Genetics and computational biology

Publications 2024

Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD (2024)
Publisher Correction: A 39 kb structural variant causing Lynch syndrome detected by optical genome mapping and nanopore sequencing
Eur J Hum Genet, 32 (5), 601-602
DOI 10.1038/s41431-023-01519-1, PubMed 38172175

Cangren P, Bertrand YJK, Braverman JM, Gilfillan GD, Hamilton MB, Oxelman B (2024)
A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera
Data Brief, 57, 111094
DOI 10.1016/j.dib.2024.111094, PubMed 39633972

Cobb L, de Muinck E, Kollias S, Skage M, Gilfillan GD, Sydenham MAK, Qiao SW, Star B (2024)
High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method
PLoS One, 19 (3), e0300865
DOI 10.1371/journal.pone.0300865, PubMed 38517905

Kristjansson D, Lee Y, Page CM, Gjessing H, Magnus MC, Jugessur A, Lyle R, Håberg SE (2024)
Sex differences in DNA methylation variations according to ART conception-evidence from the Norwegian mother, father, and child cohort study
Sci Rep, 14 (1), 22904
DOI 10.1038/s41598-024-73845-3, PubMed 39358554

Murgatroyd C, Salontaji K, Smajlagic D, Page C, Sanders F, Jugessur A, Lyle R, Tsotsi S, Haftorn K, Felix J, Walton E, Tiemeier H, Cecil C, Bekkhus M (2024)
Prenatal stress and gestational epigenetic age: No evidence of associations based on a large prospective multi-cohort study
Res Sq
DOI 10.21203/rs.3.rs-4257223/v1, PubMed 39011115

Rostami S, Rounge TB, Pestarino L, Lyle R, Fortner RT, Haaland ØA, Lie RT, Wiklund F, Bjørge T, Langseth H (2024)
Differential levels of circulating RNAs prior to endometrial cancer diagnosis
Int J Cancer, 155 (5), 946-956
DOI 10.1002/ijc.34951, PubMed 38733362

Spildrejorde M, Leithaug M, Samara A, Aass HCD, Sharma A, Acharya G, Nordeng H, Gervin K, Lyle R (2024)
Citalopram exposure of hESCs during neuronal differentiation identifies dysregulated genes involved in neurodevelopment and depression
Front Cell Dev Biol, 12, 1428538
DOI 10.3389/fcell.2024.1428538, PubMed 39055655

Publications 2023

Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD (2023)
A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing
Eur J Hum Genet, 32 (5), 513-520
DOI 10.1038/s41431-023-01494-7, PubMed 38030917

Bråten LCH, Gjefsen E, Gervin K, Pripp AH, Skouen JS, Schistad E, Pedersen LM, Wigemyr M, Selmer KK, Aass HCD, Goll G, Brox JI, Espeland A, Grøvle L, Zwart JA, Storheim K, AIM-study group (2023)
Cytokine Patterns as Predictors of Antibiotic Treatment Effect in Chronic Low Back Pain with Modic Changes: Subgroup Analyses of a Randomized Trial (AIM Study)
J Pain Res, 16, 1713-1724
DOI 10.2147/JPR.S406079, PubMed 37252109

Diaz-Lundahl S, Nørstebø SF, Klem TB, Gilfillan GD, Dalland M, Gillund P, Krogenæs A (2023)
The microbiota of uterine biopsies, cytobrush and vaginal swabs at artificial insemination in Norwegian red cows
Theriogenology, 209, 115-125
DOI 10.1016/j.theriogenology.2023.06.024, PubMed 37390751

Gjefsen E, Gervin K, Bråten LCH, Goll GL, Aass HCD, Schistad EI, Wigemyr M, Pedersen LM, Skouen JS, Vigeland MD, Selmer KK, Storheim K, Zwart JA (2023)
Longitudinal changes of serum cytokines in patients with chronic low back pain and Modic changes
Osteoarthritis Cartilage, 31 (4), 543-547
DOI 10.1016/j.joca.2023.01.001, PubMed 36640896

Haftorn KL, Denault WRP, Lee Y, Page CM, Romanowska J, Lyle R, Næss ØE, Kristjansson D, Magnus PM, Håberg SE, Bohlin J, Jugessur A (2023)
Nucleated red blood cells explain most of the association between DNA methylation and gestational age
Commun Biol, 6 (1), 224
DOI 10.1038/s42003-023-04584-w, PubMed 36849614

Lekva T, Sundaram AYF, Roland MCP, Åsheim J, Michelsen AE, Norwitz ER, Aukrust P, Gilfillan GD, Ueland T (2023)
Platelet and mitochondrial RNA is decreased in plasma-derived extracellular vesicles in women with preeclampsia-an exploratory study
BMC Med, 21 (1), 458
DOI 10.1186/s12916-023-03178-x, PubMed 37996819

