Publications
2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003
2024
Peer-reviewed publications
- Middlehurst, M., Ismail-Fawaz, A., Guillaume, A., Holder, C., Rubio, D. G., Bulatova, G., Tsaprounis, L., Mentel, L., Walter, M., Schäfer, P., and Bagnall, A. (2024).
aeon: a Python Toolkit for Learning from Time Series
Journal of Machine Learning Research. - Schäfer, P., Leser, U. (2024).
Discovering Leitmotifs in Multidimensional Time Series
PVLDB (accepted), London, UK. - Lewińska, K. E., Ernst, S., Frantz, D., Leser, U. and Hostert, P. (2024).
Global overview of usable Landsat and Sentinel-2 data for 1982-2023
Data in Brief (accepted). - Sänger, M., Garda, S., Xing, W. D., Weber-Günzel, L., Droop, P., Fuchs, B., Akbik, A. and Leser, U. (2020).
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools
Bioinformatics (accepted). - Garda, S. and Leser, U. (2024).
BELHD: Improving Biomedical Entity Linking with Homonym Disambiguation.
Bioinformatics (accepted) - de Mecquenem, N., Bosse, S., Bountris, V., Mohammadi, S., Reinert, K. and Leser, U. (2024).
CuttleFlow: Infrastructure-Specific Workflow Adaption for Improved Reusability
eScience, Osaka, Japan. - Lehmann, F., Bader, J., de Mecquenem, N., Wang, X., Bountris, V., Friederici, F., Leser, U. and Thamsen, L. (2024).
Ponder: Online Prediction of Task Memory Requirements for Scientific Workflows
eScience, Osaka, Japan. - Ermshaus, A., Schäfer, P. and Leser, U. (2024).
Multivariate Human Activity Segmentation: Systematic Benchmark with ClaSP
Int. Workshop on Advanced Analytics and Learning on Temporal Data (AALTD), Vilnius, Lithuania. - Şerbetçi, O., Wang, X. D. and Leser, U. (2024).
HU-WBI at BioASQ12B Phase A: Exploring Rank Fusion of Dense Retrievers for Biomedical Question Answering
BioASQ Challenge Workshop. - Lewińska, K. E., Franz, D., Leser, U. and Hostert, P. (2024).
Usable Observations over Europe: evaluation of compositing windows for Landsat and Sentinel-2 time series
European Journal of Remote Sensing (accepted). - Sänger, M., De Mecquenem, N., Lewińska, K. E., Bountris, V., Lehmann, F., Leser, U. and Kosch, T. (2024).
A Qualitative Assessment of Using ChatGPT as Large Language Model for Scientific Workflow Development
Gigascience 13 - Middlehurst, M. Schäfer, P., and Bagnall, A. (2024).
Bake off redux: a review and experimental evaluation of recent time series classification algorithms
Data Mining and Knowledge Discovery (accepted). - Schintke, F., Belhajjame, K., De Mecquenem, N., Frantz, D., Guarino, V., Hilbrich, M., Lehmann, F., Missier, P., Sattler, R., Sparka, J., Vu, D. and Leser, U (2024).
Validity constraints for data analysis workflows
Future Generation Computing Systems 157 - Ermshaus, A., Schäfer, P. and Leser, U. (2024).
Raising the ClaSS of Streaming Time Series Segmentation
PVLDB (accepted), Guangzhou, China - Mohammadi, S., Pourkarimi, L., Zschäbitz, M., Aretz, T., Leser, U., Reinert, K. and De Mecquenem, N. (2024).
Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures
Workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP), Paestum, Italy. - Schulz, M.-A., Albrecht, J. P., Yilmaz, A., Koch, A., Leser, U., Ritter, K. and Kainmüller, D. (2024).
TLIMB - A Transfer Learning Framework for IMage Analysis of the Brain
Workshop on Data Analytics solutions for Real-LIfe APplications (DARLI-AP), Paestum, Italy. - Ermshaus, A., Piechotta, M., Rüter, G., Keilholz, U., Leser, U. and Benary, M. (2024).
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
Bioinformatics 40(3) - Stögbauer, F., Otto, R., Jöhrens, K., Tinhofer, I., Keilholz, U., Poremba, C., Keller, U., Leser, U., Weichert, W., Boxberg, M., and Klinghammer, K. (2024).
Molecular subtyping of head and neck cancer – Clinical applicability and correlations with morphological characteristics.
Oral Oncology 149.
Other
- Herrmann, W. J., Leser, U., Möller, S., Voigt-Antons, J.-N. and Gellert, P., Eds. (2024).
The Digitalization of Healthcare for Older Adults
Berlin University Publishers. - Bagnall, A., Middlehurst, M., Forestier, G., Ismail-Fawaz, A., Guillaume, A., Rubio, D. G., Ermshaus, A., Schäfer, P., Papenbrock, T., Schmidl, S., and Wenig, P., (2024).
An Introduction to Machine Learning from Time Series
ECML-PKDD 2024 tutorial. - Badia, R., Berti-Equille, L., Ferreira da Silva, R. and Leser, U., Eds. (2024).
Integrating HPC, AI, and Workflows for Scientific Data Analysis
Dagstuhl Proceedings.
2023
Peer-reviewed publications
- Frantz, D., Schug, F., Wiedenhofer, D., Baumgart, A., Virág, D., Cooper, S., Gómez-Medina, C., Lehmann, F., Udelhoven, T., van der Linden, S., Hostert, P. & Haberl, H. (2024).
Unveiling patterns in human dominated landscapes through mapping the mass of built structures in the US.
Nature Communications 14. - Büttner, M., Leser, U., Schneider, L. and Schwendicke, F. (2023).
Natural Language Processing: Chances and Challenges in Dentistry.
Journal of Dentistry 104796. - Benary, M., Wang, X., Schmidt, M., Soll, D., Hilfenhaus, G., Nassir, M., Sigler, C., Knödler, M., Keller, U., Beule, D., Keilholz, U., Leser, U., and Rieke, DT (2023).
Leveraging Large Language Models for Decision Support in Personalized Oncology.
JAMA Network Open 6(11). - Garda, S., Weber-Genzel, L., Robert, M. and Leser, U. (2023).
BELB: a Biomedical Entity Linking Benchmark.
Bioinformatics 39(11). - Weber-Genzel, L., Barth, F., Lorenz, L., Konrath, F., Kirsten, H., Wolf, J. and Leser, U. (2023).
PEDL+: Protein-centered relation extraction from PubMed at your fingertip
Bioinformatics (accepted) - Lehmann, F., Bader, J., Thamsen, L. and Leser, U. (2023).
The Common Workflow Scheduler Interface: Status Quo and Future Plans
Workshop on Workflows in Support of Large-Scale Science (accepted). - Serbetci, O. and Leser, U. (2023).
Applicability of models trained on generated clinical German datasets on out-domain data
Nat. Conf. on Learning, Knowledge, Data, and Analysis (LWDA), Marburg, Germany. - Barth, F., Weber-Genzel, L. and Leser, U. (2023).
Biomedical Event Extraction with Generative Language Models
Nat. Conf. on Learning, Knowledge, Data, and Analysis (LWDA), Marburg, Germany. - Bader, J., Lehmann, F., Thamsen, L., Leser, U. and Kao, O. (2022).
Lotaru: Locally Predicting Workflow Task Runtimes for Resource Management on Heterogeneous Infrastructures
Future Generation Computing Systems (accepted). - Vu, A. D., Sparka, J. A., de Mecquenem, N., Kehrer, T., Leser, U. and Grunske, L. (2023).
Contract-Driven Design of Scientific Data Analysis Workflows
eScience, Cyprus. - Schäfer, P. and Leser, U. (2023).
WEASEL 2.0 - A Random Dilated Dictionary Transform for Fast, Accurate and Memory Constrained Time Series Classification
European Conference on Machine Learning, Turin, Italy (accepted). - Mohammadi, S., PourKarimi, L., Droop, F., De Mecquenem, N., Leser, U. and Knut, R. (2023).
A Mathematical Programming Approach for Resource Allocation of Data Analysis Workflows on Heterogeneous Clusters.
Journal of Supercomputing. - Ermshaus, A., Singh, S. and Leser, U. (2023).
Time Series Segmentation Applied to a New Data Set for Mobile Sensing of Human Activities
Int. Workshop on Data Analytics solutions for Real-LIfe APplications Ioanina, Greece. - Lehmann, F., Bader, J., Tschirpke, F., Thamsen, L. and Leser, U. (2023).
How Workflow Engines should talk to Resource Managers: A Proposal for a Common Workflow Scheduling Interface
Int. Conf. on Cluster, Cloud, and Internet Computing (CCGRID), Bangalore, India. - Otto, R., Detjen, K., Pamela, R., Fattohi, M., Grötzinger, C., Rindi, G., Wiedenmann, B., Sers, C. and Leser, U. (2022).
Transcriptomic deconvolution of neuroendocrine neoplasms predicts clinically relevant characteristics
Cancers 15(3) - Ermshaus, Arik, Schäfer, Patrick, Leser, Ulf (2023)
ClaSP - Parameter-free Time Series Segmentation
Data Mining and Knowledge Discovery 37. - de Mecquenem, N. (2023).
Adapting scientific workflows to changing infrastructures.
EDBT PhD Workshop, Ioannina, Greece.
Other
- Ermshaus, A., Schäfer, P., Bagnall, A., Guyet, T., Ifrim, G., Lemaire, V., Leser, U., Leverger, C. and Malinowski, S. (2023).
Human Activity Segmentation Challenge @ ECML/PKDD’23.
8th Workshop on Advanced Analytics and Learning on Temporal Data (AALTD). Turin, Italy. - Schäfer, Patrick, Leser, Ulf (2023).
WEASEL 2.0 - A Random Dilated Dictionary Transform for Fast, Accurate and Memory Constrained Time Series Classification.
arXiv:2301.10194.
2022
Peer-reviewed publications
- Schäfer, P. and Leser, U. (2022)
Motiflets - Simple and Accurate Detection of Motifs in Time Series
PVLDB, Vancouver, Canada. - Peidli, Stefan and Green, Tessa D. and Shen, Ciyue and Gross, Torsten and Min, Joseph and Garda, Samuele and Taylor-King, Jake P. and Marks, Debora S. and Luna, Augustin and Blüthgen, Nils and Sander, Chris (2022)
scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data
Workshop learning meaningful representations of life @NeurIPS. - Weber, L., Sänger, M., Garda, S., Barth, F., Alt, C. and Leser, U. (2022).
Chemical-Protein Relation Extraction with Ensembles of Carefully Tuned Pretrained Language Models
Database 2022. - J.A. Fries+, L. Weber+, N. Seelam+, G. Altay+, D. Datta*, S. Garda*, M. Kang*, R. Su*, W. Kusa*, S. Cahyawijaya*, F. Barth*, S. Ott*, M. Samwald*, S. Bach*, S. Biderman*, M. Sänger*,…, R. Martin, et al. (2022).
