Alexander Junge
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View article: Language Model Re-rankers are Fooled by Lexical Similarities
Language Model Re-rankers are Fooled by Lexical Similarities Open
Language model (LM) re-rankers are used to refine retrieval results for retrieval-augmented generation (RAG). They are more expensive than lexical matching methods like BM25 but assumed to better process semantic information and the relati…
View article: Automated Medical Coding on MIMIC-III and MIMIC-IV: A Critical Review and Replicability Study
Automated Medical Coding on MIMIC-III and MIMIC-IV: A Critical Review and Replicability Study Open
Medical coding is the task of assigning medical codes to clinical free-text\ndocumentation. Healthcare professionals manually assign such codes to track\npatient diagnoses and treatments. Automated medical coding can considerably\nalleviat…
View article: DISEASES v2 (human, integrated, full)
DISEASES v2 (human, integrated, full) Open
This file contains the full set of gene–disease associations integrated from all sources of evidence in DISEASES v2.
View article: DISEASES v2 (human, experiments, filtered)
DISEASES v2 (human, experiments, filtered) Open
This file contains the filtered non-redundant set of gene–disease associations from the TIGA database of GWAS associations in DISEASES v2.
View article: DISEASES v2 (human, knowledge, filtered)
DISEASES v2 (human, knowledge, filtered) Open
This file contains the filtered non-redundant set of gene–disease associations from curated knowledge sources in DISEASES v2.
View article: DISEASES v2 (human, experiments, full)
DISEASES v2 (human, experiments, full) Open
This file contains the full set of gene–disease associations from the TIGA database of GWAS associations in DISEASES v2.
View article: DISEASES v2 (dictionary)
DISEASES v2 (dictionary) Open
This file contains the human gene and disease names used for text mining in the DISEASES database v2.
View article: Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration Open
The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by sys…
View article: DISEASES v2 (human, knowledge, full)
DISEASES v2 (human, knowledge, full) Open
This file contains the full set of gene–disease associations from curated knowledge sources in DISEASES v2.
View article: DISEASES v2 (human, text mining, full)
DISEASES v2 (human, text mining, full) Open
This file contains the full set of gene–disease associations obtained from automatic text mining in DISEASES v2.
View article: DISEASES v2 (human, text mining, filtered)
DISEASES v2 (human, text mining, filtered) Open
This file contains the filtered non-redundant set of gene–disease associations obtained from automatic text mining in DISEASES v2.
View article: DISEASES 2.0: a weekly updated database of disease–gene associations from text mining and data integration
DISEASES 2.0: a weekly updated database of disease–gene associations from text mining and data integration Open
The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by sys…
View article: On the hunt for the alternate host of <i>Hemileia vastatrix</i>
On the hunt for the alternate host of <i>Hemileia vastatrix</i> Open
Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix , has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coff…
View article: CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision Open
Motivation Information extraction by mining the scientific literature is key to uncovering relations between biomedical entities. Most existing approaches based on natural language processing extract relations from single sentence-level co…
View article: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Open
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein …
View article: CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision
CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision Open
Information extraction by mining the scientific literature is key to uncovering relations between biomedical entities. Most existing approaches based on natural language processing extract relations from single sentence-level co-mentions, …
View article: CoCoScore Supplementary Data v1.0
CoCoScore Supplementary Data v1.0 Open
Supplementary Data: CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision# Text mining dictionariesThe entities file (entities.tsv.gz), names file (names.tsv.gz), and groups file (groups.tsv.…
View article: Bioconda: A sustainable and comprehensive software distribution for the life sciences
Bioconda: A sustainable and comprehensive software distribution for the life sciences Open
We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software pac…
View article: Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry
Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry Open
Release of bud dormancy in perennial woody plants is a temperature-dependent process and thus flowering in these species is heavily affected by climate change. The lack of cold winters in temperate growing regions often results in reduced …
View article: <b> <tt>RNAscClust</tt>:</b> clustering RNA sequences using structure conservation and graph based motifs
<b> RNAscClust:</b> clustering RNA sequences using structure conservation and graph based motifs Open
Motivation Clustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, cluste…
View article: RAIN: RNA–protein Association and Interaction Networks
RAIN: RNA–protein Association and Interaction Networks Open
Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integr…
View article: Highlights from the 11th ISCB Student Council Symposium 2015
Highlights from the 11th ISCB Student Council Symposium 2015 Open
Table of contents A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, F…
View article: RAIN v1
RAIN v1 Open
RAIN: RNA–protein Association and Interaction NetworksRAIN integrates non-coding RNA (ncRNA) and protein interaction networks in an easily accessible web interface. It contains three types of ncRNA associations: microRNA-target, ncRNA-prot…