Nilsen Husebye ES, Romanowska J, Bjørke-Monsen AL, Gilhus NE, Selmer K, Gervin K, Riedel B, Bjørk MH (2023)
Does maternal genetic liability to folate deficiency influence the risk of antiseizure medication-associated language impairment and autistic traits in children of women with epilepsy?
Am J Clin Nutr, 118 (1), 303-313
DOI 10.1016/j.ajcnut.2023.05.023, PubMed 37217097

Olstad EW, Nordeng HME, Lyle R, Gervin K (2023)
No impact of prenatal paracetamol and folic acid exposure on cord blood DNA methylation in children with attention-deficit/hyperactivity disorder
Front Genet, 14, 1204879
DOI 10.3389/fgene.2023.1204879, PubMed 37396039

Olstad EW, Nordeng HME, Sandve GK, Lyle R, Gervin K (2023)
Effects of prenatal exposure to (es)citalopram and maternal depression during pregnancy on DNA methylation and child neurodevelopment
Transl Psychiatry, 13 (1), 149
DOI 10.1038/s41398-023-02441-2, PubMed 37147306

Pedersen S, Kverneland M, Rudi K, Gervin K, Landmark CJ, Iversen PO, Selmer KK (2023)
Decreased serum concentrations of antiseizure medications in children with drug resistant epilepsy following treatment with ketogenic diet
Epilepsia Open, 8 (3), 858-866
DOI 10.1002/epi4.12746, PubMed 37057954

Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A (2023)
The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome?
Hum Genomics, 17 (1), 35
DOI 10.1186/s40246-023-00484-6, PubMed 37085889

Spildrejorde M, Samara A, Sharma A, Leithaug M, Falck M, Modafferi S, Sundaram AYM, Acharya G, Nordeng H, Eskeland R, Gervin K, Lyle R (2023)
Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol
iScience, 26 (10), 107755
DOI 10.1016/j.isci.2023.107755, PubMed 37731623

Vigeland MD, Flåm ST, Vigeland MD, Espeland A, Zucknick M, Wigemyr M, Bråten LCH, Gjefsen E, Zwart JA, Storheim K, Pedersen LM, Selmer K, Lie BA, Gervin K, The Aim Study Group (2023)
Long-Term Use of Amoxicillin Is Associated with Changes in Gene Expression and DNA Methylation in Patients with Low Back Pain and Modic Changes
Antibiotics (Basel), 12 (7)
DOI 10.3390/antibiotics12071217, PubMed 37508313

Publications 2022

Diaz-Lundahl S, Sundaram AYM, Gillund P, Gilfillan GD, Olsaker I, Krogenæs A (2022)
Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos
Front Genet, 12, 780113
DOI 10.3389/fgene.2021.780113, PubMed 35096004

Holmgren A, Hansson L, Bjerkaas-Kjeldal K, Impellizzeri AAR, Gilfillan GD, Djurovic S, Hughes T (2022)
Mapping the expression of an ANK3 isoform associated with bipolar disorder in the human brain
Transl Psychiatry, 12 (1), 45
DOI 10.1038/s41398-022-01784-6, PubMed 35091539

Håberg SE, Page CM, Lee Y, Nustad HE, Magnus MC, Haftorn KL, Carlsen EØ, Denault WRP, Bohlin J, Jugessur A, Magnus P, Gjessing HK, Lyle R (2022)
DNA methylation in newborns conceived by assisted reproductive technology
Nat Commun, 13 (1), 1896
DOI 10.1038/s41467-022-29540-w, PubMed 35393427

Kallak TK, Fransson E, Bränn E, Berglund H, Lager S, Comasco E, Lyle R, Skalkidou A (2022)
Maternal prenatal depressive symptoms and toddler behavior: an umbilical cord blood epigenome-wide association study
Transl Psychiatry, 12 (1), 186
DOI 10.1038/s41398-022-01954-6, PubMed 35513368

Nustad HE, Steinsland I, Ollikainen M, Cazaly E, Kaprio J, Benjamini Y, Gervin K, Lyle R (2022)
Modeling dependency structures in 450k DNA methylation data
Bioinformatics, 38 (4), 885-891
DOI 10.1093/bioinformatics/btab774, PubMed 34788815

Olstad EW, Nordeng HME, Sandve GK, Lyle R, Gervin K (2022)
Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures
Clin Epigenetics, 14 (1), 80
DOI 10.1186/s13148-022-01299-3, PubMed 35765087

Pedersen S, Kverneland M, Nakken KO, Rudi K, Iversen PO, Gervin K, Selmer KK (2022)
Genome-wide decrease in DNA methylation in adults with epilepsy treated with modified ketogenic diet: A prospective study
Epilepsia, 63 (9), 2413-2426
DOI 10.1111/epi.17351, PubMed 35762681

Ribarska T, Bjørnstad PM, Sundaram AYM, Gilfillan GD (2022)
Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing
BMC Genomics, 23 (1), 92
DOI 10.1186/s12864-022-08316-y, PubMed 35105301

