All Stories

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

    Article • Nature Communications, September 2025, Springer Science + Business Media

    Altuna A, Björn Grüning

  2. Unraveling the single cell spatial landscapes of melanoma brain metastases

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Altuna A

  3. Leveraging large language models for data analysis automation

    Article • PLOS One, February 2025, PLOS

    Altuna A

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

    Article • September 2024, Cold Spring Harbor Laboratory Press

    Altuna A

  5. Enhancing Biomarker-Based Oncology Trial Matching Using Large Language Models

    Article • September 2024, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • July 2024, Cold Spring Harbor Laboratory Press

    Altuna A

  7. Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

    Article • Nature Communications, April 2024, Springer Science + Business Media

    Altuna A

  8. Herpesviruses mimic zygotic genome activation to promote viral replication

    Article • December 2023, Springer Science + Business Media

    Altuna A

  9. Leveraging large language models for data analysis automation

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Altuna A

  10. Transcriptional reprogramming by mutated IRF4 in lymphoma

    Article • Nature Communications, November 2023, Springer Science + Business Media

    Altuna A

  11. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • International Journal of Molecular Sciences, February 2023, MDPI AG

    Altuna A

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

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Cancers, November 2022, MDPI AG

    Altuna A

  15. Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Genome Biology, May 2022, Springer Science + Business Media

    Altuna A

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

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Nature Machine Intelligence, February 2022, Springer Science + Business Media

    Altuna A

  19. Identifying tumor cells at the single cell level

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Nature Communications, December 2020, Springer Science + Business Media

    Altuna A

  23. Parallel genetics of regulatory sequencesin vivo

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Altuna A

  24. Deep learning for genomics using Janggu

    Article • Nature Communications, July 2020, Springer Science + Business Media

    Altuna A

  25. Evaluation of colorectal cancer subtypes and cell lines using deep learning

    Article • Life Science Alliance, December 2019, Life Science Alliance, LLC

    Altuna A

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

    Article • Nature Communications, October 2019, Springer Science + Business Media

    Altuna A

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

    Article • Aging Cell, August 2019, Wiley

    Altuna A

  28. Janggu - Deep learning for genomics

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Altuna A

  29. Global identification of functional microRNA-mRNA interactions in Drosophila

    Article • Nature Communications, April 2019, Springer Science + Business Media

    Altuna A

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

    Article • Blood, March 2019, American Society of Hematology

    Altuna A

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

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Journal of Hematology & Oncology, January 2019, Springer Science + Business Media

    Altuna A

  33. OUP accepted manuscript

    Article • Nucleic Acids Research, January 2019, Oxford University Press (OUP)

    Altuna A

  34. Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

    Article • Nucleic Acids Research, December 2018, Oxford University Press (OUP)

    Altuna A

  35. Deciphering human ribonucleoprotein regulatory networks

    Article • Nucleic Acids Research, December 2018, Oxford University Press (OUP)

    Altuna A

  36. The IκB kinase complex is a regulator of mRNA stability

    Article • The EMBO Journal, November 2018, EMBO

    Altuna A

  37. Evaluation of colorectal cancer subtypes and cell lines using deep learning

    Article • November 2018, Cold Spring Harbor Laboratory Press

    Altuna A

  38. PiGx: Reproducible genomics analysis pipelines with GNU Guix

    Article • GigaScience, October 2018, Oxford University Press (OUP)

    Altuna A

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

    Article • Developmental Cell, September 2018, Elsevier

    Altuna A

  40. Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

    Article • Cell, September 2018, Elsevier

    Altuna A

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

    Article • F1000Research, July 2018, Faculty of 1000, Ltd.

    Altuna A

  42. Reproducible genomics analysis pipelines with GNU Guix

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Altuna A

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

    Article • Cell Reports, February 2018, Elsevier

    Altuna A

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

    Article • F1000Research, January 2018, Faculty of 1000, Ltd.