BigBio: A Framework for Data-Centric Biomedical Natural Language Processing
Conference on Neural Information Processing Systems (NeurIPS), Datasets and Benchmarks Track.
+ Shared First Author, * Shared Second Author - Bader, J., Lehmann, F., Groth, A., Thamsen, L., Scheinert, D., Will, J., Leser, U. and Kao, O. (2022).
Reshi: Recommending Resources For Scientific Workflow Tasks on Heterogeneous Infrastructures
International Performance Computing and Communications Conference (IPCCC), Michigan, US. - Ermshaus, A., Schäfer, P. and Leser, U. (2022).
Window Size Selection In Unsupervised Time Series Analytics: A Review and Benchmark.
Workshop on Advanced Analytics and Learning on Temporal Data, Grenoble, France. - Münchmeyer, J., Leser, U. and Tilmann, F. (2022).
A probabilistic view on rupture predictability: all earthquakes evolve similarly.
Geophysical Research Letters 49(13). - J.A. Fries*, N. Seelam*, G. Altay*, L. Weber*, M. Kang*, D. Datta*, R. Su*, S. Garda*, B. Wang, S. Ott, M. Samwald, W. Kusa (2022).
Dataset Debt in Biomedical Language Modeling
Workshop on Challenges & Perspectives in Creating Large Language Models.
*:Equal contribution - Hilbrich, M. (2022).
Knowledge Transfer Patterns to Make Disciplinary Knowledge Explicit — Exemplified by HPC
21st Intelligent Software Methodology Tools, and Techniques (SOMET). - Hilbrich, M. and Bountris, V. (2022).
re Workflows a Language to Solve Software Management Challenges? — A ßMACH Based Analysis
21st Intelligent Software Methodology Tools, and Techniques (SOMET). - Garda, S., Lenihan-Geels, F., Proft, S., Hochmuth, S., Schülke, M., Seelow, D. and Leser, U. (2022).
RegEl corpus: Identifying DNA regulatory elements in the scientific literature.
Oxford Database 2022. - Singh, K., Münchmeyer, J., Weber, L., Leser, U. and Annika, B. (2022).
Graph Neural Networks For Learning Molecular Excitation Spectra.
Journal of Chemical Theory and Computation 18(7). - Bader, J., Lehmann, F., Thamsen, L., Will, J., Leser, U. and Kao, O. (2022).
Lotaru: Locally Estimating Runtimes of Scientific Workflow Tasks in Heterogeneous Clusters
Int. Conf. on Statistical and Scientific Database Management, Copenhagen, DK. - Hilbrich, M., Lehmann, F. (2022)
Discussing Microservices: Definitions, Pitfalls, and their Relations
IEEE International Conference on Services Computing, Barcelona, Spain. - Wang, X., Leser, U. and Weber, L. (2022).
BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering
Int. Workshop on Biomedical Language Processing (BioNLP). - Jack Woollam, Jannes Münchmeyer, Frederik Tilmann, Andreas Rietbrock, Dietrich Lange, Thomas Bornstein, Tobias Diehl, Carlo Giunchi, Florian Haslinger, Dario Jozinović, Alberto Michelini, Joachim Saul, Hugo Soto (2022).
SeisBench—A Toolbox for Machine Learning in Seismology
Seismological Research Letters, March 16, 2022 - Foster, W., Ayzel, G., Münchmeyer, J., Rettelbach, T., Kitzmann, N.H., Isson, T.T., Mutti, M., and Aberhan, M. (2022).
Machine learning identifies ecological selectivity patterns across the end-Permian mass extinction
Paleobiology, 1-15. doi:10.1017/pab.2022.1 - Simon, T., Riemer, P., Jarosch, A., Detjen, K., Di Domenico, A., Bormann, F., Menne, A., Khouja, S., Monjé, N., Childs, L. H., Lenze, D. Leser, U. ... Mamlouk, S. and Sers, C. (2022).
DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs)
Genome Medicine 14 (24). - Münchmeyer, J. Woollam, J. Rietbrock, A., Tilmann, D. et al.
Which picker fits my data? A quantitative evaluation of deep learning based seismic pickers
JGR Solid Earth 127(1)
Other
- Muenchmeyer, J., Leser, U. and Tilmann, F. (2022).
A probabilistic view on rupture predictability: all earthquakes evolve similarly
arXiv:2203.08622.
2021
Peer-reviewed publications
- Ferreira da Silva, R., Casanova, H., Chard, K., Altintas, I., Badia, R. M., ... Leser, U., ... (2021)
Community Roadmap for Scientific Workflows Research and Development
Workshop on Workflows in Support of Large-Scale Science (WORKS). St. Louis, US. - Weber, L., Sänger, M., Garda, S., Barth, F., Alt, C. and Leser, U. (2021).
Humboldt @ DrugProt: Chemical-Protein Relation Extraction with Pretrained Transformers and Entity Descriptions
7th International BioCreative Challenge Evaluation. - Hilbrich, M. and Lehmann, F. (2021)
ßMACH - A Software Management Guidance
12th Symposium on Software Performance. - Leser, U., Hilbrich, M., Draxl, C., Eisert, P., Grunske, L., Hostert, P., Kainmüller, D., Kao, O., Kehr, B., Kehrer, T. , Koch, C. , Markl, V., Meyerhenke, H., Rabl, T., Reinefeld, A., Reinert, K., Ritter, K., Scheuermann, B., Schintke, F., Schweikardt, N. and Weidlich, M. (2021)
The Collaborative Research Center FONDA
Datenbank Spektrum 21, 255–260. - Weber, L., Garda, S., Münchmeyer, J. and Leser, U. (2021).
Extend, don’t rebuild: Phrasing conditional graph modification as autoregressive sequence labelling
EMNLP, Punta Cana, Dominican Republic. - Detjen, K. M., Otto, R., Giesecke, Y., Geisler, L., Riemer, P., Jann, H., Grötzinger, C., Sers, C., Pascher, A., Lüdde, T., Leser, U., Wiedenmann, B., Sigal, M., Tacke, F., Roderburg, C. and Hammerich, L. (2021)
Elevated Flt3L predicts long-term survival in patients with high-grade gastroenteropancreatic neuroendocrine neoplasms
Cancers 13(17). - Lehmann, F., Frantz, D., Becker, S., Leser, U. and Hostert, P. (2021).
FORCE on Nextflow: Scalable Analysis of Earth Observation data on Commodity Clusters
1st Int. Workshop on Complex Data Challenges in Earth Observation. - Garda, S., Schwarz, J. M., Schuelke, M., Leser, U. and Seelow, D. (2021).
Public data sources for regulatory genomic features
Medizinische Genetik 33(2). - Ermshaus, A., Leser, U. and Schäfer, P. (2021).
ClaSP - Time Series Segmentation.
Int. Conf. on Information Management (CIKM) - Domaszewska, T. Zyla, K. Otto, R. Kaufmann, S. Weiner, J. (2021)
Gene set enrichment analysis reveals individual variability in host responses in tuberculosis patients.
Frontiers in Immunology, 2021 - Vogt, M., Leser, U. and Akbik, A. (2021).
Early Detection of Sexual Predators in Chats.
ACL-IJCAI. - Saenger, M., Weber, L. and Leser, U. (2021).
WBI at MEDIQA 2021: Summarizing Consumer Health Questions with Generative Transformers
BioNLP - MEDIQA. - Münchmeyer, J., Bindi, D., Leser, U. and Tilmann, F. (2020).
Earthquake magnitude and location estimation from real time seismic waveforms with a transformer network
Geophysical Journal International 226(2). - Kittner, M., Lamping, M., Rieke, D., Götze, J., Bajwa, B., Jelas, I., Rüter, G., Hautow, H., Sänger, M., Habibi, M., Zettwitz, M., de Bortoli, T., Ostermann, L., Ševa, J., Starlinger, J., Kohlbacher, O., Malek, N., Keilholz, U., Leser, U.
Annotation and Initial Evaluation of a Large Annotated German Oncological Corpus.
JAMIA Open 4(2). - Hazel M. Quinn, Regina Vogel, Oliver Popp, Philipp Mertins, Linxiang Lan, Clemens Messerschmidt, Alexandro Landshammer, Kamil Lisek, Sophie Chateau-Joubert, Elisabetta Marangoni, Elle Koren, Yaron Fuchs and Walter Birchmeier
YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer.
Cancer Research DOI: 10.1158/0008-5472.CAN-20-2801 - Weber, L., Sänger, M., Münchmeyer, J., Habibi, M., Leser, U. and Akbik, A. (2020).
HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition.
Bioinformatics 37(17).
Other
- Münchmeyer, J., Bindi, D., Leser, U. and Tilmann, F. (2020).
Earthquake magnitude and location estimation from real time seismic waveforms with a transformer network.
arXiv:2101.02010.
2020
Peer-reviewed publications
- Münchmeyer, J., Bindi, D., Leser, U. and Tilmann, F. (2020).
The transformer earthquake alerting model: A new versatile approach to earthquake early warning.
Geophysical Journal International 225(1). - Reimann, M., Schrezenmeier, J. Richter-Pechanska, P. Dolnik, A., Hick, T.P., Schleich, K. Cai, X. Fan, D., Lohneis, P. Masswig, S., Denker, S., Busse, A., Knittel, G., Flümann, R., Childs, D., Childs, L., Gätjens-Sanchez, A.M., Bullinger, L. Rosenwald, A., Reinhardt, H-C. Schmitt C-A. (2020)
Adaptive T-cell immunity controls senescence-prone MyD88- or CARD11-mutant B-cell lymphomas.
Blood 2020 Nov 24. doi: 10.1182/blood.2020005244. - Habibi, M., Starlinger, J. and Leser, U. (2020).
TabSim: A Siamese Neural Network for Accurate Estimation of Table Similarity.
IEEE Big Data. - Klinghammer K., Politz O., Eder T., Otto R., Raguse J., Albers A., Kaufmann A., Tinhofer I., Hoffmann J., Keller U., Keilholz U (2020).
Combination of copanlisib with cetuximab improves tumor response in cetuximab-resistant patient-derived xenografts of head and neck cancer.
Oncotarget. 2020; 11: 3688-3697 - Xing, W. D., Weber, L. and Leser, U. (2020).
Biomedical Event Extraction as Multi-turn Question Answering.
Int. Workshop on Health Text Mining and Information Analysis. - Saenger, M. and Leser, U. (2020).
Large-scale Entity Representation Learning for Biomedical Relationship Extraction.
Bioinformatics 37(2). - Messerschmidt, C., Obermayer, B., Klinghammer, K., Ochsenreither, S., Treue, D., Stenzinger, A., Glimm, H., Fröhling, S., Kindler, T., Brandts, C.H., Schulze-Osthoff, K., Weichert, W., Tinhofer, I., Klauschen, F., Keilholz, U., Beule, D., Rieke, D.T. (2020).
Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC.
International Journal of Cancer 147(8) - Schleich, K., Kase, J., Dörr, J. R., Trescher, S., Bhattacharya, A., Yu, Y., Wailes, E. M., Fan, D. N. Y., Lohneis, P., Milanovic, M., Lau, A., Lenze, D., Hummel, M., Chapuy, B., Leser, U., Reimann, M., Lee, S., Schmitt, C.A. (2020).