Samara A, Falck M, Spildrejorde M, Leithaug M, Acharya G, Lyle R, Eskeland R (2022)
Robust neuronal differentiation of human embryonic stem cells for neurotoxicology
STAR Protoc, 3 (3), 101533
DOI 10.1016/j.xpro.2022.101533, PubMed 36123835

Samara A, Spildrejorde M, Sharma A, Falck M, Leithaug M, Modafferi S, Bjørnstad PM, Acharya G, Gervin K, Lyle R, Eskeland R (2022)
A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D
iScience, 25 (11), 105279
DOI 10.1016/j.isci.2022.105279, PubMed 36304110

Soares JZ, Valeur J, Šaltytė Benth J, Knapskog AB, Selbæk G, Arefi G, Gilfillan GD, Tollisen A, Bogdanovic N, Pettersen R (2022)
Vitamin D in Alzheimer's Disease: Low Levels in Cerebrospinal Fluid Despite Normal Amounts in Serum
J Alzheimers Dis, 86 (3), 1301-1314
DOI 10.3233/JAD-215536, PubMed 35180126

Tønne E, Due-Tønnessen BJ, Vigeland MD, Amundsen SS, Ribarska T, Åsten PM, Sheng Y, Helseth E, Gilfillan GD, Mero IL, Heimdal KR (2022)
Whole-exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways
Am J Med Genet A, 188 (5), 1464-1475
DOI 10.1002/ajmg.a.62663, PubMed 35080095

Umu SU, Langseth H, Zuber V, Helland Å, Lyle R, Rounge TB (2022)
Serum RNAs can predict lung cancer up to 10 years prior to diagnosis
Elife, 11
DOI 10.7554/eLife.71035, PubMed 35147498

Yadav A, Verhaegen S, Filis P, Domanska D, Lyle R, Sundaram AYM, Leithaug M, Østby GC, Aleksandersen M, Berntsen HF, Zimmer KE, Fowler PA, Paulsen RE, Ropstad E (2022)
Exposure to a human relevant mixture of persistent organic pollutants or to perfluorooctane sulfonic acid alone dysregulates the developing cerebellum of chicken embryo
Environ Int, 166, 107379
DOI 10.1016/j.envint.2022.107379, PubMed 35792514

Publications 2021

Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor JA, Xu Z, Lie RT, Gjessing HK, Jugessur A (2021)
Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts
NAR Genom Bioinform, 3 (2), lqab035
DOI 10.1093/nargab/lqab035, PubMed 33987535

Gjefsen E, Gervin K, Goll G, Bråten LCH, Wigemyr M, Aass HCD, Vigeland MD, Schistad E, Pedersen LM, Pripp AH, Storheim K, Selmer KK, Zwart JA (2021)
Macrophage migration inhibitory factor: a potential biomarker for chronic low back pain in patients with Modic changes
RMD Open, 7 (2)
DOI 10.1136/rmdopen-2021-001726, PubMed 34344830

Gomes JDA, Olstad EW, Kowalski TW, Gervin K, Vianna FSL, Schüler-Faccini L, Nordeng HME (2021)
Genetic Susceptibility to Drug Teratogenicity: A Systematic Literature Review
Front Genet, 12, 645555
DOI 10.3389/fgene.2021.645555, PubMed 33981330

Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Norli ES, Evenrød IM, Andreassen BK, Franzenburg S, Franke A, Rayner S, Gervin K, Lie BA (2021)
Methotrexate Treatment of Newly Diagnosed RA Patients Is Associated With DNA Methylation Differences at Genes Relevant for Disease Pathogenesis and Pharmacological Action
Front Immunol, 12, 713611
DOI 10.3389/fimmu.2021.713611, PubMed 34867944

Haftorn KL, Lee Y, Denault WRP, Page CM, Nustad HE, Lyle R, Gjessing HK, Malmberg A, Magnus MC, Næss Ø, Czamara D, Räikkönen K, Lahti J, Magnus P, Håberg SE, Jugessur A, Bohlin J (2021)
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies
Clin Epigenetics, 13 (1), 82
DOI 10.1186/s13148-021-01055-z, PubMed 33875015

Kaitetzidou E, Gilfillan GD, Antonopoulou E, Sarropoulou E (2021)
Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns
Genomics, 114 (1), 266-277
DOI 10.1016/j.ygeno.2021.12.010, PubMed 34933072

Kallak TK, Bränn E, Fransson E, Johansson Å, Lager S, Comasco E, Lyle R, Skalkidou A (2021)
DNA methylation in cord blood in association with prenatal depressive symptoms
Clin Epigenetics, 13 (1), 78
DOI 10.1186/s13148-021-01054-0, PubMed 33845866

