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Other IDs

ResearcherID: A-4424-2012
Scopus Author ID: 13407674400

Keywords

Bioinformatics, Computational Genomics, epigenomics

Countries

Germany

Activities

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Employment (5)

Max Delbrück Centrum für Molekulare Medizin Berlin Buch: Berlin-Buch, Berlin, DE

2014 to present | Group Leader/Head of Bioinformatics Platform (Berlin Institute of Medical Systems Biology)
Employment
Source: Self-asserted source
ALTUNA AKALIN

Friedrich Miescher Institute for Biomedical Research: Basel, BS, CH

2013 to 2014 | Postdoctoral Fellow
Employment
Source: Self-asserted source
ALTUNA AKALIN

Joan and Sanford I Weill Medical College of Cornell University: New York, NY, US

2012 to 2013 | Senior Research Associate
Employment
Source: Self-asserted source
ALTUNA AKALIN

Joan and Sanford I Weill Medical College of Cornell University: New York, NY, US

2010 to 2012 | Postdoctoral associate
Employment
Source: Self-asserted source
ALTUNA AKALIN

RIKEN Yokohama: Yokohama, JP

2007-09-01 to 2007-12-19 | Visiting PhD Student
Employment
Source: Self-asserted source
ALTUNA AKALIN

Education and qualifications (2)

Universitetet i Bergen: Bergen, NO

2005 to 2010 | PhD
Education
Source: Self-asserted source
ALTUNA AKALIN

Sabanci Universitesi: Istanbul, TR

2001 to 2005 | B.Sc
Education
Source: Self-asserted source
ALTUNA AKALIN

Works (50 of 80)

Items per page:
Page 1 of 2

Leveraging large language models for data analysis automation

PLOS ONE
2025-02-21 | Journal article
DOI: 10.1371/journal.pone.0317084
Contributors: Jacqueline A. Jansen; Diego A. Forero; Artür Manukyan; Nour Al Khoury; Altuna Akalin
Source: check_circle
Crossref

Evaluating large language model workflows in clinical decision support: referral, triage, and diagnosis

2024-09-28 | Preprint
DOI: 10.1101/2024.09.27.24314505
Contributors: Farieda Gaber; Maqsood Shaik; Vedran Franke; Altuna Akalin
Source: check_circle
Crossref

Enhancing Biomarker-Based Oncology Trial Matching Using Large Language Models

2024-09-19 | Preprint
DOI: 10.1101/2024.09.13.612922
Contributors: Nour Al Khoury; Maqsood Shaik; Ricardo Wurmus; Altuna Akalin
Source: check_circle
Crossref

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond

2024-07-18 | Preprint
DOI: 10.1101/2024.07.16.603606
Contributors: Bora Uyar; Taras Savchyn; Ricardo Wurmus; Ahmet Sarigun; Mohammed Maqsood Shaik; Vedran Franke; Altuna Akalin
Source: check_circle
Crossref

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

Nature Communications
2024-04-11 | Journal article
DOI: 10.1038/s41467-024-46794-8
Contributors: Trendelina Rrustemi; Katrina Meyer; Yvette Roske; Bora Uyar; Altuna Akalin; Koshi Imami; Yasushi Ishihama; Oliver Daumke; Matthias Selbach
Source: check_circle
Crossref

Herpesviruses mimic zygotic genome activation to promote viral replication

2023-12-13 | Preprint
DOI: 10.21203/rs.3.rs-3125635/v1
Contributors: Florian Full; Stephanie Walter; Eva Neugebauer; Jiang Tan; Nir Drayman; Vedran Franke; Savaş Tay; Markus Landthaler; Altuna Akalin; Armin Ensser et al.
Source: check_circle
Crossref

Leveraging large language models for data analysis automation

2023-12-12 | Preprint
DOI: 10.1101/2023.12.11.571140
Contributors: Jacqueline A Jansen; Artür Manukyan; Nour Al Khoury; Altuna Akalin
Source: check_circle
Crossref

Transcriptional reprogramming by mutated IRF4 in lymphoma

Nature Communications
2023-11-07 | Journal article
DOI: 10.1038/s41467-023-41954-8
Contributors: Nikolai Schleussner; Pierre Cauchy; Vedran Franke; Maciej Giefing; Oriol Fornes; Naveen Vankadari; Salam A. Assi; Mariantonia Costanza; Marc A. Weniger; Altuna Akalin et al.
Source: check_circle
Crossref

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

2023-08-03 | Preprint
DOI: 10.1101/2023.08.01.551433
Contributors: Trendelina Rrustemi; Katrina Meyer; Yvette Roske; Bora Uyar; Altuna Akalin; Koshi Imami; Yasushi Ishihama; Oliver Daumke; Matthias Selbach
Source: check_circle
Crossref

