Authors: Andreas+Prlić
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Journal Article

Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models

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Muhammad Nabeel Asim, Tayyaba Asif, Faiza Hassan, Andreas Dengel
Database, Volume 2025, 2025, baaf027, https://doi.org/10.1093/database/baaf027
Published: 30 May 2025
Journal Article

Improved insights into the SABIO-RK database via visualization

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Dorotea Dudaš, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller
Database, Volume 2023, 2023, baad011, https://doi.org/10.1093/database/baad011
Published: 31 March 2023
Journal Article

The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization

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R Travis Moreland, Anh-Dao Nguyen, Joseph F Ryan, Andreas D Baxevanis
Database, Volume 2020, 2020, baaa029, https://doi.org/10.1093/database/baaa029
Published: 09 May 2020
Journal Article

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

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Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates, Daniel Zerbino, Paul Flicek
Database, Volume 2017, 2017, bax020, https://doi.org/10.1093/database/bax020
Published: 18 March 2017
Journal Article

The Ensembl gene annotation system

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Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Y. Amy Tang … Stephen M. J. Searle
Database, Volume 2016, 2016, baw093, https://doi.org/10.1093/database/baw093
Published: 23 June 2016
Journal Article

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria

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Miguel A. Ibarra-Arellano, Adrián I. Campos-González, Luis G. Treviño-Quintanilla, Andreas Tauch, Julio A. Freyre-González
Database, Volume 2016, 2016, baw089, https://doi.org/10.1093/database/baw089
Published: 30 May 2016
Journal Article

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

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Norbert Kilian, Tilo Henning, Patrick Plitzner, Andreas Müller, Anton Güntsch, Ben C. Stöver, Kai F. Müller, Walter G. Berendsohn, Thomas Borsch
Database, Volume 2015, 2015, bav094, https://doi.org/10.1093/database/bav094
Published: 30 September 2015
Journal Article

EpiFactors: a comprehensive database of human epigenetic factors and complexes

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Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium, Finn Drabløs
Database, Volume 2015, 2015, bav067, https://doi.org/10.1093/database/bav067
Published: 07 July 2015
Journal Article

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

Tudor Groza, Sebastian Köhler, Sandra Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson
Database, Volume 2015, 2015, bav005, https://doi.org/10.1093/database/bav005
Published: 27 February 2015
Journal Article

Determining similarity of scientific entities in annotation datasets

Guillermo Palma, Maria-Esther Vidal, Eric Haag, Louiqa Raschid, Andreas Thor
Database, Volume 2015, 2015, bau123, https://doi.org/10.1093/database/bau123
Published: 27 February 2015
Journal Article

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

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Stephan Pabinger, Rene Snajder, Timo Hardiman, Michaela Willi, Andreas Dander, Zlatko Trajanoski
Database, Volume 2014, 2014, bau004, https://doi.org/10.1093/database/bau004
Published: 14 February 2014
Journal Article

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

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Mariana Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz, Ulf Leser
Database, Volume 2013, 2013, bat020, https://doi.org/10.1093/database/bat020
Published: 18 April 2013
Journal Article

MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes

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Andreas Braun, Bettina Halwachs, Martina Geier, Katrin Weinhandl, Michael Guggemos, Jan Marienhagen, Anna J. Ruff, Ulrich Schwaneberg, Vincent Rabin, Daniel E. Torres Pazmiño, Gerhard G. Thallinger, Anton Glieder
Database, Volume 2012, 2012, bas028, https://doi.org/10.1093/database/bas028
Published: 21 June 2012
Journal Article

The Histone Database: an integrated resource for histones and histone fold-containing proteins

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Leonardo Mariño-Ramírez, Kevin M. Levine, Mario Morales, Suiyuan Zhang, R. Travis Moreland, Andreas D. Baxevanis, David Landsman
Database, Volume 2011, 2011, bar048, https://doi.org/10.1093/database/bar048
Published: 22 October 2011
Journal Article

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

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Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice David, Frederik Decouttere, Jacques Rougemont, Bart Deplancke
Database, Volume 2011, 2011, bar040, https://doi.org/10.1093/database/bar040
Published: 14 September 2011
Journal Article

Ensembl BioMarts: a hub for data retrieval across taxonomic space

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Rhoda J. Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel Staines, Paul Derwent, Arnaud Kerhornou, Paul Kersey, Paul Flicek
Database, Volume 2011, 2011, bar030, https://doi.org/10.1093/database/bar030
Published: 23 July 2011
Journal Article

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

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Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlić, Gregory B. Quinn, Peter W. Rose, Chaitali Shah, Jasmine Young, Benjamin Yukich, Helen M. Berman, Philip E. Bourne
Database, Volume 2011, 2011, bar003, https://doi.org/10.1093/database/bar003
Published: 03 March 2011
Journal Article

HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population

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Nicolas J. Tourasse, Ole Andreas Økstad, Anne-Brit Kolstø
Database, Volume 2010, 2010, baq017, https://doi.org/10.1093/database/baq017
Published: 30 July 2010
Journal Article

The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family

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R. Travis Moreland, Joseph F. Ryan, Christopher Pan, Andreas D. Baxevanis
Database, Volume 2009, 2009, bap004, https://doi.org/10.1093/database/bap004
Published: 17 April 2009