H3K9me3-mediated epigenetic regulation of senescence in 2 mice predicts outcome of lymphoma patients.
Nature Communications 11:3651. - Habibi, M., Starlinger, J. and Leser, U. (2020).
A Permutation Invariant Neural Network for Table Orientation Classification.
Data Mining and Knowledge Discovery. - Schäfer, P. and Leser, U. (2020)
TEASER: Early and Accurate Time Series Classification
Data Mining and Knowledge Discovery, DOI:10.1007/s10618-020-00690-z. - Weber, L., Thobe, K., Lozano, O. A. M., Wolf, J. and Leser, U. (2020).
PEDL: Extracting protein-protein associations using deep language models and distant supervision.
Int. Conf. on Intelligent Systems in Molecular Biology, Bioinformatics 36. - Chondrogiannis, T., Bouros, P., Gamper, J., Leser, U. and Blumenthal, D. B. (2020).
Finding k-Shortest Paths with Limited Overlap.
VLDB Journal 2020:1-25. - Muenchmeyer, J., Bindi, D., Sippl, C., Leser, U. and Tilmann, F. (2020).
Low uncertainty multi-feature magnitude estimation with 3D corrections and boosting tree regression: application to North Chile.
Geophysical Journal International, 220:1.
Other
- J Münchmeyer, D Bindi, U Leser, F Tilmann (2020).
The transformer earthquake alerting model: A new versatile approach to earthquake early warning
arXiv:2009.06316. - Weber, L., Sänger, M., Münchmeyer, J., Habibi, M., Leser, U. and Akbik, A. (2020).
HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition
arXiv:2008.07347. - Simon, T., Mamlouk, S., Riemer, P., Bormann, F., Klinger, B., Menne, A., Teichmann, D., Wanke-Möhr, K., Pacyna-Gengelbach, M., Khouja, S., et al. (2020).
An Integrative Genetic, Epigenetic and Proteomic Characterization of Pancreatic Neuroendocrine Neoplasms (PanNENs) defines Distinct Molecular Features of α- and β-cell like Subgroups
bioRxiv 2020.06.12.146811. - Schiefer, C., Bux, M., Brandt, J., Messerschmidt, C., Reinert, K., Beule, D. and Leser, U. (2020)
Portability of Scientific Workflows in NGS Data Analysis: A Case Study
arXiv:2006.03104
2019
Peer-reviewed publications
- Habibi, M., Rheinlaender, A., Thielemann, W., Adams, R., Fischer, P., Krolkiewicz, S., Wiegandt, D. L. and Leser, U. (2019)
PatSeg: a Sequential Patent Segmentation Approach.
Big Data Research: 100133. - Kulbe, H., Otto, R., Darb-Esfahani, S., Lammert, H., Abubaker, S., Welsch, G., Chekerov, R., Schäfer, R., Dragun, D., Hummel, M., Leser, U., Sehouli, J., and Braicu, E. (2019)
Discovery and validation of novel biomarkers for detection of epithelial ovarian cancer.
Cells 8(7). - Sänger, M., Weber, L., Kittner, M. and Leser, U. (2019).
Classifying German Animal Experiment Summaries with Multi-lingual BERT at CLEF eHealth 2019 Task 1.
CLEF Working Notes. - Weber, L., Münchmeyer, J., Rocktäschel, T., Habibi, M. and Leser, U. (2019).
HUNER: Improving Biomedical NER with Pretraining.
Bioinformatics 36(1). - Trescher, S. and Leser, U. (2019).
Estimation of Transcription Factor Activity in Knockdown Studies.
Nature Scientific Reports 9(1). - Seva, J., Wiegandt, D., Goetze, J., Lamping, M., Rieke, D. T., Schaefer, R., Jähnichen, P., Kittner, M., Pallarz, S., Starlinger, J., Keilholz, Ul., and Leser, U. (2019)
VIST – A Variant-Information Search Tool for Precision Oncology
BMC Bioinformatics 20(1). - Pallarz, S., Benary, M., Lamping, M., Rieke, D., Starlinger, J., Sers, C., Wiegandt, D. L., Seibert, M., Seva, J., Schäfer, R., Keilholz, U., and Leser, U. (2019)
Comparative Analysis of Public Knowledge Bases for Precision Oncology
Journal of Clinical Oncology - Precision Oncology 3. - Witt, C., Von Santen, J. and Leser, U. (2019).
Learning Low-Wastage Memory Allocations for Scientific Workflows at IceCube
Int. Conf. on High Performance Computing & Simulation, Dublin, Ireland. - Witt, C., Wagner, D. and Leser, U. (2019).
Feedback-Based Resource Allocation for Batch Scheduling of Scientific Workflows
Int. Conf. on High Performance Computing & Simulation, Dublin, Ireland. - Weber, L., Minervini, P., Münchmeyer, J., Leser, U. and Rocktäschel, T. (2019).
NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language
ACL, Florence, Italy. - Seva, J., Götze, J., Lamping, M., Rieke, D. T., Schäfer, R. and Leser, U. (2019).
Information Retrieval for Precision Oncology.
German Conference on Business, Technology, and the Web (BTW), Rostock, Germany. - Witt, C., Bux, M., Gusew, W. and Leser, U. (2019).
Predictive Performance Modeling for Distributed Batch Processing using Black-Box Monitoring and Machine Learning.
Information Systems, 82:33-55. - Sprenger, S., Schäfer, P. and Leser, U. (2019).
BB-Tree: A practical and efficient main-memory index structure for multidimensional workloads.
Int. Conf. on Extending Database Technologies (EDBT) Lisbon, Portugal. - Otto, R., Rössler, J.-N., Sers, C., Mamlouk, S. and Leser, U. (2018).
Robust in-silico identification of Cancer Cell Lines based on RNA and targeted DNA sequencing data.
Nature Scientific Reports, 9:367. - Sprenger, S., Schäfer, P. and Leser, U. (2019).
BB-Tree: A main-memory index structure for multidimensional range queries.
Int. Conf. on Data Engineering, Macau, China.
Other
- Schäfer, P. and Leser, U. (2019).
TEASER: Early and Accurate Time Series Classification.
arXiv:1908.03405. - Weber, Leon, Minervini, Pasquale, Münchmeyer, Jannes, Leser, Ulf, Rocktäschel, Tim (2019).
NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language.
arXiv:1906.06187.
2018
Peer-reviewed publications
- Chondrogiannis, T., Bouros, P., Gamper, J., Leser, U. and Blumenthal, D. B. (2018).
Finding k-Dissimilar Paths with Minimum Collective Length.
SIGSPATIAL, Washington, US - Starlinger, J., Pallarz, S., Seva, J., Rieke, D., Sers, C., Keilholz, U. and Leser, U. (2018).
Variant Information Systems for Precision Oncology.
BMC Medical Decision Making. - Witt, C., Wheating, S. and Leser, U. (2018).
LOS: Level Order Sampling for Task Graph Scheduling on Heterogeneous Resources.
Workshop on Workflows in Support of Large-Scale Science, Dallas, US. - Loster, M., Hegner, M., Naumann, F. and Leser, U. (2018).
Dissecting Company Names using Sequence Labeling
LWDA, Mannheim, Germany. - Schäfer, P., and Leser, U. (2018).
Multivariate Time Series Classification with WEASEL+MUSE.
3rd ECML/PKDD Workshop on Advanced Analytics and Learning on Temporal Data, Dublin, Ireland. - Seva, J., Wackerbauer, M. and Leser, U. (2018).
Identifying Key Sentences for Precision Oncology Using Semi-Supervised Learning.
BioNLP, Melbourne, Australia. - Sprenger, S., Schäfer, P. and Leser, U. (2018).
Multidimensional Range Queries on Modern Hardware.
Int. Conf. on Scientific and Statistical Database Management, Bozen, Italy. - Fier, F., Augsten, N., Bouros, P., Leser, U. and Freytag , J.-C. (2018).
Set Similarity Joins on MapReduce: An Experimental Survey.
Int. Conf. on Very Large Databases, Rio de Janeiro, Brazil. - Wandelt, S., Sun, X. and Leser, U. (2018).
Column-wise compression of open relational data.
Information Sciences. - Roller, R., Kittner, M., Weissenborn, D. and Leser, U. (2018).
Cross-lingual Candidate Search for Biomedical Concept Normalization.
Int. Workshop on Multilingual Biomedical Text Processing, Tokyo, Japan. - Krause, T., Leser, U., Luedeling, A. and Druskat, S. (2018).
Designing a Re-Usable and Embeddable Corpus Search Library.
Workshop on the Challenges in the Management of Large Corpora, Miyazaki, Japan. - Sprenger, S., Zeuch, S. and Leser, U. (2018).
Exploiting automatic vectorization to employ SPMD on SIMD registers.
Joint Workshop of HardBD and Active, Paris, France. - Becker S, Szyska M, Mensen A, Hocke A, Hellwig K, Otto R, Olfe L, Vuong L, Tietze-Bürger C, Dörner T, Dörken B, Scheibenbogen C, Schröder J, Arnold R and Na I. (2017).
A comparative analysis of human bone marrow-resident and peripheral memory B cells.
Journal of Allergy and Clinical Immunology, doi: 10.1016/j.jaci.2017.12.983. - Schäfer, P., Pflugmacher, D., Hostert, P. and Leser, U. (2018).
Classifying land cover from satellite images using time series analytics.
2nd Int. Workshop on Data Analytics Solutions for Real-Life Applications, Vienna, Austria.
Other
- Chondrogiannis, T., Bouros, P., Gamper, J., Leser, U. and Blumenthal, D. B. (2018).
Finding k-Dissimilar Paths with Minimum Collective Length.
arXiv:1809.06831. - Sprenger, S., Schäfer, P. and Leser, U. (2018).
Multidimensional Range Queries on Modern Hardware.
arXiv:1801.03644.
2017
Peer-reviewed publications
- Schäfer, P. and Leser, U. (2017).
Fast and Accurate Time Series Classification with WEASEL.
In Proceedings of the 2017 ACM on Conference on Information and Knowledge Management (CIKM '17) - Brandt, J., Reisig, W. and Leser, U. (2017).
Computation Semantics of the Functional Scientific Workflow Language Cuneiform.
Journal of Functional Programming 27. - Ševa, J., Kittner, M., Roller, R. and Leser, U. (2017).
Multi-lingual ICD-10 coding using a hybrid rule-based and supervised classification approach at CLEF eHealth 2017.
CLEF Working Papers. - Kougka, G., Gounaris, A. and Leser, U. (2017).
Modeling Data Flow Execution in a Parallel Environment.
DaWaK, Lyon, France. - Klinghammer, K., Otto, R., Raguse, J.-D., Albers, A. E., Tinhofer, I., Fichtner, I., Leser, U., Keilholz, U. and Hoffmann, J. (2017).
