Erik FaesslerFriedrich Schiller University Jena | FSU · Department of German Linguistics
Erik Faessler
Diplom
About
37
Publications
4,134
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
559
Citations
Citations since 2017
Introduction
I am active in the field of information retrieval and information extraction with a focus on the biomedical field.
Currently I investigate possibilities to enhance gene mention normalization (i.e. the mapping of textual mentions of gene names onto a database identifier) with state-of-the-art deep learning techniques.
Additional affiliations
April 2009 - present
Position
- Researcher
Description
- PhD candidate with the main subjects of biomedical information retrieval and information extraction.
Education
October 2002 - March 2009
Field of study
- Computer Science: Artificial Intelligence (major), Linguistics (minor), Computational Linguistics (minor)
Publications
Publications (37)
Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR-S6K and RAF-MEK-ERK-RSK pathways. However, despite their functional importance, knowledge about t...
Background:
Childhood asthma is a result of a complex interaction of genetic and environmental components causing epigenetic and immune dysregulation, airway inflammation and impaired lung function. Although different microarray based EWAS studies have been conducted, the impact of epigenetic regulation in asthma development is still widely unknow...
Motivation
Knowledge about interactions between genes and proteins is vital for bio-molecular research. A large part of this knowledge is published in written text and not accessible in a structured way. To remedy this situation, several repositories of automatically extracted interaction facts were proposed over the years. However, existing soluti...
Aryl hydrocarbon receptor (AHR) activation by tryptophan (Trp) catabolites enhances tumor malignancy and suppresses anti-tumor immunity. The context specificity of AHR target genes has so far impeded systematic investigation of AHR activity and its upstream enzymes across human cancers. A pan-tissue AHR signature, derived by natural language proces...
From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and...
The PI3K/Akt pathway promotes skeletal muscle growth and myogenic differentiation. Although its importance in skeletal muscle biology is well documented, many of its substrates remain to be identified. We here studied PI3K/Akt signaling in contracting skeletal muscle cells by quantitative phosphoproteomics. We identified the extended basophilic pho...
Genes and proteins are the fundamental entities of molecular genetics and deeper knowledge about their interactions constitutes a cornerstone for advancing precision medicine. We here introduce PROGENE (formerly called FSU-PRGE), a corpus that reflects our efforts to cope with this important class of named entities within the framework of a long-la...
The 2019 Precision Medicine Track at TREC (TREC-PM) aimed at identifying relevant documents from two collections, namely PubMed (biomedical abstracts) and ClinicalTrials.gov (clinical trials), given 40 precision medicine topics representing (virtual) patients. The organizers also proposed a new subtask on treatment retrieval from PubMed. We describ...
All cells and organisms exhibit stress-coping mechanisms to ensure survival. Cytoplasmic protein-RNA assemblies termed stress granules are increasingly recognized to promote cellular survival under stress. Thus, they might represent tumor vulnerabilities that are currently poorly explored. The translation-inhibitory eIF2α kinases are established as...
The TREC-PM challenge aims for advances in the field of information retrieval applied to precision medicine. Here we describe our experimental setup and the achieved results in its 2018 edition. We explored the use of unsupervised topic models, supervised document classification, and rule-based query-time search term boosting and expansion. We part...
This paper introduces the Jena Document Information System (JeDIS). The focus lies on its capability to partition annotation graphs into modules. Annotation modules are defined in terms of types from the annotation schema. Modules allow easy manipulation of their annotations (deletion or update) and the creation of alternative annotations of indivi...
We introduce ADOnIS, an information system which coherently integrates two important, yet mostly disparate data sources, namely structured, tabular data, and unstructured data in terms of publications. The integration is achieved by providing the underlying background knowledge of the domains involved in terms of adequately tailored ontologies. Onc...
We present Joyce, a scalable tool for identifying and assembling relevant (pieces of) ontologies from a repository of source ontologies, thus enabling the effective and efficient reuse of formalized domain knowledge. Joyce includes a conceptual filter to identify relevant classes, minimizes unintended redundancies, i.e. concept duplicates, and excl...
Supplementary Figures 1-39, Supplementary Tables 1-7, Supplementary References.
List of differentially regulated phosphopeptides. Phosphopeptides showing fold ratio larger than 2 or 1.5 fold changes (FC) and p-values lower than 0.05 between time points 5 minutes, 10 minutes and 15 minutes after amino acid readdition compared to the starting time (0 minutes).
SBML model including only the canonical amino acid input on mTORC1.
SBML model including four amino acids input in the network (simple p70-S6K module).
List of differentially regulated phosphosites. Phosphosites showing fold ratio larger than 2 or 1.5 fold changes (FC) and p-values lower than 0.05 between time points 5 minutes, 10 minutes and 15 minutes after amino acid readdition compared to the starting time (0 minutes).
Text mining input and results for the detection of molecular event partners of AMPK reported in scientific texts (Medline and PubMed Central). Genes and proteins were mapped to their respective UniProt ID to avoid ambiguity. The event partners as well as the textual contexts of the events themselves are listed.
