientific article published on 16 August 2019

Variant information systems for precision oncology

scientific article published on 21 November 2018

What makes a gene name? Named entity recognition in the biomedical literature

scientific article

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