Basal subtype is predictive for response to cetuximab treatment in patient derived xenografts of squamous cell head and neck cancer.
Int. Journal of Cancer, 141(6). - Kittner, M., Bajwa, B., Rieke, D., Lamping, M., Starlinger, J. and Leser, U. (2017).
Design of an Information Extraction Pipeline for German Clinical Texts.
Workshop on Extraction and Processing of Rich Semantics from Medical Texts. - Habibi, M., Weber, L., Neves, M., Wiegandt, D. L. and Leser, U. (2017).
Deep Learning with Word Embeddings improves Biomedical Named Entity Recognition.
Bioinformatics, 33(14); special issue of ISMB/ECCB, Prague, Czech. - Rheinländer, A., Leser, U. and Graefe, G. (2017).
Optimization of Complex Data Flows with User-Defined Functions.
ACM Computing Surveys, 50(3). - Sänger, M., Leser, U. and Klinger, R. (2017).
Fine-grained Opinion Mining from Mobile App Reviews with Word Embedding Features.
Int. Conf. on Natural Language & Information Systems, Liege, Belgium. - Trescher, S., Münchmeyer, Y. and Leser, U. (2017).
Estimating Genome-Wide Regulatory Activity from Multi-Omics Data Sets using Mathematical Optimization.
BMC Systems Biology, 11:41. - Otto, R., Sers, C. and Leser, U. (2017).
Robust In-Silico identification of Cancer Cell Lines based on Next Generation Sequencing.
OncoTarget, 8(21):34310-34320. - Mamlouk, S., Childs, L. H., Aust, D., Heim, D., Melching, F., Oliveira, C., Wol, T., Durek, P., Schumacher, D., Bläker, H., von Winterfeld, M Gastl, B, Möhr, K, Menne, A, Zeugner, S, Redmer, T, Lenze, D, Tierling, S, Möbs, M, Weichert, W, Folprecht, G, Blanc, E, Beule, D, Schäfer, R, Morkel, M Klauschen, F, Leser, U, Sers, C (2017).
DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer
Nature communications 8:14093 - Bux, M., Brandt, J., Witt, C., Dowling, J. and Leser, U. (2017).
Hi-WAY: Execution of Scientific Workflows on Hadoop YARN
Int. Conf. on Extending Database Technology, Venice, Italy. - Chondrogiannis, T., Bouros, P., Gamper, J. and Leser, U. (2017).
Exact and Approximate Algorithms for Finding k-Shortest Paths with Limited Overlap.
Int. Conf. on Extending Database Technologies (EDBT), Venice, Italy. - Krause, T., Leser, U. and Lüdeling, A. (2017).
graphANNIS: A Fast Query Engine for Deeply Annotated Linguistic Corpora.
Language Technology and Computational Linguistics 31. - Schäfer, P. and Leser, U. (2017).
Scalability of Univariate Time Series Classifiers.
BTW, Stuttgart, Germany
Other
- Schäfer, P. and Leser, U. (2017).
Multivariate Time Series Classification with WEASEL+MUSE.
arXiv:1711.11343. - Schäfer, P. and Leser, U. (2017).
Fast and Accurate Time Series Classification with WEASEL
arXiv:1701.07681
2016
Peer-reviewed publications
- Habibi, M. Wiegandt, D. L., Schmedding, F. and Leser, U. (2016).
Recognizing Chemicals in Patents - A Comparative Analysis.
Journal of Cheminformatics 8:59. - Starlinger, J., Kittner, M., Blankenstein, O. and Leser, U. (2016).
How to improve information extraction from German medical records/a>
it - Information Technology. - Sprenger, S., Zeuch, S. and Leser, U. (2016).
Cache-Sensitive Skip List: Efficient Range Queries on modern CPUs
ADMS-IMDM workshops, New Delhi, India. - Wiegandt, D., Starlinger, J. and Leser, U. (2016).
Graph n-grams for Scientific Workflow Similarity Search
LWDA, Potsdam, Germany. - Habibi, M., Wiegandt, D. L., Schmedding, F. and Leser, U. (2016).
Performance of Gene Name Recognition Tools on Patents
Semantic Mining in Biomedicine, Potsdam, Germany. - Heinemann, F., Huber, T., Meisel, C., Bundschus, M. and Leser, U. (2016).
Reflection of successful anti-cancer drug development processes in the literature.
Drug Discovery Today 21(11): 1740–1744. - Lichtblau, Y., Zimmermann, K., Haldemann, B., Lenze, D., Hummel, M. and Leser, U. (2016).
Comparative assessment of differential network analysis methods.
Briefings in Bioinformatics bbw061. - Kunkel, A., Rheinländer, A., Schiefer, C., Helmer, S., Bouros, P., and Leser, U. (2016).
PIEJoin: Towards Parallel Set Containment Joins.
SSDBM, Budapest, Hungary. - Childs, L., Mamlouk, S., Brandt, J., Sers, C. and Leser, U. (2016).
SoFIA: A Data Integration Framework for Annotating High-Throughput Data Sets.
Bioinformatics 32(17): 2590-2597. - Thomas, P., J. Hakenberg, T. Rocktäschel, Y. Lichtblau and U. Leser (2016).
SETH detects and normalizes genetic variants in text.
Bioinformatics 32(18): 2883-2885. - Rheinländer, A., Lehmann, M., Kunkel, A., Meier, J. and Leser, U. (2016).
Potential and Pitfalls of Domain-Specific Information Extraction at Web Scale.
SIGMOD, San Francisco, USA. - Jargosch, M., S. Kroeger, E. Gralinska, U. Klotz, Z. Fang, W. Chen, U. Leser, J. Selbig, D. Groth and R. Baumgrass (2016).
Data integration for identification of important transcription of STAT6-mediated cell fate decisions.
Genetics and Molecular Research, 15(2). - Sänger, M., U. Leser, S. Kemmerer, P. Adolphs and R. Klinger (2016).
SCARE – The Sentiment Corpus of App Reviews with Fine-grained Annotations in German
LREC, Portoroz, Slovenia. - Gohlke, B.-O., J. Nickel, R. Otto, M. Dunkel and R. Preissner (2016).
CancerResource—updated database of cancer-relevant proteins, mutations and interacting drugs.
Nucleic Acid Research, 44(D1):D932-7. - Hakenberg, J., W.-Y. Cheng, P. Thomas, Y.-C. Wang, A. V. Uzilov and R. Chen (2016).
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.
BMC Bioinformatics, 17:24. - Sips, M., Witt, C., Rawald, T. and Marwan, N. (2016).
Torwards Visual Analytics for the Exploration of Large Sets of Time Series.
Recurrence Plots and Their Quantifications: Expanding Horizons (pp. 3-17). Springer International Publishing.
2015
Peer-reviewed publications
- Wandelt, S. and U. Leser (2015).
Sequence factorization with multiple references.
PLOS ONE, 10(9):e0139000. - P. Köthur, C. Witt, M. Sips, N. Marwan, S. Schinkel, and D. Dransch (2015).
Visual Analytics for Correlation-Based Comparison of Time Series Ensembles.
Comput. Graph. Forum 34(3): 411-420 - Chondrogiannis, T., P. Bouros, J. Gamper and U. Leser (2015).
Alternative Routing: k-Shortest Paths with Limited Overlap.
SIGSPATIAL, Seattle, Washington, USA. - Bessani, A., J. Brandt, M. Bux, V. Cogo, L. Dimitrova, J. Dowling, A. Gholami, K. Hakimzadeh, M. Hummel, M. Ismail, E. Laure, U. Leser, J.-E. Litton, R. Martinez, S. Niazi, J. Reichel and K. Zimmermann (2015).
BiobankCloud: a Platform for the Secure Sorage, Sharing, and Processing of Large Biomedical Data Sets.
1st Int. Workshop on Data Management and Analytics for Medicine and Healthcare, Hawaii, US.. - Taliun, D., J. Gamper, U. Leser and C. Pattaro (2015).
Fast Sampling-based Whole-Genome Haplotype Block Recognition
Transactions on Computational Biology and Bioinformatics, 13(2):315-25. - Starlinger, J., S. Cohen-Boulakia, S. Khannac, S. B. Davidson and U. Leser (2015).
Effective and Efficient Similarity Search in Scientific Workflow Repositories
Future Generation Computer Systems, 56, pp 584–594. - Alves, F., V. Cogo, S. Wandelt, U. Leser and A. N. Bessani (2015).
On-Demand Indexing for Referential Compression of DNA Sequences.
PLOS ONE, 10(7) - Bux, M., J. Brandt, C. Lipka, K. Hakimzadeh, J. Dowling and U. Leser (2015).
SAASFEE: Scalable Scientific Workflow Execution Engine.
PVLDB, Hawaii, US. - Rheinländer, A., Heise, A., Hueske, F., Leser, U., and Naumann, F. (2015).
SOFA: An Extensible Logical Optimizer for UDF-heavy Data Flows
Information Systems 52:96-125. - Lehmann, R., Childs, L., Thomas, P., Abreu, M., Fuhr, L., Herzel, H., Leser, U. and Relógio, A. (2015).
Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach.
PLOS ONE 10(5). - Zimmermann, K., Jentsch, M., Rasche, A., Hummel, M. and Leser, U. (2015).
Algorithms for differential splicing detection using exon arrays: a comparative assessment
BMC Genomics 16:136. - Rawald, T., Sips, M., Marwan, N. and Leser, U. (2015).
Massively Parallel Analysis of Similarity Matrices on Heterogeneous Hardware
Int. Workshop on Data (Co-)Processing on Heterogeneous Hardware (DAPHNE). - Brandt, J., Bux, M. and Leser, U. (2015).
Cuneiform -- A Functional Language for Large Scale Scientific Data Analysis
EDBT Workshop Beyond Map&Reduce, Bruessels, Belgium. - Thomas, P., Durek, P., Solt, I., Klinger, B., Witzel, F., Schulthess, P., Mayer, Y., Tikk, D., Blüthgen, N. and Leser, U. (2015).
Computer-assisted curation of a human regulatory core network from the biological literature.
Bioinformatics 31(8): 1258-1266. - Neves, M. and U. Leser (2015).
Question Answering for Biology
Methods 74:36–46.
2014
Peer-reviewed publications
- Bégay, V., Smink, J. J., Loddenkemper, C., Zimmermann, K., Rudolph, C., Scheller, M., Steinemann, D., Leser, U., Schlegelberger, B., Stein, H., et al. (2014).
Deregulation of the endogenous C/EBPβ LIP isoform predisposes to tumorigenesis
Journal of Molecular Medicine, Nov 2014. - Wandelt, S. and U. Leser (2014).
MRCSI: Compressing and Searching String Collections with Multiple References
PVLDB, Kona, Hawaii, US. - Wandelt, S. and Sun, X. (2014).
Efficient Compression of 4D-Trajectory Data in Air Traffic Management.
IEEE Transactions on Intelligent Transportation Systems, 16(2). - Bux, M. and Leser, U. (2014).
DynamicCloudSim: Simulating Heterogeneity in Computational Clouds.