Phosphoproteomic identification data. Contains excerpts from the output files "proteinGroups" including information on protein group identification and quantification, "peptides" including information about peptide identification and quantification and "PhosphoSTY" containing information about phosphopeptide identification and quantification as wel...
SBML model similar to Supplementary Model 2, but including a more complex p70-S6K module.
Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as a key mediator. However, little is known about whether aa, independently of mTORC1, activate other kinases of the mTOR signalling network. To delineate aa-stimulated mTOR network dynamics, we...
We introduce JCoRe 2.0, the relaunch of a UIMA-based open software repository for full-scale natural language processing originating from the Jena University Language & Information Engineering (JULIE) Lab. In an attempt to put the new release of JCoRe on firm software engineering ground, we uploaded it to GitHub, a social coding platform, with an u...
The automatic processing of non-English clinical documents is massively hampered by the lack of publicly available medical language resources for training, testing and evaluating NLP components. We suggest sharing statistical models derived from access-protected clinical documents as a reasonable substitute and provide solutions for sentence splitt...
We report on basic design decisions and novel annotation procedures underlying the development of PathoJen, a corpus of Medlineabstracts annotated for pathological phenomena, including diseases as a proper subclass. This named entity type is known to be hard to delineate and capture by annotation guidelines. We here propose a two-category encoding...
In our approach to event extraction, dependency graphs constitute the fundamental data structure for knowledge capture. Two types of trimming operations pave the way to more effective relation extraction. First, we simplify the syntactic representation structures resulting from parsing by pruning informationally irrelevant lexical material from dep...
Among the many proposals to promote alternatives to costly to create gold standards, just recently the idea of a fully automatically, and thus cheaply, to set up silver standard has been launched. However, the current construction policy for such a silver standard requires crucial parameters (such as similarity thresholds and agreement cut-offs) to...
We describe the approach to event extrac- tion which the JULIELab Team from FSU Jena (Germany) pursued to solve Task 1 in the "BioNLP'09 Shared Task on Event Ex- traction". We incorporate manually curated dictionaries and machine learning method- ologies to sort out associated event triggers and arguments on trimmed dependency graph structures. Tri...
We present JNET, a highly configurable named entity tagger.
Projects
Projects (2)
We seek to answer fundamental questions about the subsurface: What biota live there? How do they interact with and reflect their environment? How do they reflect surface properties? Answers are required to understand how increasing human activities impact this zone and the services it provides.
Understanding the Links Between Surface and Subsurface Biogeosphere
The Collaborative Research Center AquaDiva focusses on the important roles of water (Aqua) and biodiversity (Diva)
for shaping the structure, properties and functions of the subsurface , defined here as the zone that begins below the highest density of plant roots (~0.3 meters) down into the first aquifers (~100 meters).
Our project seeks to answer fundamental questions about this
part of the Earth’s Critical Zone (CZ): What biota live there? How do they interact with and reflect their environment? How do they reflect surface properties?
The CZ is increasingly impacted by humans, yet we have little understanding of the consequences for ecosystem services such as groundwater quality and supply, stabilization of carbon, and trace
gas cycling on which people in turn rely.
The overall research question of the CRC AquaDiva "How do surface conditions and local geology set the functional biodiversity of the subsurface?" requires us to explore how these factors interact to shape the subsurface environment and its impacts.
To answer this question we established a Critical Zone Exploratory (CZE) which builds on a three-factor experimental design, i.e., land use (factor 1), CZ subsurface
compartment (factor 2), and alkaline versus acidic geologic setting (factor 3). Within this approach, we apply a combination of complementary field and laboratory investigations
at different spatial scales to determine how surface conditions and geologic constraints impact
subsurface biodiversity and function.
We concentrate on investigating how processes of fluid flow, matter and energy transport link surface processes (atmosphere, climate, vegetation, and topsoil horizons) to subsurface
biodiversity and function along gradients of land management and surface biodiversity within a
transect underlain by limestone and siliciclastic rocks.
Our efforts build on an infrastructure of existing
wide bore groundwater wells, the characterization of surface properties in the Biodiversity
Exploratory Hainich-Dün, and a grassland biodiversity experiment (The Jena Experiment).
The AquaDiva-research team is organized into three scientific teams: BIODIV investigators will identify and trace biomarkers of specific organisms, functions or processes and further use molecular-based methods to study subsurface functional biodiversity.
FLUX investigators will use a range of tracer methods, field monitoring, and models to determine the rates of vertical and lateral transport of water, energy, genetic material, mobile organic matter, colloids, particles, elements, and gases.
GEOFACTS investigators will focus on the geological and physical structures of the subsurface as well as the chemical interactions
with the biota, such as mineral formation and weathering.
The research teams are supprted by the INFRA projects that manage and coordinate common sampling and analysis, data sharing, analysis and archiving, and a doctoral program for students in the project.
