All Stories

  1. Leveraging large language models for data analysis automation

    Article • PLOS One, February 2025, PLOS

    Altuna A

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

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

    Altuna A

  3. 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

  4. 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

  5. Janggu - Deep learning for genomics

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Altuna A

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

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

    Altuna A

  7. 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

  8. 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

  9. 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

  10. OUP accepted manuscript

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

    Altuna A

  11. 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

  12. Deciphering human ribonucleoprotein regulatory networks

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

    Altuna A

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

    Article • The EMBO Journal, November 2018, EMBO

    Altuna A

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

    Article • November 2018, Cold Spring Harbor Laboratory Press

    Altuna A

  15. PiGx: Reproducible genomics analysis pipelines with GNU Guix

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

    Altuna A

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

    Article • Developmental Cell, September 2018, Elsevier

    Altuna A

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

    Article • Cell, September 2018, Elsevier

    Altuna A

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

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

    Altuna A

  19. Reproducible genomics analysis pipelines with GNU Guix

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Altuna A

  20. 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

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

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

    Altuna A

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

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

    Altuna A

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

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Altuna A

  24. Strategies for analyzing bisulfite sequencing data

    Article • Journal of Biotechnology, November 2017, Elsevier

    Altuna A

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

    Article • October 2017, Springer Science + Business Media

    Altuna A

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

    Article • Molecular Systems Biology, October 2017, EMBO

    Altuna A

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

    Article • Nature Communications, September 2017, Nature

    Altuna A

  28. 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

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

    Article • March 2017, Cold Spring Harbor Laboratory Press

    Altuna A

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

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

    Altuna A

  31. Strategies for analyzing bisulfite sequencing data

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Altuna A

  32. 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

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

    Article • Nature, January 2015, Nature

    Altuna A

  34. 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

  35. 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

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

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

    Altuna A

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

    Article • Nature, February 2014, Nature

    Altuna A, Piero Carninci, Dr ir Wilfred van IJcken

  38. 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

  39. Induction of sarcomas by mutant IDH2

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

    Altuna A

  40. 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

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

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

    Altuna A

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

    Article • PLoS Genetics, June 2012, PLOS

    Altuna A

  43. 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

  44. 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

  45. Promoter architecture of mouse olfactory receptor genes

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

    Altuna A, Piero Carninci

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

    Article • PLOS One, September 2011, PLOS

    Altuna A, Marian Seda

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

    Article • Developmental Biology, April 2010, Elsevier

    Altuna A

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

    Article • Cell, April 2010, Elsevier

    Piero Carninci, Altuna A

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

    Article • Cell, March 2010, Elsevier

    Altuna A, Piero Carninci

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

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

    Altuna A

  51. 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

  52. 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

  53. Transcriptional features of genomic regulatory blocks

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

    Altuna A

  54. Differential Evolution of the 13 Atlantic Salmon Hox Clusters

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

    Altuna A

  55. 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

  56. Complex Loci in Human and Mouse Genomes

    Article • PLoS Genetics, January 2006, PLOS

    Altuna A, Piero Carninci