Future Generation Computer Systems 46:85-99. - Starlinger, J., Cohen-Boulakia, S., Khanna, S., Davidson, S. B. and Leser, U. (2014).
Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity.
eScience, Guarujá, Brazil. - Bölling, C., Weidlich, M., Holzhütter, H. (2014)
SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.
Journal of Biomedical Semantics, 5(Suppl 1):S1. - Starlinger, J., Brancotte, B., Cohen-Boulakia, S. and Leser, U. (2014)
Similarity Search for Scientific Workflows.
PVLDB, Hangzhou, China. - Alexandrov, A., Bergmann, R., Ewen, S., Freytag, J.-C., Hueske, F., Heise, A., Kao, O., Leich, M., Leser, U., Markl, V., Naumann, F., Peters, M., Rheinländer, A., Sax, M., Schelter, S., Höger, M., Tzoumas, K., Warneke, D. (2014)
The Stratosphere Platform for Big Data Analytics.
VLDB Journal, 23(6):939-964. - Wandelt, S. and Leser, U. (2014)
RRCA: Ultra-fast Multiple In-Species Genome Alignments
Int. Conf. on Algorithms for Computational Biology, Barcelona, Spain. - Relógio, A., Thomas, P., Medina-Pérez, P., Reischl, S., Bervoets, S., Gloc, E., Riemer, P., Mang-Fatehi, S., Maier, B., Schaefer, R., Leser, U., Herzel, HP., Kramer, A., Sers, C. (2014)
Ras – mediated deregulation of the circadian clock in cancer.
PLoS Genetics. - Döhling, L., Lewandowski, J. and Leser, U. (2014)
A Study in Domain-Independent Information Extraction for Disaster Management.
Workshop on Disaster Management and Principled Large-scale information Extraction, Reijkjavik, Island. - Wandelt, S., Deng, D., Gerdjikov, S., Mishra, S., Mitankin, P., Patil, M., Siragusa, E., Tiskin, A., Wang, W., Wang, J., Leser, U. (2014)
State-of-the-art in String Similarity Search and Join.
SIGMOD Record 43(1). - Rheinländer, A., Beckmann, M., Kunkel, A., Heise, A., Stoltmann, T. and Leser, U. (2014)
Versatile optimization of UDF-heavy data flows with Sofa (Demo)
SIGMOD, Snowbird, USA. - Döhling, L. and Leser, U. (2014)
Extracting and Aggregating Temporal Events from Text.
4th Temporal Web Analytics Workshop, Seoul, Korea.
2013
Peer-reviewed publications
- Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J., Mah, N., Neves, M., Andrade-Navarro, M., Leser, U. and Kurtz, A. (2013)
CellFinder: A Cell Data Repository.
Nucleic Acids Research 2013. - Huber, T., Rocktäschel, T., Weidlich, M., Thomas, P. and Leser, U. (2013)
Extended Feature Set for Chemical Named Entity Recognition and Indexing
Biocreative IV. Bethesda, MD, USA. - Scheller, M., Schönheit, J., Zimmermann, K., Leser, U., Rosenbauer, F. and Leutz, A. (2013)
Crosstalk between Wnt/β-catenin and Irf8 in leukemia progression and drug resistance.
Journal of Experimental Medicine, 210(11):2239-2256 . - Wandelt, S. and Leser, U. (2013)
FRESCO: Referential Compression of Highly-Similar sequences
Transactions on Computational Biology and Bioinformatics 10(5): 1275-1288. - Sacharidis, D. and Bouros, P. (2013)
Routing Directions: Keeping it Fast and Simple
International Conference on Advances in Geographic Information Systems (SIGSPATIAL'13), Orlando, Florida, USA. - Jansen, L., Fuellen, G., Leser, U. and Kurtz, A. (2013)
Using Ontologies to Study Cell Transitions
Journal of Biomedical Semantics, 4:25. - Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J.-F., Nguyen-Dobinsky, T.-N., Leser, U. and Kurtz, A. (2013)
CELDA - An Ontology for the Comprehensive Representation of Cells in Complex Systems.
BMC Bioinformatics vol 14. - Wandelt, S., Starlinger, J., Bux, M. and Leser, U. (2013)
RCSI: Scalable similarity search in thousand(s) of genomes
PVLDB, Hangzhou, China. - Wandelt, S. and Leser, U. (2013)
QGramProjector: Q-gram projection for indexing highly-similar strings.
Advances in Databases and Information Systems, Genoa, Italy. - Wandelt, S., Bux , M. and Leser, U. (2013)
Trends in Genome Compression.
Current Bioinformatics, 9(3). - Thomas, P. and Leser, U. (2013)
HistoNer: Histone modification extraction from text
BioLINK Special Interest Group, in conjunction with ISBM/ECCB 2013 Conference, Berlin, Germany. - Jacob, C., Thomas, P. and Leser, U. (2013)
Comprehensive Benchmark of Gene Ontology Concept Recognition tools
BioLINK Special Interest Group, in conjunction with ISBM/ECCB 2013 Conference, Berlin, Germany. - Bux, M. and Leser, U. (2013)
DynamicCloudSim: Simulating Heterogeneity in Computational Clouds.
Int. Workshop on Scalable Workflow Enactment Engines and Technologies (SWEET'13), in conjunction with ACM SIGMOD Conference, New York, USA. - Stoltmann, T., Zimmermann, K., Koschmieder, A. and Leser, U. (2013)
OmixAnalyzer - A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets.
Int. Conf. on Data Integration for the Life Sciences (DILS). - Rocktäschel, T., Huber, T., Weidlich, M. and Leser, U. (2013).
WBI-NER: The impact of domain-specific features on the performance of identifying and classifying mentions of drugs.
DDI Challenge at Semeval.
Ranked first in competition - Thomas, P., Neves, M., Rocktäschel, T. and Leser, U. (2013).
WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting.
DDI Challenge at Semeval.Ranked second in competition - Neves, M., Damaschun, A., Mah, N., Lekschas, F., Seltmann, S., Stachelscheid, H., Fontaine, J.-F., Kurtz, A. and Leser, U. (2013).
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts
Database (Oxford) Vol. 2013, Article ID bat020. - Tikk, D., Solt, I., Thomas, P. and Leser, U. (2013).
A Detailed Error Analysis of 13 Kernel Methods for Protein-Protein Interaction Extraction.
Supp Material: Instance based difficulty levels
BMC Bioinformatics vol. 14. - Leich, M., Adamek, J., Schubotz, M., Heise, A., Rheinländer, A. and Markl , V. (2013).
Applying Stratosphere for Big Data Analytics
15. GI-Fachtagung Datenbanksysteme für Business, Technologie und Web (BTW), March 11 - 15, 2013, Magdeburg, Germany. - Thomas, P., Starlinger, J. and Leser, U. (2013).
Experiences from Developing the Domain-Specific Entity Search Engine GeneView
BTW, Magdeburg, Germany. - Pirk, H., Funke, F., Grund, M., Neumann, T., Leser, U., Manegold, S., Kemper, A. and Kersten, M.
CPU and Cache Efficient Management of Memory-Resident Databases.
Int. Conf. on Data Engineering, Brisbane, Australia
Ranked first in competitionOther
- Astrid Rheinländer, Arvid Heise, Fabian Hueske, Ulf Leser, Felix Naumann
SOFA: An Extensible Logical Optimizer for UDF-heavy Dataflows.
Technical Report CoRR/arXiv:1311.6335 - Marc Bux, Ulf Leser
Parallelization in Scientific Workflow Management Systems.
Technical Report CoRR/arXiv:1303.7195
2012
Peer-reviewed publications
- Neves, M. and Leser, U.
A Survey on Annotation Tools for the Biomedical Literature.
Briefings in Bioinformatics, 14(4). - Wandelt, S. and Leser, U.
Adaptive efficient compression of genomes.
Algorithms for Molecular Biology 7(30), 2012 - Wandelt, S. and Leser, U.
String Searching in Referentially Compressed Genomes.
Int. Conf. on Knowledge Discovery and Information Retrieval, Barcelona, Spain.Best Paper Award - Leser, U. and Liebermeister, W.
Knowledge Management for Systems Biology.
In Dubitzky, W., Wolkenhauer, O., Cho, K.-H. and Yokota, H. (ed). Book "Encyclopedia of Systems Biology". - Jansen, L., Fuellen, G., Leser, U. and Kurtz, A. (2012)
Using Ontologies to Study Cell Transitions.
Int. Workshop on Ontologies in Biomedicine and Life Sciences, Dresden, Germany. - Joosten, M., Seitz, V., Zimmermann, K., Sommerfeld, A., Berg, E., Lenze, D., Leser, U., Stein, H. and Hummel, M.
Histone acetylation and DNA demethylation of T-cells result in an anaplastic large cell lymphoma-like phenotype.
Haematologica 98(2). - Bauckmann, J., Abedjan, Z., Müller, H., Leser, U. and Naumann, F. (2012)
Discovering Conditional Inclusion Dependencies
Int. Conf. on Information and Knowledge Management, Hawaii. - Wandelt, S., Rheinländer, A., Bux, M., Thalheim, L., Haldemann, B. and Leser, U.
Data Management Challenges in Next Generation Sequencing
Datenbank-Spektrum 12(3). - Heise, A., Rheinländer, A., Leich, M., Naumann, F., and Leser, U.
Meteor/Sopremo: An Extensible Query Language and Operator Model.
Int. Workshop on End-to-end Management of Big Data, in conjunction with VLDB, Istanbul, Turkey, 2012. - Thomas, P., Starlinger, J., Vowinkel, A., Arzt, S. and Leser, U.
GeneView: A comprehensive semantic search engine for PubMed.
Nucl. Acids Res. 40 (W1): W585-W591, 2012. - Hueske, F., Peters, M., Sax, M.J., Rheinländer, A., Bergmann, R., Krettek, A., and Tzoumas, K.
Opening the Black Boxes in Dataflow Optimization.
38th Int. Conf. on Very Large Data Bases (VLDB), Istanbul, Turkey, 2012. - Koschmieder, A. and Leser, U.
Regular Path Queries on Large Graphs
International Conference on Scientific and Statistical Database Management (SSDBM) 2012. - Boelling, C., Dumontier, M., Weidlich, M. and Holzhütter, H.
Role-based representation and inference of biochemical processes
International Conference on Biomedical Ontology. - Rocktäschel, T., Weidlich, M. and Leser, U..
ChemSpot: A Hybrid System for Chemical Named Entity Recognitions
Bioinformatics 28 (12): 1633-1640, 2012 - Trissl, S., Hussels, P. and Leser, U.
InterOnto - Ranking Inter-Ontology Links
Int. Conf. on Data Integration for the Life Sciences, Washington, USA, 2012 - Starlinger, J., Cohen-Boulakia, S. and Leser, U.
(Re)Use in Public Scientific Workflow Repositories
Int. Conf. on Scientific and Statistical Database Management, Chania, Greece, 2012 - Fenz, D., Lange, D., Rheinländer, A., Naumann, F. and Leser, U.