Kværner AS, Birkeland E, Bucher-Johannessen C, Vinberg E, Nordby JI, Kangas H, Bemanian V, Ellonen P, Botteri E, Natvig E, Rognes T, Hovig E, Lyle R, Ambur OH, de Vos WM, Bultman S, Hjartåker A, Landberg R, Song M, Blix HS, Ursin G, Randel KR, de Lange T, Hoff G, Holme Ø et al. (2021)
The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants
BMC Cancer, 21 (1), 930
DOI 10.1186/s12885-021-08640-8, PubMed 34407780

Lind A, Barlinn R, Landaas ET, Andresen LL, Jakobsen K, Fladeby C, Nilsen M, Bjørnstad PM, Sundaram AYM, Ribarska T, Müller F, Gilfillan GD, Holberg-Petersen M (2021)
Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory
J Clin Virol, 141, 104906
DOI 10.1016/j.jcv.2021.104906, PubMed 34273860

Olstad EW, Nordeng HME, Gervin K (2021)
Prenatal medication exposure and epigenetic outcomes: a systematic literature review and recommendations for prenatal pharmacoepigenetic studies
Epigenetics, 17 (4), 357-380
DOI 10.1080/15592294.2021.1903376, PubMed 33926354

Wojewodzic MW, Leithaug M, Lauritzen M, Lyle R, Haglund S, Rubin CJ, Ewels PA, Grotmol T, Rounge TB (2021)
Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes
Clin Epigenetics, 13 (1), 107
DOI 10.1186/s13148-021-01097-3, PubMed 33980276

Publications 2020

Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Lillegraven S, Aga AB, Evenrød IM, Norli ES, Andreassen BK, Franzenburg S, Franke A, Haavardsholm EA, Rayner S, Gervin K, Lie BA (2020)
Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4⁺ Memory Than in CD4⁺ Naïve T Cells
Front Immunol, 11, 194
DOI 10.3389/fimmu.2020.00194, PubMed 32117312

Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Rayner S, Lie BA, Gilfillan GD (2020)
An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits
RNA Biol, 17 (9), 1284-1292
DOI 10.1080/15476286.2020.1761081, PubMed 32436772

Lee Y, Haftorn KL, Denault WRP, Nustad HE, Page CM, Lyle R, Lee-Ødegård S, Moen GH, Prasad RB, Groop LC, Sletner L, Sommer C, Magnus MC, Gjessing HK, Harris JR, Magnus P, Håberg SE, Jugessur A, Bohlin J (2020)
Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
BMC Genomics, 21 (1), 747
DOI 10.1186/s12864-020-07168-8, PubMed 33109080

Umu SU, Langseth H, Keller A, Meese E, Helland Å, Lyle R, Rounge TB (2020)
A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis
Mol Oncol, 14 (2), 235-247
DOI 10.1002/1878-0261.12620, PubMed 31851411

Publications 2019

Cernilogar FM, Hasenöder S, Wang Z, Scheibner K, Burtscher I, Sterr M, Smialowski P, Groh S, Evenroed IM, Gilfillan GD, Lickert H, Schotta G (2019)
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
Nucleic Acids Res, 47 (17), 9069-9086
DOI 10.1093/nar/gkz627, PubMed 31350899

Fosslie M, Manaf A, Lerdrup M, Hansen K, Gilfillan GD, Dahl JA (2019)
Going low to reach high: Small-scale ChIP-seq maps new terrain
Wiley Interdiscip Rev Syst Biol Med, 12 (1), e1465
DOI 10.1002/wsbm.1465, PubMed 31478357

Furi L, Crawford LA, Rangel-Pineros G, Manso AS, De Ste Croix M, Haigh RD, Kwun MJ, Engelsen Fjelland K, Gilfillan GD, Bentley SD, Croucher NJ, Clokie MR, Oggioni MR (2019)
Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host
J Bacteriol, 201 (19)
DOI 10.1128/JB.00370-19, PubMed 31285240

Gervin K, Salas LA, Bakulski KM, van Zelm MC, Koestler DC, Wiencke JK, Duijts L, Moll HA, Kelsey KT, Kobor MS, Lyle R, Christensen BC, Felix JF, Jones MJ (2019)
Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data
Clin Epigenetics, 11 (1), 125
DOI 10.1186/s13148-019-0717-y, PubMed 31455416

Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Farmer A, Henderson JM, Hussong MA, Moll P, Nguyen L, McNulty A, Shaffer JM, Shore S, Yip HK, Vitkovska J, Rayner S, Lie BA, Gilfillan GD (2019)
Systematic assessment of commercially available low-input miRNA library preparation kits
RNA Biol, 17 (1), 75-86
DOI 10.1080/15476286.2019.1667741, PubMed 31559901

Khezri A, Narud B, Stenseth EB, Johannisson A, Myromslien FD, Gaustad AH, Wilson RC, Lyle R, Morrell JM, Kommisrud E, Ahmad R (2019)
DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation
BMC Genomics, 20 (1), 897
DOI 10.1186/s12864-019-6307-8, PubMed 31775629

