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List of works by Altuna Akalin

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

scientific article published in March 2019

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An optimized algorithm for detecting and annotating regional differential methylation

scientific article

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

scientific article published on 29 January 2019

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia

scientific article

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

scientific article published on 06 May 2020

Cell-type specialization is encoded by specific chromatin topologies

scientific article published on 17 November 2021

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

scientific article published on 6 February 2010

Complex Loci in human and mouse genomes

scientific article

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

scientific article

Deep learning for genomics using Janggu

scientific article published on 13 July 2020

Differential evolution of the 13 Atlantic salmon Hox clusters

scientific article

Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions

scientific article

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

scientific article

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

scientific article published on 03 September 2013

Evaluation of colorectal cancer subtypes and cell lines using deep learning

scientific article published on 02 December 2019

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

scientific article published on 02 August 2018

Genomation: a toolkit to summarize, annotate and visualize genomic intervals

scientific article published on 21 November 2014

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

scientific article

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

scientific article published on 26 March 2007

Global identification of functional microRNA-mRNA interactions in Drosophila

scientific article published on 09 April 2019

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

article published in 2017

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

scientific article published on 01 June 2019

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

scientific article published on 30 May 2022

Induction of sarcomas by mutant IDH2

scientific article published on September 2013

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

scientific article published on 06 September 2018

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

scientific article

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

scientific article published in February 2018

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

scientific article published on 19 October 2021

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

scientific article published in 2024

PiGx: Reproducible genomics analysis pipelines with GNU Guix

Promoter architecture of mouse olfactory receptor genes

scientific journal article

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

scientific article published on 21 February 2017

RNA localization is a key determinant of neurite-enriched proteome

scientific article published on 19 September 2017

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

scientific article published on 16 October 2017

Reproducible genomics analysis pipelines with GNU Guix

article published in 2018

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

scientific article published on 25 October 2019

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

scientific article published on 11 December 2020

Strategies for analyzing bisulfite sequencing data

scientific article

Strategies for analyzing bisulfite sequencing data

The IκB kinase complex is a regulator of mRNA stability

scientific article published on 22 November 2018

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

scientific article published on 05 June 2017

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

scientific article (publication date: 4 January 2016)

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

scientific article published on 09 August 2019

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

scientific article

Transcriptional features of genomic regulatory blocks

scientific article published on 19 April 2009

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

scientific article

Two independent transcription initiation codes overlap on vertebrate core promoters

scientific article published on 16 February 2014

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

scientific article published on 31 October 2017

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

article

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

scientific article

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

scholarly article published 13 December 2017

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

scientific article published on 3 January 2018

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