Efficient Similarity Search in a Very Large String Sets
Int. Conf. on Scientific and Statistical Database Management, Chania, Greece, 2012 - Thomas, P., Bobić, T., Leser, U., Hofmann-Apitius, M. and Klinger, R.
Weakly Labeled Corpora as Silver Standard for Drug-Drug and Protein-Protein Interaction.
In Proceedings of the Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM) on Language Resources and Evaluation Conference (LREC), Istanbul, Turkey. 2012 - Neves, M., Damaschun, A., Kurtz, A. and Leser, U.
Annotating and evaluating text for stem cell research.
Workshop on Building and Evaluating Resources for Biomedical Text Mining, Istanbul, Turkey. 2012 - Bobic, T., Klinger, R., Thomas, P., and Hofmann-Apitius, M.
Improving Distantly Supervised Extraction of Drug-Drug and Protein-Protein Interactions.
In Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning (ROBUS-UNSUP) on European Conference of the Association for Computational Linguistics (EACL), Avignon, France. 2012 - Müller, H., Freytag, J.-C. and Leser, U.
Improving Data Quality by Source Analysis.
ACM Journal of Data and Information Quality Volume 2 Issue 4, February 2012
Other
- Bauckmann, J., Abedjan, Z., Leser, U., Müller, H. and Naumann, F.
Covering or Complete? Discovering Conditional Inclusion Dependencies.
Technical Report 62, Hasso-Plattner-Institut Potsdam. - Koschmieder, A. and Leser, U.
Regular Path Queries on Large Graphs.
Technical Report No 240, Department of Computer Science, Humboldt-Universität zu Berlin.
2011
Peer-reviewed publications
- Döhling, L. and Leser, U. (2011).
EquatorNLP: Pattern-based Information Extraction for Disaster Response
In Proceedings of Terra Cognita 2011 Workshop, Bonn, Germany. - Thomas, P., Solt, I., Klinger, R. and Leser, U. (2011).
Learning Protein Protein Interaction Extraction using Distant Supervision
In Proceedings of Robust Unsupervised and Semi-Supervised Methods in Natural Language Processing 2011, Hissar, Bulgaria - Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., Nenadic, G. and Bergman, C. (2011).
The GNAT library for local and remote gene mention normalization
Bioinformatics 27(19): 2769-2771. - Rheinländer, A. and Leser, U. (2011).
Scalable Sequence Similarity Search and Join in Main Memory on Multi-Cores
2nd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Bordeaux, France. - Thomas, P., Neves, M. L., Solt, I., Tikk, D. and Leser, U. (2011).
Relation Extraction for Drug-Drug Interactions using Ensemble Learning
DDIExtraction Workshop, SpainRanked First in the DDI challenge - Cohen-Boulakia, S. and Leser, U. (2011).
Search, Adapt, and Reuse: The Future of Scientific Workflows
SIGMOD Record 40(2) - Arighi, C.N., Roberts, P., Agarwal, S., Bhattacharya, S., Cesareni, G., Chatr-aryamontri, A., Clematide, S., Gaudet, P., Giglio, M.G., Harrow, I., Huala, E., Krallinger, M., Leser, U., Li, D., Liu, F., Lu, Z., Maltais, L., Okazaki, N., Perfetto, L., Rinaldi, F., Sætre, R., Salgado, D., Srinivasan, P., Thomas, P.E., Toldo, L., Hirschman L., and Wu, C.H (2011).
BioCreative III Interactive Task: an Overview
BMC Bioinformatics, 12(Suppl 8):S8. - Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011).
PiPa: Custom Integration of Protein Interactions and Pathways
GI-Jahrestagung 2011, Workshop "Daten In den Lebenswissenschaften". - Groth, P., Leser, U. and Weiss, B. (2011).
Phenotype Mining for Functional Genomics and Gene Discovery.
In Yu, B. and Hinchcliffe, M. (ed). Book "In Silico Tools for Gene Discovery", Springer. - Thomas, P., Klinger, R., Furlong, L., Hofmann-Apitius, M. and Friedrich, C. (2011).
Challenges in the Association of Human Variation Names with Unique Database Identifier
BMC Bioinformatics 2011, 12(Suppl 4):S4. - Thomas, P., Pietschmann, S., Solt, I., Tikk, D. and Leser, U. (2011).
Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text
BioNLP 2011, Portland US - Seitz, V., Thomas, P., Zimmermann, K., Paul, U., Ehlers, A., Joosten, M., Dimitrova, L., Lenze, D., Sommerfeld, A., Oker, E., Leser, U., Stein, H., and Hummel, M. (2011).
Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation
Hematologica , 96(6):863-70. - Koschmieder, A., Zimmermann, K., Trißl, S., Stoltmann, T. and Leser, U.
Tools for Managing and Analyzing Microarray Data
Briefings in Bioinformatics 2012 13: 46-60. - Jaeger, S., Sers, C. and Leser, U. (2011).
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
BMC Genomics 2010, 11:717. - Cohen-Boulakia, S. and Leser, U. (2011).
Next Generation Data Integration for the Life Sciences (Tutorial)
Int. Conf. on Data Engineering, Hannover, Germany.
Other
- Starlinger, J., Schmeck, B. and Leser, U.
Challenges in Automatic Diagnosis Extraction from Medical Examination Summaries
CIKM 2011, Workshop on Web Science and Information Exchange in the Medical Web. - Döhling, L., Woith, H., Fahland, D. and Leser, U.
Equator: Faster Decision Making for Geoscientists
GI-Jahrestagung 2011, Workshop "Workshop zur IT-Unterstützung von Rettungskräften".
2010
Peer-reviewed publications
- Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG.
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Molecular System Biology, 2010. - Castillo, R., Rothe, C. and Leser, U.
RDFMatView: Indexing RDF Data using Materialized SPARQL Queries
6th Int. WS on Scalable Semantic Web Knowledge Bases, Shanghai, China. - Ngyuen, L. Q., Tikk, D. and Leser, U.
Simple Tricks for Improving Pattern-Based Information Extraction from the Biomedical Literature
Journal of Biomedical Semantics. - Jaeger, S., Ertaylan, G., van Dijk, D., Leser, U. and Sloot, P. M.
Inference of Surface Membrane Factors of HIV-1 Infection through Functional Interaction Networks
PLoS ONE 5(10): e13139, 2010. - Roger Castillo
RDFMatView: Indexing RDF Data for SPARQL Queries.
International Semantic Web Conference 2010, Doctoral Consortium, Shanghai, China. - Rheinländer, A., and Leser, U.
Fast Similarity Search and Similarity Join in Oracle DB.
In Proceedings of DOAG'10, Nürnberg, 2010. - Domonkos Tikk, Illés Solt
Improving textual medication extraction using combined conditional random fields and rule-based systems
Journal of the American Medical Informatics Association 2010;17:540-544. - Trissl, S. and U. Leser
Estimating Result Size and Execution Times for Graph Queries
Workshop on Querying Graph Structured Data, Novi Sad, Serbia. - Kabisch, T., Dragut, E., Yu, C. and Leser, U.
Deep Web Integration with VisQI
Int. Conf. on Very Large Databases, Singapore. - Groth, P., Kalev, I., Kirov, I., Traikov, B., Leser, U. and Weiss, B.
Phenoclustering: Online mining of cross-species phenotypes
Bioinformatics, 26(15): p. 1924-1925 - Senger, C., Seidling, H. M., Quinzler, R., Leser, U. and Haefeli, W. E.
Design and evaluation of an ontology-based drug application database
Methods of Information in Medicine 49(6) - Roger Castillo, Ulf Leser
Selecting Materialized Views for RDF Data
2nd Int. Workshop on Semantic Web Information Management, Vienna, AustriaSelected as one of two best papers - Tikk, D., Thomas, P., Palaga, P., Hakenberg, J. and Leser, U.
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
PLOS Computational Biology, 6(7) - Illés Solt, Domonkos Tikk, Ulf Leser
Species identification for gene name normalization
Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium - Domonkos Tikk, Peter Palaga, Ulf Leser
A fast and effective dependency graph kernel for PPI relation extraction
Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium - André Koschmieder
Cost-Based Optimization of Regular Path Queries on Large Graphs
Grundlagen von Datenbanken, Bad Helmstedt, Germany - Rheinländer, A., Knobloch, M., Hochmuth, N. and Leser, U.
Prefix Tree Indexing for Similarity Search and Similarity Join on Genomic Data
Int. Conf. on Statistical and Scientific Databases, Heideberg, Germany - Brauer, F., Huber, M., Hackenbroich, G., Leser, U., Naumann, F. and Barczynski, W.
Graph-Based Concept Identification and Disambiguation for Enterprise Search
19th Int. World Wide Web Conference, Raleigh, US - Hakenberg, J., Solt, I., Tikk, D., Nguyen, V. H., Tari, L., Nguyen, Q. L., Baral, C. and Leser, U.
Molecular event extraction from Link Grammar parse trees
Int. Journal of Computational Intelligence 7(4): 665-680. - Ferenc P. Szidarovszky, Illes Solt, Domonkos Tikk
A Simple Ensemble Method for Hedge Identification
Proceedings of the Fourteenth Conference on Computational Natural Language Learning: Shared Task, Uppsala, Sweden, 15-16 July 2010
Other
- Freytag, J.-C., Kao, O., Leser, U., Markl, V., and Naumann, F.
Stratosphere - Informationsmanagement 'above the cloud'
Datenbank Spektrum. - Solt, I., Gerner, M., Thomas, P., Nenadic, G., Bergman, C. M., Leser, U. and Hakenberg, J.
Gene mention normalization in full texts using GNAT and LINNAEUS.
Proceedings of BioCreative III, Bethesda, USA, 2010. pp 137-142. - Thomas, P., Starlinger, J., Jacob, C., Solt, I., Hakenberg, J. and Leser, U.
GeneView Gene-Centric Ranking of Biomedical Text
Proceedings of BioCreative III, Bethesda, USA, 2010. pp 137-142. - Lakes, T., Leser, U. and Senf, C.
An urban health risk analysis for Berlin: exploration and integration of spatio-temporal information on the urban environment.
EnvironInfo 2010, Bonn, Germany. - Karin Zimmermann and Ulf Leser
Analysis of Affymetrix Exon Arrays.
Technical Report 235, Department for Computer Science, Humboldt-Universität zu Berlin - Bauckmann, J., Leser, U. and Naumann, F.
Efficient and exact computation of inclusion dependencies for data integration
Technical Report 34. Hasso-Plattner-Institiut Potsdam - Philip Groth, Bertram Weiss, Ulf Leser
Ontologies improve cross-species phenotype analysis (Extended Version)
Meeting of the Special Interest Group on Bio-Ontologies, Boston, US - Philippe Thomas, Domonkos Tikk, Ulf Leser
A fair benchmark of kernel methods for PPI extraction
Workshop on Advances in Bio Text Mining (BioTM 2010), Ghent, Belgium - Roger Castillo, Christian Rothe, and Ulf Leser
RDFMatView: Indexing RDF Data for SPARQL Queries.