Publications 2018

Dahl JA, Gilfillan GD (2018)
How low can you go? Pushing the limits of low-input ChIP-seq
Brief Funct Genomics, 17 (2), 89-95
DOI 10.1093/bfgp/elx037, PubMed 29087438

Eguíluz-Gracia I, Malmstrom K, Dheyauldeen SA, Lohi J, Sajantila A, Aaløkken R, Sundaram AYM, Gilfillan GD, Makela M, Baekkevold ES, Jahnsen FL (2018)
Monocytes accumulate in the airways of children with fatal asthma
Clin Exp Allergy, 48 (12), 1631-1639
DOI 10.1111/cea.13265, PubMed 30184280

Hjorthaug HS, Gervin K, Mowinckel P, Munthe-Kaas MC (2018)
Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation
PLoS One, 13 (12), e0208699
DOI 10.1371/journal.pone.0208699, PubMed 30540848

Ribarska T, Gilfillan GD (2018)
Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers
Methods Mol Biol, 1689, 157-166
DOI 10.1007/978-1-4939-7380-4_14, PubMed 29027173

Rounge TB, Umu SU, Keller A, Meese E, Ursin G, Tretli S, Lyle R, Langseth H (2018)
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Sci Rep, 8 (1), 17650
DOI 10.1038/s41598-018-35974-4, PubMed 30518766

Santoro F, Pettini E, Kazmin D, Ciabattini A, Fiorino F, Gilfillan GD, Evenroed IM, Andersen P, Pozzi G, Medaglini D (2018)
Transcriptomics of the Vaccine Immune Response: Priming With Adjuvant Modulates Recall Innate Responses After Boosting
Front Immunol, 9, 1248
DOI 10.3389/fimmu.2018.01248, PubMed 29922291

Segorbe D, Wilkinson D, Mizeranschi A, Hughes T, Aaløkken R, Váchová L, Palková Z, Gilfillan GD (2018)
An optimized FAIRE procedure for low cell numbers in yeast
Yeast, 35 (8), 507-512
DOI 10.1002/yea.3316, PubMed 29577419

Stüken A, Haverkamp THA, Dirven HAAM, Gilfillan GD, Leithaug M, Lund V (2018)
Microbial Community Composition of Tap Water and Biofilms Treated with or without Copper-Silver Ionization
Environ Sci Technol, 52 (6), 3354-3364
DOI 10.1021/acs.est.7b05963, PubMed 29461810

Wilkinson D, Maršíková J, Hlaváček O, Gilfillan GD, Ježková E, Aaløkken R, Váchová L, Palková Z (2018)
Transcriptome Remodeling of Differentiated Cells during Chronological Ageing of Yeast Colonies: New Insights into Metabolic Differentiation
Oxid Med Cell Longev, 2018, 4932905
DOI 10.1155/2018/4932905, PubMed 29576850

Wilkinson D, Váchová L, Hlaváček O, Maršíková J, Gilfillan GD, Palková Z (2018)
Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms
Oxid Med Cell Longev, 2018, 4950591
DOI 10.1155/2018/4950591, PubMed 29765496

Publications 2017

de Muinck EJ, Trosvik P, Gilfillan GD, Hov JR, Sundaram AYM (2017)
A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform
Microbiome, 5 (1), 68
DOI 10.1186/s40168-017-0279-1, PubMed 28683838

Gervin K, Nordeng H, Ystrom E, Reichborn-Kjennerud T, Lyle R (2017)
Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD
Clin Epigenetics, 9, 77
DOI 10.1186/s13148-017-0376-9, PubMed 28785368

Hanssen EN, Lyle R, Egeland T, Gill P (2017)
Degradation in forensic trace DNA samples explored by massively parallel sequencing
Forensic Sci Int Genet, 27, 160-166
DOI 10.1016/j.fsigen.2017.01.002, PubMed 28088090

Lee S, Norheim F, Gulseth HL, Langleite TM, Kolnes KJ, Tangen DS, Stadheim HK, Gilfillan GD, Holen T, Birkeland KI, Jensen J, Drevon CA (2017)
Interaction between plasma fetuin-A and free fatty acids predicts changes in insulin sensitivity in response to long-term exercise
Physiol Rep, 5 (5)
DOI 10.14814/phy2.13183, PubMed 28270597

Maršíková J, Wilkinson D, Hlaváček O, Gilfillan GD, Mizeranschi A, Hughes T, Begany M, Rešetárová S, Váchová L, Palková Z (2017)
Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling
BMC Genomics, 18 (1), 814
DOI 10.1186/s12864-017-4214-4, PubMed 29061122