    Altuna A

  45. Using gene networks to make sense of single cell biology

    Article • F1000Research, January 2018, Faculty of 1000, Ltd.

    Altuna A

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

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Altuna A

  47. Strategies for analyzing bisulfite sequencing data

    Article • Journal of Biotechnology, November 2017, Elsevier

    Altuna A

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

    Article • October 2017, Springer Science + Business Media

    Altuna A

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

    Article • Molecular Systems Biology, October 2017, EMBO

    Altuna A

  50. RNA localization is a key determinant of neurite-enriched proteome

    Article • Nature Communications, September 2017, Nature

    Altuna A

  51. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

    Article • Nucleic Acids Research, June 2017, Oxford University Press (OUP)

    Björn Grüning, Altuna A

  52. HOT or not: Examining the basis of high-occupancy target regions

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Altuna A

  53. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

    Article • Nucleic Acids Research, February 2017, Oxford University Press (OUP)

    Altuna A

  54. Strategies for analyzing bisulfite sequencing data

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Altuna A

  55. The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Dr A. Bulak Arpat, Altuna A, Gina Cannarozzi, Lukas Weber

  56. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

    Article • Nature, January 2015, Nature

    Altuna A

  57. DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia

    Article • Cell Reports, December 2014, Elsevier

    Dr. Xinyang Zhao, Altuna A

  58. DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

    Article • Nucleic Acids Research, November 2014, Oxford University Press (OUP)

    Altuna A

  59. genomation: a toolkit to summarize, annotate and visualize genomic intervals

    Article • Bioinformatics, November 2014, Oxford University Press (OUP)

    Altuna A

  60. Two independent transcription initiation codes overlap on vertebrate core promoters

    Article • Nature, February 2014, Nature

    Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

  61. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

    Article • Frontiers in Cellular Neuroscience, January 2014, Frontiers

    Altuna A, Piero Carninci

  62. Induction of sarcomas by mutant IDH2

    Article • Genes & Development, September 2013, Cold Spring Harbor Laboratory Press

    Altuna A

  63. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

    Article • Genome Research, September 2013, Cold Spring Harbor Laboratory Press

    Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

  64. An optimized algorithm for detecting and annotating regional differential methylation

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Altuna A

  65. Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

    Article • PLoS Genetics, June 2012, PLOS

    Altuna A

  66. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

    Article • Proceedings of the National Academy of Sciences, March 2012, Proceedings of the National Academy of Sciences

    Altuna A, Piero Carninci

  67. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

    Article • Genome Biology, January 2012, Springer Science + Business Media

    Altuna A

  68. Promoter architecture of mouse olfactory receptor genes

    Article • Genome Research, December 2011, Cold Spring Harbor Laboratory Press

    Altuna A, Piero Carninci

  69. Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

    Article • PLOS One, September 2011, PLOS

    Altuna A, Marian Seda

  70. Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

    Article • Developmental Biology, April 2010, Elsevier

    Altuna A

  71. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

    Article • Cell, April 2010, Elsevier

    Piero Carninci, Altuna A

  72. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

    Article • Cell, March 2010, Elsevier

    Altuna A, Piero Carninci

  73. Translog, a web browser for studying the expression divergence of homologous genes

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Altuna A

  74. Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish

    Article • Developmental Dynamics, September 2009, Wiley

    Altuna A

  75. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

    Article • Nature Genetics, April 2009, Nature

    Altuna A, Piero Carninci, Professor Nikolai Petrovsky

  76. Transcriptional features of genomic regulatory blocks

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Altuna A

  77. Differential Evolution of the 13 Atlantic Salmon Hox Clusters

    Article • Molecular Biology and Evolution, April 2008, Oxford University Press (OUP)

    Altuna A

  78. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

    Article • Genome Research, March 2007, Cold Spring Harbor Laboratory Press

    Altuna A

  79. Complex Loci in Human and Mouse Genomes

    Article • PLoS Genetics, January 2006, PLOS

    Altuna A, Piero Carninci