Technical Report No 234, Department for Computer Science, Humboldt-Universität zu Berlin
2009
Peer-reviewed publications
- Böhm C and Leser U
Graph-Based Ontology Construction from Heterogeneous Evidences
Int. Semantic Web Conference, Washington, USSelected as ISWC-Spotlight paper - Dragut E, Kabisch T, Leser U, Yu C.
A Hierarchical Approach to Model Web Query Interfaces for Web Source Integration
VLDB, Lyon, France - Illés Solt, Domonkos Tikk
Yet another rule-based approach for extracting medication information from discharge summaries
The Third i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data, 11/2009, San Francisco, CA, USA. - Rostin A, Albrecht O, Bauckmann J, Naumann F, Leser U.
A Machine-Learning Approch to Foreign Key Detection
WebDB, Provedence, US - De Stasio A, Ertelt M, Kemmner W, Leser U, Ceccarelli M
Exploiting Scientific Workflows for Large-Scale Gene Expression Data Analysis
24th of the International Symposium on Computer and Information Sciences (ISCIS), Cyprus - Hakenberg J, Tari L, Gonzalez G, Solt I, Tikk D, Rheinländer A, Ngyuen QL, and Leser U
Molecular event extraction from Link Grammar parse trees
BioNLP shared task 2009 - Starlinger J, Leitner F, Valencia A, and Leser U
SOA-based Integration of Text Mining Services
Service Cup 2009Third prize in the international Service Cup 2009 contest. - Palaga P, Nguyen QL, Leser U, and Hakenberg J
High-Performance Information Extraction with AliBaba (Demo)
Extending Database Technology (EDBT), St. Petersburg, Russia. - Chiarcos C, Dipper S, Götze M, Leser U, Lüdeling A, Ritz J, and Stede M
A Flexible Framework for Integrating Annotations from Different Tools and Tagsets
Traitement Automatique des Langues, Special Issue on Platforms for Natural Language Processing. - Hakenberg, J., Plake, C. and Leser, U.
Ali Baba: Text Mining for Systems Biology
In Lodhi, H. and Muggleton, S. (eds) "Elements of Computational Systems Biology". Wiley & Sons - Schiemann, T., Leser, U. and Hakenberg, J.
Word Sense Disambiguation in Biomedical Applications: A Machine Learning Approach
In Prince, V. and Roche, M. (eds) Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global. - Leser U.
Semantic Integration of Life Science Entities
In: Öszu T, Liu L, editors. Encyclopedia of Database Systems, Springer - Leser U., Trißl S.
Graph Management in the Life Sciences
In: Öszu T, Liu L, editors. Encyclopedia of Database Systems, Springer - Illés Solt, Domonkos Tikk, Viktor Gál, Zsolt T Kardkovács
Semantic Classification of Diseases in Discharge Summaries Using a Context-aware Rule-based Classifier
Journal of the American Medical Informatics Association, 2009;16:580-584.
Other
- Hakenberg, J.
Mining relations from the biomedical literature.
Dissertation (HU edoc) - Groth, P.
Knowledge management and discovery for genotype/phenotype data.
Dissertation (HU edoc)
2008
Peer-reviewed publications
- Hakenberg, J., Plake, C., Royer, L., Strobelt, H., Leser U., and Schroeder. M.
Gene mention normalization and interaction extraction with context models and sentence motifs
Genome Biology, 2008;9 Suppl 2:S14 (2008). - Groth, P., Weiss, B. and Leser, U.
Hunting for gene function: Using phenotype data mining as a large-scale discovery tool
BioSapiens Workshop on Automated Function Prediction, at ISMB 2008. - Jaeger, S., Gaudan, S., Leser, U. and Rebholz-Schuhmann, D.
Integrating Protein-Protein Interactions and Text Mining for Protein Function Prediction
Workshop on Data Integration for the Life Sciences (DILS), Evry, France.Appeared in BMC Bioinformatics, Selected Best Papers from DILS08 - Quilitz, B. and Leser, U.
Querying Distributed RDF Data Sources with SPARQL
European semantic Web Conference (ESWC), Teneriffa, Spain (2008). - Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz and Ulf Leser
Mining phenotypes for gene function prediction
BMC Bioinformatics, 9:136 (2008).
Other
- Anke Lüdeling, Ulf Leser
Bioinformatics methods in calculating language relationships
Tutorial at the European Summer School in Logic, Language and Information (ESSLI), Hamburg (2008) - Mirko Hochmuth, Anke Lüdeling, Ulf Leser
Simulating and reconstructing language change
Institut für Informatik der Humboldt-Universität zu Berlin, Technical Report (2008) - Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann, Eds. (2008). Proceedings of the Dagstuhl Workshop on "Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives". Available from the Dagstuhl DROPS server.
- Jens Dittrich, Ulf Leser, Betram Ludaescher, Dave Maier, Louiqa Raschid, Eds. (2008). Proceedings Workshop on Information Integration Methods, Architectures, and Systems" (IIMAS), Cancun, Mexico.
2007
Peer-reviewed publications
- Jaeger, S. and Leser, U.
High-Precision Function Prediction using Conserved Interactions
German Conference on Bioinformatics (GCB), Springer LNI, pp 145-162, Potsdam, Germany (2007). - Silke Trißl, Florian Zipser, and Ulf Leser
Applying GRIPP to XML Documents containing XInclude and XLink Elements
XML Tage, Berlin, Germany, (2007). - Jana Bauckmann
Automatically Integrating Life Science Data Sources
PhD Workshop in conjunction with VLDB 2007, Vienna, Austria (2007). - Philipp Hussels, Silke Trissl, and Ulf Leser
What's new? What's certain? - Scoring Search Results in the Presence of Overlapping Data Sources
4th Workshop on Data Integration in the Life Sciences (DILS07), Philadelphia, USA. 2007
In Lecture Notes in Computer Science, Volume 4544/2007, Pages 231-246. [SpringerLink] - Hakenberg, J., Schröder, M. and Leser, U.
Consenus Pattern Alignment to find protein--protein interactions in text
Proc 2nd BioCreative Challenge Evaluation Workshop. Madrid, Spain, April 23-25, pages 213–215. - Silke Trissl
Cost-based Optimization of Graph Queries
1st PhD Workshop on Innovative Database Research (IDAR) in conjunction with ACM SIGMOD Conference, Beijing, China, 2007. - Silke Trissl, Ulf Leser
Fast and Practical Indexing and Querying of Very Large Graphs
ACM SIGMOD Conference, Bejing, China, pages 845-856, 2007. [ACM] - Fahland, D., Gläßer, T. M., Quilitz, B., Weißleder, S. and Leser, U.
HUODINI - Flexible Information Integration for Disaster Management
4th International Conference on Information Systems for Crisis Response and Management (ISCRAM), Delft, NL (2007) - Heese, R., Leser, U., Quilitz, B. and Rothe, C.
Index Support for SPARQL
Poster Paper, European Semantic Web Conference (ESWC), Innsbruck, Austria (2007) - Jana Bauckmann, Ulf Leser, Felix Naumann, Véronique Tietz
Efficiently Detecting Inclusion Dependencies
International Conference on Data Engineering (ICDE), Istanbul, Turkey, pp 1448-1450 (2007)
Other
- Philip Groth, Bertram Weiss, Ulf Leser
Making use of Phenotype Data - an Ongoing Challenge
Poster, ISMB/ECCB 2007, Vienna, Austria (2007) - Georg Basler, Jan Hummel, Karin Köhl, Jan Hannemann, Joachim Kopka, Ulf Leser, Dirk Walther, Joachim Selbig
Linking metabolite profiles and experiment data for large-scale comparative metabolome analyses
Poster, German Conference on Bioinformatics, Potsdam, Germany (2007) - Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann
Protein Function Predicted using Protein Interaction Graphs and Publications
Poster, German Conference on Bioinformatics, Potsdam, Germany (2007)
2006
Peer-reviewed publications
- Gunnar Kleinau, Mara Brehm, Urs Wiedemann, Dirk Labudde, Ulf Leser, Gerd Krause
Implications for molecular mechanisms of glycoprotein hormone receptors using a new Sequence-Structure-Function Analysis resource.
Journal of Molecular Endocrinology, Nov. 16 (2006) - Heiko Müller, Ulf Leser, Johann-Christoph Freytag
Classification of Contradiction Patterns.
30th Annual Conference of the Gesellschaft für Klassifikation, Berlin, Germany (2006)
Proceedings by Springer - Heiko Müller, Johann-Christoph Freytag, Ulf Leser
Describing Differences between Databases.
Conference on Information and Knowledge Management (CIKM), Arlington, USA (2006) - Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
Ali Baba: Accessing PubMed using graphs.
German Conference on Bioinformatics (GCB), September 20-22, Tübingen, Germany (2006) - [Conference]
- Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser
Ali Baba: PubMed as a graph.
Bioinformatics, 22(19):2444-2445 (2006) - Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
Collecting a Large Corpus from all of Medline.
Second International Symposium on Semantic Mining in Biomedicine (SMBM). Jena, Germany (2006)
[Abstract] - [SMBM'06] - [Proceedings] - Jana Bauckmann, Ulf Leser, Felix Naumann
Efficiently Computing Inclusion Dependencies for Schema Discovery.
Workshop InterDB (with ICDE06), Atlanta (2006) - Uwe Radetzki, Ulf Leser, S.C. Schulze-Rauschenbach, J. Zimmermann, J. Lussem, T. Bode, A.B. Cremers
Adapters, shims, and glue - service interoperability for in silico experiments.
Bioinformatics, 22(9):1137-1143 (2006) - Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner
A structural keystone for drug design.
Journal of Integrative Bioinformatics (2006) - Lukas Faulstich, Ulf Leser, Thorsten Vitt
Implementing a Linguistic Query Language for Historic Texts.
International Workshop on Query Languages and Query Processing, Springer-Verlag, München (2006).
Books
- Ulf Leser, Felix Naumann
Informationsintegration
dpunkt.verlag (2006)
[ Book web site] - Ulf Leser, Felix Naumann, Barbara Eckman (editors)
Data Integration in the Life Sciences
Proceedings of the Third International Workshop, Hinxton, July 2006.
Springer LNCS Series: Lecture Notes in Bioinformatics, Vol. 4075, (2006)
[ SpringerLink] [Workshop] - Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel Berrar, Werner Dubitzky (editors)
Knowledge Discovery in Life Science Literature
Proceedings of the International Workshop KDLL 2006 in conjunction with PAKDD 2006, Singapore, April 2006.