Disintegration of the NuRD Complex in Primary Human Muscle Stem Cells in Critical Illness Myopathy

International Journal of Molecular Sciences
2023-02 | Journal article | Author
DOI: 10.3390/ijms24032772
Contributors: Joanna Schneider; Devakumar Sundaravinayagam; Alexander Blume; Andreas Marg; Stefanie Grunwald; Eric Metzler; Helena Escobar Fernandez; Stefanie Müthel; Haicui Wang; PD Dr. med. Tobias Wollersheim et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute

Decoding single-cell multiomics: scMaui - A deep learning framework for uncovering cellular heterogeneity in presence of batch Effects and missing data

2023-01-20 | Preprint
DOI: 10.1101/2023.01.18.524506
Contributors: Yunhee Jeong; Jonathan Ronen; Wolfgang Kopp; Pavlo Lutsik; Altuna Akalin
Source: check_circle
Crossref

Identifying tumor cells at the single-cell level using machine learning

Genome Biology
2022-12 | Journal article
DOI: 10.1186/s13059-022-02683-1
Contributors: Jan Dohmen; Artem Baranovskii; Jonathan Ronen; Bora Uyar; Vedran Franke; Altuna Akalin
Source: check_circle
Crossref

Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction

Cancers
2022-11-15 | Journal article
DOI: 10.3390/cancers14225604
Contributors: Artem Baranovskii; Irem B. Gündüz; Vedran Franke; Bora Uyar; Altuna Akalin
Source: check_circle
Crossref
grade
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Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

2022-06-17 | Preprint
DOI: 10.1101/2022.06.15.496249
Contributors: Artem Baranovskii; Irem B. Gunduz; Vedran Franke; Bora Uyar; Altuna Akalin
Source: check_circle
Crossref

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

2022-02-27 | Preprint
DOI: 10.1101/2022.02.26.482114
Contributors: Lisa-Marie Appel; Irina Grishkovskaya; Johannes Benedum; Vedran Franke; Anton Polyansky; Andrea Neudolt; Anna Wunder; Bojan Zagrovic; Altuna Akalin; Kristina Djinovic-Carugo et al.
Source: check_circle
Crossref

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

Nature Machine Intelligence
2022-02-23 | Journal article
DOI: 10.1038/s42256-022-00443-1
Contributors: Wolfgang Kopp; Altuna Akalin; Uwe Ohler
Source: check_circle
Crossref

Identifying tumor cells at the single cell level

2021-10-16 | Other
DOI: 10.1101/2021.10.15.463909
Contributors: Jan Dohmen; Artem Baranovskii; Jonathan Ronen; Bora Uyar; Vedran Franke; Altuna Akalin
Source: check_circle
Crossref

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

2021-05-12 | Other
DOI: 10.1101/2021.05.11.443540
Contributors: Wolfgang Kopp; Altuna Akalin; Uwe Ohler
Source: check_circle
Crossref

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression

2021-03-24 | Preprint
DOI: 10.1101/2021.03.24.436599
Contributors: Stephanie Walter; Vedran Franke; Nir Drayman; Emanuel Wyler; Savaş Tay; Markus Landthaler; Altuna Akalin; Armin Ensser; Florian Full
Source: check_circle
Crossref

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

Nature Communications
2020-12-11 | Journal article
DOI: 10.1038/s41467-020-20064-9
Contributors: Minchul Kim; Vedran Franke; Bettina Brandt; Elijah D. Lowenstein; Verena Schöwel; Simone Spuler; Altuna Akalin; Carmen Birchmeier
Source: check_circle
Crossref

Parallel genetics of regulatory sequencesin vivo

2020-07-29 | Preprint
DOI: 10.1101/2020.07.28.224998
Contributors: Jonathan Froehlich; Bora Uyar; Margareta Herzog; Kathrin Theil; Petar Glažar; Altuna Akalin; Nikolaus Rajewsky
Source: check_circle
Crossref

Deep learning for genomics using Janggu

Nature Communications
2020-07-13 | Journal article
DOI: 10.1038/s41467-020-17155-y
Contributors: Wolfgang Kopp; Remo Monti; Annalaura Tamburrini; Uwe Ohler; Altuna Akalin
Source: check_circle
Crossref

Autocrine LTA signaling drives NF-κB and JAK-STAT activity and myeloid gene expression in Hodgkin lymphoma

Blood
2019 | Journal article
DOI: 10.1182/blood-2018-08-871293
EID:

2-s2.0-85064113208
Contributors: Von Hoff, L.; Kärgel, E.; Franke, V.; McShane, E.; Schulz-Beiss, K.W.; Patone, G.; Schleussner, N.; Kolesnichenko, M.; Hübner, N.; Daumke, O. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Deciphering human ribonucleoprotein regulatory networks

Nucleic Acids Research
2019 | Journal article
DOI: 10.1093/nar/gky1185
EID:

2-s2.0-85060657242
Contributors: Mukherjee, N.; Wessels, H.-H.; Lebedeva, S.; Sajek, M.; Ghanbari, M.; Garzia, A.; Munteanu, A.; Yusuf, D.; Farazi, T.; Hoell, J.I. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Global identification of functional microRNA-mRNA interactions in Drosophila

Nature Communications
2019 | Journal article
DOI: 10.1038/s41467-019-09586-z
EID:

2-s2.0-85064076995
Contributors: Wessels, H.-H.; Lebedeva, S.; Hirsekorn, A.; Wurmus, R.; Akalin, A.; Mukherjee, N.; Ohler, U.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia

Journal of Hematology and Oncology
2019 | Journal article
DOI: 10.1186/s13045-018-0692-3
EID:

2-s2.0-85059937122
Contributors: James, A.R.; Schroeder, M.P.; Neumann, M.; Bastian, L.; Eckert, C.; Gökbuget, N.; Tanchez, J.O.; Schlee, C.; Isaakidis, K.; Schwartz, S. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

Nature Communications
2019 | Journal article
DOI: 10.1038/s41467-019-12894-z
EID:

2-s2.0-85074142939
Contributors: Wyler, E.; Franke, V.; Menegatti, J.; Kocks, C.; Boltengagen, A.; Praktiknjo, S.; Walch-Rückheim, B.; Bosse, J.; Rajewsky, N.; Grässer, F. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans

Aging Cell
2019 | Journal article
DOI: 10.1111/acel.13012
EID:

2-s2.0-85070325124
Contributors: Müthel, S.; Uyar, B.; He, M.; Krause, A.; Vitrinel, B.; Bulut, S.; Vasiljevic, D.; Marchal, I.; Kempa, S.; Akalin, A. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Evaluation of colorectal cancer subtypes and cell lines using deep learning

Life Science Alliance
2019-12 | Journal article
DOI: 10.26508/lsa.201900517
Contributors: Jonathan Ronen; Sikander Hayat; Altuna Akalin
Source: check_circle
Crossref

Janggu - Deep learning for genomics

2019-07-14 | Other
DOI: 10.1101/700450
Contributors: Wolfgang Kopp; Remo Monti; Annalaura Tamburrini; Uwe Ohler; Altuna Akalin
Source: check_circle
Crossref

HOT or not: examining the basis of high-occupancy target regions

Nucleic Acids Research
2019-06-20 | Journal article
DOI: 10.1093/nar/gkz460
Contributors: Katarzyna Wreczycka; Vedran Franke; Bora Uyar; Ricardo Wurmus; Selman Bulut; Baris Tursun; Altuna Akalin
Source: check_circle
Crossref
grade
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Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

Nucleic Acids Research
2019-03-18 | Journal article
DOI: 10.1093/nar/gky1270
Contributors: Camilla Ciolli Mattioli; Aviv Rom; Vedran Franke; Koshi Imami; Gerard Arrey; Mandy Terne; Andrew Woehler; Altuna Akalin; Igor Ulitsky; Marina Chekulaeva
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

2019-03-04 | Other
DOI: 10.1101/566992
Contributors: Emanuel Wyler; Vedran Franke; Jennifer Menegatti; Kocks Christine; Anastasiya Boltengagen; Samantha Praktiknjo; Barbara Walch-Rückheim; Nikolaus Rajewsky; Friedrich Grässer; Altuna Akalin et al.
Source: check_circle
Crossref

FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells

Developmental Cell
2018 | Journal article
DOI: 10.1016/j.devcel.2018.07.006
EID:

2-s2.0-85053857310
Contributors: Kolundzic, E.; Ofenbauer, A.; Bulut, S.I.; Uyar, B.; Baytek, G.; Sommermeier, A.; Seelk, S.; He, M.; Hirsekorn, A.; Vucicevic, D. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

Cell
2018 | Journal article
DOI: 10.1016/j.cell.2018.08.019
EID:

2-s2.0-85053074162
Contributors: Meyer, K.; Kirchner, M.; Uyar, B.; Cheng, J.-Y.; Russo, G.; Hernandez-Miranda, L.R.; Szymborska, A.; Zauber, H.; Rudolph, I.-M.; Willnow, T.E. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