Reppe S, Lien TG, Hsu YH, Gautvik VT, Olstad OK, Yu R, Bakke HG, Lyle R, Kringen MK, Glad IK, Gautvik KM (2017)
Distinct DNA methylation profiles in bone and blood of osteoporotic and healthy postmenopausal women
Epigenetics, 12 (8), 674-687
DOI 10.1080/15592294.2017.1345832, PubMed 28650214

Sarropoulou E, Sundaram AYM, Kaitetzidou E, Kotoulas G, Gilfillan GD, Papandroulakis N, Mylonas CC, Magoulas A (2017)
Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili
Gigascience, 6 (12), 1-13
DOI 10.1093/gigascience/gix108, PubMed 29126158

Umu SU, Langseth H, Bucher-Johannessen C, Fromm B, Keller A, Meese E, Lauritzen M, Leithaug M, Lyle R, Rounge TB (2017)
A comprehensive profile of circulating RNAs in human serum
RNA Biol, 15 (2), 242-250
DOI 10.1080/15476286.2017.1403003, PubMed 29219730

Publications 2016

Beulig F, Urich T, Nowak M, Trumbore SE, Gleixner G, Gilfillan GD, Fjelland KE, Küsel K (2016)
Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure
Nat Microbiol, 1, 15025
DOI 10.1038/nmicrobiol.2015.25, PubMed 27571979

Gervin K, Andreassen BK, Hjorthaug HS, Carlsen KCL, Carlsen KH, Undlien DE, Lyle R, Munthe-Kaas MC (2016)
Intra-individual changes in DNA methylation not mediated by cell-type composition are correlated with aging during childhood
Clin Epigenetics, 8, 110
DOI 10.1186/s13148-016-0277-3, PubMed 27785156

Gervin K, Page CM, Aass HC, Jansen MA, Fjeldstad HE, Andreassen BK, Duijts L, van Meurs JB, van Zelm MC, Jaddoe VW, Nordeng H, Knudsen GP, Magnus P, Nystad W, Staff AC, Felix JF, Lyle R (2016)
Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition
Epigenetics, 11 (9), 690-698
DOI 10.1080/15592294.2016.1214782, PubMed 27494297

Lee S, Norheim F, Langleite TM, Noreng HJ, Storås TH, Afman LA, Frost G, Bell JD, Thomas EL, Kolnes KJ, Tangen DS, Stadheim HK, Gilfillan GD, Gulseth HL, Birkeland KI, Jensen J, Drevon CA, Holen T, NutriTech Consortium (2016)
Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging
Physiol Rep, 4 (21)
DOI 10.14814/phy2.13019, PubMed 27821717

Lekva T, Lyle R, Roland MC, Friis C, Bianchi DW, Jaffe IZ, Norwitz ER, Bollerslev J, Henriksen T, Ueland T (2016)
Gene expression in term placentas is regulated more by spinal or epidural anesthesia than by late-onset preeclampsia or gestational diabetes mellitus
Sci Rep, 6, 29715
DOI 10.1038/srep29715, PubMed 27405415

Samarakoon PS, Sorte HS, Stray-Pedersen A, Rødningen OK, Rognes T, Lyle R (2016)
cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data
BMC Genomics, 17, 51
DOI 10.1186/s12864-016-2374-2, PubMed 26764020

Sarropoulou E, Tsalafouta A, Sundaram AY, Gilfillan GD, Kotoulas G, Papandroulakis N, Pavlidis M (2016)
Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)
BMC Genomics, 17, 506
DOI 10.1186/s12864-016-2874-0, PubMed 27461489

Sorte HS, Osnes LT, Fevang B, Aukrust P, Erichsen HC, Backe PH, Abrahamsen TG, Kittang OB, Øverland T, Jhangiani SN, Muzny DM, Vigeland MD, Samarakoon P, Gambin T, Akdemir ZH, Gibbs RA, Rødningen OK, Lyle R, Lupski JR, Stray-Pedersen A (2016)
A potential founder variant in CARMIL2/RLTPR in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction
Mol Genet Genomic Med, 4 (6), 604-616
DOI 10.1002/mgg3.237, PubMed 27896283

Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR et al. (2016)
Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders
J Allergy Clin Immunol, 139 (1), 232-245
DOI 10.1016/j.jaci.2016.05.042, PubMed 27577878

Sundaram AY, Hughes T, Biondi S, Bolduc N, Bowman SK, Camilli A, Chew YC, Couture C, Farmer A, Jerome JP, Lazinski DW, McUsic A, Peng X, Shazand K, Xu F, Lyle R, Gilfillan GD (2016)
A comparative study of ChIP-seq sequencing library preparation methods
BMC Genomics, 17 (1), 816
DOI 10.1186/s12864-016-3135-y, PubMed 27769162

Svendsen AJ, Gervin K, Lyle R, Christiansen L, Kyvik K, Junker P, Nielsen C, Houen G, Tan Q (2016)
Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study
Front Immunol, 7, 510
DOI 10.3389/fimmu.2016.00510, PubMed 27909437

