Translog, a web browser for studying the expression divergence of homologous genes. - Xianjun Dong; Altuna Akalin; Yogita Sharma; Boris Lenhard (BMC Bioinform., 2010)

An optimized algorithm for detecting and annotating regional differential methylation. - Sheng Li; Francine E. Garrett-Bakelman; Altuna Akalin; Paul Zumbo; Ross L. Levine; Bik L. To; Ian D. Lewis; Anna L. Brown; Richard J. D'Andrea; Ari Melnick; Christopher E. Mason (BMC Bioinform., 2013)

Two independent transcription initiation codes overlap on vertebrate core promoters. - Vanja Haberle; Nan Li; Yavor Hadzhiev; Charles Plessy; Christopher Previti; Chirag Nepal; Jochen Gehrig; Xianjun Dong; Altuna Akalin; Ana Maria Suzuki; Wilfred F. J. van IJcken; Olivier Armant; et al. (Nat., 2014)

genomation: a toolkit to summarize, annotate and visualize genomic intervals. - Altuna Akalin; Vedran Franke; Kristian Vlahovicek; Christopher E. Mason; Dirk Schübeler (Bioinform., 2015)

DoRiNA 2.0 - upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. - Kai Blin; Christoph Dieterich; Ricardo Wurmus; Nikolaus Rajewsky; Markus Landthaler; Altuna Akalin (Nucleic Acids Res., 2015)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

netSmooth: Network-smoothing based imputation for single cell RNA-seq. - Jonathan Ronen; Altuna Akalin (F1000Research, 2018)

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning. - Wolfgang Kopp; Altuna Akalin; Uwe Ohler (Nat. Mach. Intell., 2022)

Compass: A Comprehensive Tool for Accurate and Efficient Molecular Docking in Inference and Fine-Tuning. - Ahmet Sarigün; Vedran Franke; Altuna Akalin (CoRR, 2024)

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data. - Yunhee Jeong; Jonathan Ronen; Wolfgang Kopp; Pavlo Lutsik; Altuna Akalin (BMC Bioinform., 2024)

Enhancing biomarker based oncology trial matching using large language models. - Nour Alkhoury; Maqsood Shaik; Ricardo Wurmus; Altuna Akalin (npj Digit. Medicine, 2025)

Evaluating large language model workflows in clinical decision support for triage and referral and diagnosis. - Farieda Gaber; Maqsood Shaik; Fabio Allega; Agnes Julia Bilecz; Felix Busch; Kelsey Goon; Vedran Franke; Altuna Akalin (npj Digit. Medicine, 2025)

PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning. - Ahmet Sarigün; Bora Uyar; Vedran Franke; Altuna Akalin (CoRR, 2025)