Halfdan Rydbeck
About Halfdan Rydbeck
I contribute to the bioinformatics part of projects analyzing proteomics data of plasma samples from prematurely born children. In one such project longitudinal data on concentrations of plasma proteins is analyzed together with data on volumes of different brain regions and with other clinical outcomes. In another one methods for identifying biomarkers are being applied to find protein concentrations in cord blood that can be used as a less labor intensive and cheaper way to read out blood stemcell concentration to determine suitability for transplantation.
The analyses includes regular analytical steps like normalisation, tests for differential expression, correlation networks and enrichment analyses. The algorithms and tools for these tasks are not yet mature but evolving at something of a yearly rate. The analyses are performed in Rstudio where the workhorses are the R package collections Bioconductor and Tidyverse. Reports are generated with R notebooks and the R package Bookdown. Github and GitKraken is used for code version control. Recently applied R packages are DEqMS for differential expression analysis of mass spectrometry data, WGCNA for proteins correlation analysis and ReactomeGSA for pathway analysis.
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Transcriptome network analysis links perinatal Staphylococcus epidermidis infection to microglia reprogramming in the immature
hippocampus
Giacomo Gravina, Maryam Ardalan, Tetyana Chumak, Halfdan Rydbeck, Xiaoyang Wang, Carl Joakim Ek, Carina Mallard
Glia - 2023 -
The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell
count
Anders K. Nilsson, Halfdan Rydbeck, Annika Thorsell, Sofia Frändberg, Helena Barreto Henriksson, Camilla Hesse, Gunnel Hellgren, Pia Lundgren, Ann Hellström
Stem Cell Research - 2022 -
Expression of S100A Alarmins in Cord Blood Monocytes Is Highly Associated With Chorioamnionitis and Fetal Inflammation in Preterm
Infants
Veronika Golubinskaya, Henri Puttonen, Ing Marie Fyhr, Halfdan Rydbeck, Ann Hellström, Bo Jacobsson, Holger Nilsson, Carina Mallard, Karin Sävman
Frontiers in Immunology - 2020 -
Independent losses of a xenobiotic receptor across teleost
evolution
Marta Eide, Halfdan Rydbeck, Ole K. Tørresen, Roger Lille-Langøy, Pål Puntervoll, Jared V. Goldstone, Kjetill S. Jakobsen, John Stegeman, Anders Goksøyr, Odd A. Karlsen
Scientific Reports - 2018 -
ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data
sets
Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig
PLoS ONE - 2015 -
The Genomic HyperBrowser: an analysis web server for genome-scale
data.
Geir K. Sandve, Sveinung Gundersen, Morten Johansen, Ingrid K. Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck, Kai Trengereid, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Matús Kalas, Tonje Lien, Morten B. Rye, Arnoldo Frigessi, Eivind Hovig
Nucleic acids research - 2013 -
Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression
data
Marieke L. Kuijjer, Halfdan Rydbeck, Stine H. Kresse, Emilie P. Buddingh, Ana B. Lid, Helene Roelofs, Horst Bürger, Ola Myklebost, Pancras C.W. Hogendoorn, Leonardo A. Meza-Zepeda, Anne Marie Cleton-Jansen
Genes Chromosomes and Cancer - 2012 -
Integrative Analysis Reveals Relationships of Genetic and Epigenetic Alterations in
Osteosarcoma
Stine H. Kresse, Halfdan Rydbeck, Magne Skårn, Heidi M. Namløs, Ana H. Barragan-Polania, Anne Marie Cleton-Jansen, Massimo Serra, Knut Liestøl, Pancras C.W. Hogendoorn, Eivind Hovig, Ola Myklebost, Leonardo A. Meza-Zepeda
PLoS ONE - 2012 -
The differential disease
regulome
Geir K. Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K. Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig
BMC Genomics - 2011 -
Evaluation of high-resolution microarray platforms for genomic profiling of bone
tumours
Stine H. Kresse, Karoly Szuhai, Ana H. Barragan-Polania, Halfdan Rydbeck, Anne Marie Cleton-Jansen, Ola Myklebost, Leonardo A. Meza-Zepeda
BMC Research Notes - 2010 -
The Genomic HyperBrowser: Inferential genomics at the sequence
level
Geir K. Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K. Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig
Genome Biology - 2010 -
Incorporating prior biological information in linkage studies increases power and limits multiple
testing.
Francesca Lantieri, Halfdan Rydbeck, Paola Griseri, Isabella Ceccherini, Marcella Devoto
BMC proceedings - 2007 -
Univariate and bivariate variance component linkage analysis of a whole-genome scan for loci contributing to bone mineral
density
Marcella Devoto, Loretta D. Spotila, Deborah L. Stabley, Gina N. Wharton, Halfdan Rydbeck, Jarmo Korkko, Richard Kosich, Darwin Prockop, Alan Tenenhouse, Katia Sol-Church
European Journal of Human Genetics - 2005