Tekpli X, Urbanucci A, Hashim A, Vågbø CB, Lyle R, Kringen MK, Staff AC, Dybedal I, Mills IG, Klungland A, Staerk J (2016)
Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Epigenetics Chromatin, 9, 21
DOI 10.1186/s13072-016-0070-8, PubMed 27252783

Trucchi E, Mazzarella AB, Gilfillan GD, Lorenzo MT, Schönswetter P, Paun O (2016)
BsRADseq: screening DNA methylation in natural populations of non-model species
Mol Ecol, 25 (8), 1697-713
DOI 10.1111/mec.13550, PubMed 26818626

Wikenius E, Moe V, Kjellevold M, Smith L, Lyle R, Waagbø R, Page CM, Myhre AM (2016)
The Association between Hair Cortisol and Self-Reported Symptoms of Depression in Pregnant Women
PLoS One, 11 (9), e0161804
DOI 10.1371/journal.pone.0161804, PubMed 27584584

Publications 2015

Lekva T, Berg JP, Lyle R, Heck A, Bollerslev J, Ueland T (2015)
Alternative splicing of placental lactogen (CSH2) in somatotroph pituitary adenomas
Neuro Endocrinol Lett, 36 (2), 136-42
PubMed 26071582

Ollikainen M, Ismail K, Gervin K, Kyllönen A, Hakkarainen A, Lundbom J, Järvinen EA, Harris JR, Lundbom N, Rissanen A, Lyle R, Pietiläinen KH, Kaprio J (2015)
Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat
Clin Epigenetics, 7 (1), 39
DOI 10.1186/s13148-015-0073-5, PubMed 25866590

Reppe S, Noer A, Grimholt RM, Halldórsson BV, Medina-Gomez C, Gautvik VT, Olstad OK, Berg JP, Datta H, Estrada K, Hofman A, Uitterlinden AG, Rivadeneira F, Lyle R, Collas P, Gautvik KM (2015)
Methylation of bone SOST, its mRNA, and serum sclerostin levels correlate strongly with fracture risk in postmenopausal women
J Bone Miner Res, 30 (2), 249-56
DOI 10.1002/jbmr.2342, PubMed 25155887

Rounge TB, Lauritzen M, Langseth H, Enerly E, Lyle R, Gislefoss RE (2015)
microRNA Biomarker Discovery and High-Throughput DNA Sequencing Are Possible Using Long-term Archived Serum Samples
Cancer Epidemiol Biomarkers Prev, 24 (9), 1381-7
DOI 10.1158/1055-9965.EPI-15-0289, PubMed 26108462

Willemsen G, Ward KJ, Bell CG, Christensen K, Bowden J, Dalgård C, Harris JR, Kaprio J, Lyle R, Magnusson PK, Mather KA, Ordoňana JR, Perez-Riquelme F, Pedersen NL, Pietiläinen KH, Sachdev PS, Boomsma DI, Spector T (2015)
The Concordance and Heritability of Type 2 Diabetes in 34,166 Twin Pairs From International Twin Registers: The Discordant Twin (DISCOTWIN) Consortium
Twin Res Hum Genet, 18 (6), 762-71
DOI 10.1017/thg.2015.83, PubMed 26678054

Publications 2014

Misceo D, Holmgren A, Louch WE, Holme PA, Mizobuchi M, Morales RJ, De Paula AM, Stray-Pedersen A, Lyle R, Dalhus B, Christensen G, Stormorken H, Tjønnfjord GE, Frengen E (2014)
A dominant STIM1 mutation causes Stormorken syndrome
Hum Mutat, 35 (5), 556-64
DOI 10.1002/humu.22544, PubMed 24619930

Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flåm ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E, Malaspinas AS (2014)
Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans
Curr Biol, 24 (21), 2518-25
DOI 10.1016/j.cub.2014.09.057, PubMed 25447991

Samarakoon PS, Sorte HS, Kristiansen BE, Skodje T, Sheng Y, Tjønnfjord GE, Stadheim B, Stray-Pedersen A, Rødningen OK, Lyle R (2014)
Identification of copy number variants from exome sequence data
BMC Genomics, 15 (1), 661
DOI 10.1186/1471-2164-15-661, PubMed 25102989

Squadrito ML, Baer C, Burdet F, Maderna C, Gilfillan GD, Lyle R, Ibberson M, De Palma M (2014)
Endogenous RNAs modulate microRNA sorting to exosomes and transfer to acceptor cells
Cell Rep, 8 (5), 1432-46
DOI 10.1016/j.celrep.2014.07.035, PubMed 25159140

Star B, Nederbragt AJ, Hansen MH, Skage M, Gilfillan GD, Bradbury IR, Pampoulie C, Stenseth NC, Jakobsen KS, Jentoft S (2014)
Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA
PLoS One, 9 (3), e89676
DOI 10.1371/journal.pone.0089676, PubMed 24608104