Nuclear Organization in the Spinal Cord Depends on Motor Neuron Lamination Orchestrated by Catenin and Afadin Function

Cell Reports
2018 | Journal article
DOI: 10.1016/j.celrep.2018.01.059
EID:

2-s2.0-85042035348
Contributors: Dewitz, C.; Pimpinella, S.; Hackel, P.; Akalin, A.; Jessell, T.M.; Zampieri, N.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

The IκB kinase complex is a regulator of mRNA stability

EMBO Journal
2018 | Journal article
DOI: 10.15252/embj.201798658
EID:

2-s2.0-85057061708
Contributors: Mikuda, N.; Kolesnichenko, M.; Beaudette, P.; Popp, O.; Uyar, B.; Sun, W.; Tufan, A.B.; Perder, B.; Akalin, A.; Chen, W. et al.
Source: Self-asserted source
ALTUNA AKALIN via Scopus - Elsevier

PiGx: reproducible genomics analysis pipelines with GNU Guix

GigaScience
2018-12-01 | Journal article
DOI: 10.1093/gigascience/giy123
Contributors: Ricardo Wurmus; Bora Uyar; Brendan Osberg; Vedran Franke; Alexander Gosdschan; Katarzyna Wreczycka; Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Evaluation of colorectal cancer subtypes and cell lines using deep learning

2018-11-07 | Other
DOI: 10.1101/464743
Contributors: Jonathan Ronen; Sikander Hayat; Altuna Akalin
Source: check_circle
Crossref

netSmooth: Network-smoothing based imputation for single cell RNA-seq

F1000Research
2018-07-10 | Journal article
DOI: 10.12688/f1000research.13511.3
Contributors: Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref

Reproducible genomics analysis pipelines with GNU Guix

2018-04-11 | Other
DOI: 10.1101/298653
Contributors: Ricardo Wurmus; Bora Uyar; Brendan Osberg; Vedran Franke; Alexander Gosdschan; Katarzyna Wreczycka; Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref

netSmooth: Network-smoothing based imputation for single cell RNA-seq

F1000Research
2018-01-24 | Journal article
DOI: 10.12688/f1000research.13511.2
Contributors: Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

netSmooth: Network-smoothing based imputation for single cell RNA-seq [version 1; referees: awaiting peer review]

2018-01-03 | Journal article
DOI: 10.12688/f1000research.13511.1
Part of ISSN: 2046-1402
Contributors: Jonathan Ronen; Altuna Akalin
Source: check_circle
F1000
grade
Preferred source (of 2)‎

netSmooth: Network-smoothing based imputation for single cell RNA-seq

2017-12-13 | Other
DOI: 10.1101/234021
Contributors: Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref

Strategies for analyzing bisulfite sequencing data.

Journal of biotechnology
2017-11 | Journal article
DOI: 10.1016/j.jbiotec.2017.08.007
PMID: 28822795
Source: Self-asserted source
ALTUNA AKALIN via Europe PubMed Central
grade
Preferred source (of 2)‎

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

Molecular Systems Biology
2017-10 | Journal article
DOI: 10.15252/msb.20177754
PMID: 29038337
PMC: PMC5658700
Source: Self-asserted source
ALTUNA AKALIN via Europe PubMed Central
grade
Preferred source (of 2)‎

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.

Genome biology
2017-10 | Journal article
DOI: 10.1186/s13059-017-1329-5
PMID: 29089033
PMC: PMC5663069
Source: Self-asserted source
ALTUNA AKALIN via Europe PubMed Central
grade
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RNA localization is a key determinant of neurite-enriched proteome.

Nature communications
2017-09 | Journal article
DOI: 10.1038/s41467-017-00690-6
PMID: 28928394
PMC: PMC5605627
Source: Self-asserted source
ALTUNA AKALIN via Europe PubMed Central
grade
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The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Nucleic acids research
2017-06 | Journal article
DOI: 10.1093/nar/gkx409
PMID: 28582575
PMC: PMC5570170
Source: Self-asserted source
ALTUNA AKALIN via Europe PubMed Central
grade
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RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

Nucleic Acids Research
2017-06-02 | Journal article
DOI: 10.1093/nar/gkx120
Contributors: Bora Uyar; Dilmurat Yusuf; Ricardo Wurmus; Nikolaus Rajewsky; Uwe Ohler; Altuna Akalin
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Items per page:
Page 1 of 2

Peer review (4 reviews for 4 publications/grants)

Review activity for European heart journal. (1)
Review activity for Genome medicine. (1)
Review activity for Nature biotechnology. (1)
Review activity for Nature communications (1)
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