Springer LNCS Series: Lecture Notes in Bioinformatics, Vol. 3886, (2006)
[Information] [ SpringerLink] [Workshop]
Other
- Silke Trißl, Ulf Leser
GRIPP - Indexing and Querying Graphs based on Pre- and Postorder Numbering
Technical Report No 207, Department for Computer Science, Humboldt-Universität zu Berlin (2006) - Jana Bauckmann, Ulf Leser, Felix Naumann, Joachim Schmid
Data Profiling: Effiziente Fremdschlüsselerkennung mit Aladin
German Information Quality Conference & Workshop, Bad Soden, Germany, (2006) - Artin Avanes, Timo Mika Gläßer, Markus Scheidgen
Self-Organizing Information Systems for Disaster Management
3. GI/ITG KuVS Fachgespräch "Ortsbezogene Anwendungen und Dienste", Berlin, Germany, (2006) - Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
Ali Baba
Demo at NuGO WP8 Workshop on text mining and knowledge extraction and its application for nutrigenomics research, June 1-2 (2006)
[Workshop] - Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
Ali Baba - Visualizing biological networks from PubMed query results.
Poster at Data Integration in the Life Sciences (DILS), Hinxton, UK (2006). - Heiko Müller, J-C Freytag, Ulf Leser
On the Distance of Databases.
Technical Report No 199, Department for Computer Science, Humboldt-Universität zu Berlin (2006) - Rainer Dietrich et al.
Das Interdisziplinäre Zentrum für Sprachliche Bedeutung .
Humboldt Spektrum 4/2006 - Jana Bauckmann
Efficiently Identifying Inclusion Dependencies in RDBMS
18. Workshop über Grundlagen von Datenbanken (2006)
2005
Peer-reviewed publications
- Ulf Leser and Jörg Hakenberg
What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature.
Briefings in Bioinformatics, 6(4):357-369 (2005)
[Abstract] [ PubMed] - Heiko Müller, Melanie Weis, Jens Bleiholder, Ulf Leser
Erkennen und Bereinigen von Datenfehlern in naturwissenschaftlichen Daten.
Datenbank Spektrum, Vol. 15, pp. 26-35 (2005). - Ulf Leser
A Query Language for Biological Networks.
3rd European Conference on Computational Biology, Madrid, Spain (2005).
Appeared in Bioinformatics, 21(suppl_2):ii33-ii39. - Silke Trissl, Ulf Leser
Querying ontologies in relational database systems.
2nd Workshop on Data Integration in the Life Sciences (DILS05), San Diago, USA (2005).
In Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 63 - 79. [SpringerLink] - Fouzia Moussouni, Emilie Guréin, Gwenaelle Marquet, Anita Burgun, Olivier Loréal. Laure Berti-Equille, Ulf Leser
Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW.
2nd Workshop on Data Integration in the Life Sciences (DILS05), San Diago, USA (2005).
In Lecture Notes in Computer Science, Volume 3615, Aug 2005, Pages 158 - 174. [ SpringerLink] - Daniel Schober, Ulf Leser, Martin Zenke, Jens Reich
GandrKB: Ontological Microarray Annotation and Visualization.
Bioinformatics, 1;21(11):2785-2786 (2005) - Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata.
Proc Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany (August 2005)
[Abstract] [LLL'05] - Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer
Systematic Feature Evaluation for Gene Name Recognition.
BMC Bioinformatics, 6(Suppl 1):S9, April 2005
[Abstract] [ PubMed] - Jörg Hakenberg, Juliane Rutsch, Ulf Leser
Tuning Text Classification for Hereditary Diseases with Section Weighting.
First International Symposium on Semantic Mining in Biomedicine (SMBM), pp. 34-37. Hinxton, UK (2005)
[Abstract] [ Proceedings] [SMBM'05] - Kristian Rother, Silke Trißl , Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser
Columba: An Integrated Database of Proteins, Structures, and Annotations.
BMC Bioinformatics 2005, 6:81. [BMC Bioinformatics] - Kristian Rother, Elke Michalsky, Ulf Leser
How well are protein structures annotated in secondary databases?.
PROTEINS, 60(4):571-76. (2005) - Conrad Plake, Jörg Hakenberg, Ulf Leser
Learning Patterns for Information Extraction from Free Text.
Workshop des Arbeitskreises Knowledge Discovery (AKKD), Karlsruhe, Germany (2005)
[Abstract] - Conrad Plake, Jörg Hakenberg, Ulf Leser
Optimizing Syntax Patterns for Discovering Protein-Protein Interactions.
ACM SAC, Bioinformatics track, 1:195-201. Santa Fe, USA (2005)
[Abstract] [SAC 2005] - Ulf Leser, Felix Naumann
(Almost) Hands-Off Information Integration for the Life Sciences.
Conference on Innovative Database Research (CIDR 2005), Asilomar, CA.
Invited publications
- Anke Lüdeling, Thorwald Poschenrieder und Lukas Faulstich.
DeutschDiachronDigital - Ein diachrones Korpus des Deutschen.
Jahrbuch für Computerphilologie 2005.
[Abstract, PDF]
Other
- Ulf Leser and Jörg Hakenberg
Text Mining: Automatische Analyse biomedizinischer Texte .
GenomXPress, 4.05, pp. 20-22 (2005).
[Full issue] - Ramakrishnan, R., Agrawal, R., Freytag, J.-C., Bollinger, T., Clifton, C. W., Dzeroski, S., Hipp, J., Keim, D., Kramer, S., Kriegel, H.-P., Leser, U., et al.
Data Mining: The Next Generation. Report from a Dagstuhl Perspectives Workshop..
Seminar Proceedings, Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany. (2005) - Ulf Leser
A Query Language for Biological Networks.
Institut für Informatik der Humboldt-Universität zu Berlin, Technical Report 187 (2005) - Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Ulf Leser, and Edda Klipp
Recognition and Extraction of Entities related to Enzyme Kinetics.
Poster at Biotext - a biomedical text mining workshop, London, UK, 9 November 2005.
[Workshop] - Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp
Finding Kinetic Data Using Text Mining.
Poster at 5th Int Workshop on Bioinformatics and Systems Biology, Berlin, Germany, 25 August 2005.
[PDF] - Silke Trissl
Anfragen in Ontologien in relationalen Datenbanken (German).
17. GI-Workshop über 'Grundlagen von Datenbanken', Wörlitz, Germany (2005).
[PDF] - Stephan Rieche, Ulf Leser
Versionierung in relationalen Datenbanken.
Studierendenprogramm der 11. GI-Fachtagung für Datenbanksysteme in Business, Technologie und Web (BTW 2005), Karlsruhe. - Lukas C. Faulstich, Ulf Leser und Anke Lüdeling
Storing and querying historical texts in a relational database.
Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.176 (2005) - Lukas C. Faulstich, Ulf Leser
Implementing Linguistic Query Languages Using LoToS.
Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.195 (2005)
Press
- Interview Prof. Leser mit der Berliner Morgenpost vom 16.7.2005: " Strategien gegen Studienabbrecher und Langzeitstudenten"
- Interview in der Saarbrücker Zeitung zu Dagstuhl Seminare: "Ein Mekka für Forscher"
2004
Peer-reviewed publications
- S. Jurk, U. Leser, J.L. Marzo
Cooperative Transaction Processing between Client and Server
Eighth East-European Conference on Advances in Databases and Information Systems, Budapest, Hungary (2004) - Heiko Müller, Ulf Leser, Johann-Christoph Freytag
Mining for Patterns in Contradictory Data
International Workshop on Information Quality in Information Systems (in conjunction with SIGMOD 2004), Paris, France (2004) - Stefanie Dipper, Lukas Faulstich, Ulf Leser, Anke Lüdeling
Challenges in Modelling a Richly Annotated Diachronic Corpus of German
Workshop on XML-based Richly Annotated Corpora (in conjunction with LREC 2004), Lissabon, Portugal (2004) - Kristian Rother, Heiko Müller, Silke Trissl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser
COLUMBA: Multidimensional Data Integration of Protein Annotations
International Workshop on Data Integration in the Life Sciences, Leipzig, Germany (2004) - Jörg Hakenberg, Sebastian Schmeier, Axel Kowald, Edda Klipp, Ulf Leser
Finding Kinetic Parameters Using Text Mining
OMICS: A Journal of Integrative Biology, Special Issue on Data Mining meets Integrative Biology, 8(2):131-152. (2004)
[Abstract] [ PubMed] - Felix Naumann, Johann-Christoph Freytag, Ulf Leser
Completeness of Integrated Information Sources
Journal on Information Systems, 29(7):583-615 (2004).
Other
- Emil Kroymann, Sebastian Thiebes, Anke Lüdeling, Ulf Leser
Eine vergleichende Analyse von historischen und diachronen digitalen Korpora
Institut für Informatik der Humboldt-Universität zu Berlin, Informatik-Bericht Nr.174
[Paper] - Uwe Radetzki, Ulf Leser, Armin B. Cremers
IRIS: A Mediator-Based Approach Achieving Interoperability of Web Services in Life Science Applications
3rd E-BioSci / ORIEL Annual Workshop, UK, October 2004
[Paper] - Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Condrad Plake, Tobias Scheffer
A Support Vector Machine Classifier for Gene Name Recognition
EMBO Workshop: A critical assessment of text mining methods in molecular biology. Granada, Spain, March 2004
[Abstract] [Paper] - Silke Trissl, Kristian Rother, Heiko Müller, Ulf Leser
Columba - A Database of Annotations of Protein Structure
HGM-Poster 2004
[Abstract] [Poster] - Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, Edda Klipp
Fighting the Data Acquisition Bottleneck
Int Conf Systems Biology (ICSB), October 2004, Heidelberg, Germany.
[Abstract] - Silke Trissl, Kristian Rother, Ulf Leser
Columba - A Database of annotated protein structure
ECCB-Poster 2004
[Abstract] [Poster] - Stefan Günther, Kristian Rother, Silke Trissl
The usefulness of integrated databases: a case study of COLUMBA
ECCB-Poster 2004
[Abstract] [Poster]
2003
Peer-reviewed publications
- Ulf Leser, Peter Rieger
Integration molekularbiologischer Daten
Datenbankspektrum Ausgabe 6, (in German) pp. 56-66 (2003)
[Full Text] - Jörg Hakenberg, Alexander Nussbaum, Hansjörg Schild, Hans-Georg Rammensee, Christina Kuttler, Hermann-Georg Holzhütter, Peter-M. Kloetzel, Stefan H.E. Kaufmann, Hans-Joachim Mollenkopf
MAPPP - MHC-I Antigenic Peptide Processing Prediction.
Applied Bioinformatics, 2(3):155-158 (2003)
[Abstract] [PubMed] - Felix Naumann, Johann-Christoph Freytag, Ulf Leser
Completeness of Information Sources
Workshop on Data Quality in Cooperative Information Systems, Siena, Italy (2003)
[Full Text] - Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, Ulf Leser
Text Mining for Systems Biology Using Statistical Learning Methods
3. Workshop des Arbeitskreises Knowledge Discovery, Karlsruhe, Germany (2003)
[Abstract] [Full text]
Other
- Tobias Scheffer, Ulf Leser (editors)
Data Mining and Text Mining for Bioinformatics
Proceedings of the European Workshop in conjunction with ECML/PDKK, Dubrovnik, Croatia
[Full text] - Kristian Rother, Silke Trissl, Heiko Müller, Patrick May, Rene Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius Frömmel
Columba - A Database of Annotations of Protein Structure
ECCB-Poster 2003
[Abstract] [Poster]