Publications by authors named "Altuna Akalin"

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Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond.
Bora Uyar, Taras Savchyn, Amirhossein Naghsh Nilchi, Ahmet Sarigun, Ricardo Wurmus, Altuna Akalin

Nat Commun· September 2025

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Leveraging large language models for data analysis automation.
Jacqueline A Jansen, Artür Manukyan, Nour Al Khoury, Altuna Akalin

PLoS One· May 2025

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Enhancing biomarker based oncology trial matching using large language models.
Nour Alkhoury, Maqsood Shaik, Ricardo Wurmus, Altuna Akalin

NPJ Digit Med· May 2025

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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, Altuna Akalin

NPJ Digit Med· May 2025

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Publisher Correction: Herpesviruses mimic zygotic genome activation to promote viral replication.
Eva Neugebauer, Stephanie Walter, Jiang Tan, Nir Drayman, Vedran Franke, Altuna Akalin

Nat Commun· March 2025

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Herpesviruses mimic zygotic genome activation to promote viral replication.
Eva Neugebauer, Stephanie Walter, Jiang Tan, Nir Drayman, Vedran Franke, Altuna Akalin

Nat Commun· January 2025

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Cytosolic nucleic acid sensors and interferon beta-1 activation drive radiation-induced anti-tumour immune effects in human pancreatic cancer cells.
Sylvia Kerschbaum-Gruber, Ava Kleinwächter, Katerina Popova, Alexandra Kneringer, Lisa-Marie Appel, Altuna Akalin

Front Immunol· October 2024

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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 Bioinformatics· August 2024

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A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
Dominik Szabó, Vedran Franke, Simona Bianco, Mykhailo Y Batiuk, Eleanor J Paul, Altuna Akalin

bioRxiv· May 2024

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Pathogenic mutations of human phosphorylation sites affect protein-protein interactions.
Trendelina Rrustemi, Katrina Meyer, Yvette Roske, Bora Uyar, Altuna Akalin

Nat Commun· April 2024

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Herpesviruses mimic zygotic genome activation to promote viral replication.
Florian Full, Stephanie Walter, Eva Neugebauer, Jiang Tan, Nir Drayman, Altuna Akalin

Res Sq· December 2023

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Transcriptional reprogramming by mutated IRF4 in lymphoma.
Nikolai Schleussner, Pierre Cauchy, Vedran Franke, Maciej Giefing, Oriol Fornes, Altuna Akalin

Nat Commun· November 2023

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The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Johannes Benedum, Vedran Franke, Lisa-Marie Appel, Lena Walch, Melania Bruno, Altuna Akalin

Nat Commun· November 2023

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Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation.
Rafael R C Cuadrat, Adelheid Kratzer, Hector Giral Arnal, Anja C Rathgeber, Katarzyna Wreczycka, Altuna Akalin

NAR Genom Bioinform· June 2023

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Disintegration of the NuRD Complex in Primary Human Muscle Stem Cells in Critical Illness Myopathy.
Joanna Schneider, Devakumar Sundaravinayagam, Alexander Blume, Andreas Marg, Stefanie Grunwald, Altuna Akalin

Int J Mol Sci· February 2023

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The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Lisa-Marie Appel, Vedran Franke, Johannes Benedum, Irina Grishkovskaya, Xué Strobl, Altuna Akalin

Nat Commun· January 2023

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A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.

Sci Immunol· January 2023

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SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Vic-Fabienne Schumann, Rafael Ricardo de Castro Cuadrat, Emanuel Wyler, Ricardo Wurmus, Aylina Deter, Altuna Akalin

Sci Total Environ· December 2022

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Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction.
Artem Baranovskii, Irem B Gündüz, Vedran Franke, Bora Uyar, Altuna Akalin

Cancers (Basel)· November 2022

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Rapid Inflammasome Activation Is Attenuated in Post-Myocardial Infarction Monocytes.
Hector Giral, Vedran Franke, Minoo Moobed, Maja F Müller, Laura Lübking, Altuna Akalin

Front Immunol· May 2022

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Identifying tumor cells at the single-cell level using machine learning.
Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Bora Uyar, Vedran Franke, Altuna Akalin

Genome Biol· May 2022

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Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
Alison C McGarvey, Wolfgang Kopp, Dubravka Vučićević, Kenny Mattonet, Rieke Kempfer, Altuna Akalin

Cell Genom· January 2022

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The SEQC2 epigenomics quality control (EpiQC) study.
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Altuna Akalin

Genome Biol· December 2021

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Author Correction: The SEQC2 epigenomics quality control (EpiQC) study.
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Altuna Akalin

Genome Biol· December 2021

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Cell-type specialization is encoded by specific chromatin topologies.
Warren Winick-Ng, Alexander Kukalev, Izabela Harabula, Luna Zea-Redondo, Dominik Szabó, Altuna Akalin

Nature· November 2021

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