Stormo C, Kringen MK, Lyle R, Olstad OK, Sachse D, Berg JP, Piehler AP (2014)
RNA-sequencing analysis of HepG2 cells treated with atorvastatin
PLoS One, 9 (8), e105836
DOI 10.1371/journal.pone.0105836, PubMed 25153832

Publications 2013

Lekva T, Berg JP, Lyle R, Heck A, Ringstad G, Olstad OK, Michelsen AE, Casar-Borota O, Bollerslev J, Ueland T (2013)
Epithelial splicing regulator protein 1 and alternative splicing in somatotroph adenomas
Endocrinology, 154 (9), 3331-43
DOI 10.1210/en.2013-1051, PubMed 23825128

Peña-Diaz J, Hegre SA, Anderssen E, Aas PA, Mjelle R, Gilfillan GD, Lyle R, Drabløs F, Krokan HE, Sætrom P (2013)
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
Nucleic Acids Res, 41 (5), 2846-56
DOI 10.1093/nar/gks1336, PubMed 23325852

Weedon-Fekjær MS, Sheng Y, Herse F, Lyle R, Sugulle M, Dechend R, Staff AC (2013)
OP008. Different dysregulation of placental mirnas in early- and late-onset preeclampsia
Pregnancy Hypertens, 3 (2), 65
DOI 10.1016/j.preghy.2013.04.024, PubMed 26105854

Publications 2012

Forsberg LA, Rasi C, Razzaghian HR, Pakalapati G, Waite L, Thilbeault KS, Ronowicz A, Wineinger NE, Tiwari HK, Boomsma D, Westerman MP, Harris JR, Lyle R, Essand M, Eriksson F, Assimes TL, Iribarren C, Strachan E, O'Hanlon TP, Rider LG, Miller FW, Giedraitis V, Lannfelt L, Ingelsson M, Piotrowski A et al. (2012)
Age-related somatic structural changes in the nuclear genome of human blood cells
Am J Hum Genet, 90 (2), 217-28
DOI 10.1016/j.ajhg.2011.12.009, PubMed 22305530

Gervin K, Vigeland MD, Mattingsdal M, Hammerø M, Nygård H, Olsen AO, Brandt I, Harris JR, Undlien DE, Lyle R (2012)
DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes
PLoS Genet, 8 (1), e1002454
DOI 10.1371/journal.pgen.1002454, PubMed 22291603

Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R (2012)
Limitations and possibilities of low cell number ChIP-seq
BMC Genomics, 13, 645
DOI 10.1186/1471-2164-13-645, PubMed 23171294

Hansen JS, Nygaard UC, Lyle R, Lovik M (2012)
Early life interventions to prevent allergy in the offspring: the role of maternal immunization and postnatal mucosal allergen exposure
Int Arch Allergy Immunol, 158 (3), 261-75
DOI 10.1159/000332963, PubMed 22398405

Hekman KE, Yu GY, Brown CD, Zhu H, Du X, Gervin K, Undlien DE, Peterson A, Stevanin G, Clark HB, Pulst SM, Bird TD, White KP, Gomez CM (2012)
A conserved eEF2 coding variant in SCA26 leads to loss of translational fidelity and increased susceptibility to proteostatic insult
Hum Mol Genet, 21 (26), 5472-83
DOI 10.1093/hmg/dds392, PubMed 23001565

Leidenroth A, Sorte HS, Gilfillan G, Ehrlich M, Lyle R, Hewitt JE (2012)
Diagnosis by sequencing: correction of misdiagnosis from FSHD2 to LGMD2A by whole-exome analysis
Eur J Hum Genet, 20 (9), 999-1003
DOI 10.1038/ejhg.2012.42, PubMed 22378277

Munthe-Kaas MC, Bertelsen RJ, Torjussen TM, Hjorthaug HS, Undlien DE, Lyle R, Gervin K, Granum B, Mowinckel P, Carlsen KH, Carlsen KC (2012)
Pet keeping and tobacco exposure influence CD14 methylation in childhood
Pediatr Allergy Immunol, 23 (8), 747-54
DOI 10.1111/pai.12021, PubMed 23194293

Nilsen TS, Knudsen GP, Gervin K, Brandt I, Røysamb E, Tambs K, Orstavik R, Lyle R, Reichborn-Kjennerud T, Magnus P, Harris JR (2012)
The Norwegian Twin Registry from a public health perspective: a research update
Twin Res Hum Genet, 16 (1), 285-95
DOI 10.1017/thg.2012.117, PubMed 23186607

Sorte H, Mørkrid L, Rødningen O, Kulseth MA, Stray-Pedersen A, Matthijs G, Race V, Houge G, Fiskerstrand T, Bjurulf B, Lyle R, Prescott T (2012)
Severe ALG8-CDG (CDG-Ih) associated with homozygosity for two novel missense mutations detected by exome sequencing of candidate genes
Eur J Med Genet, 55 (3), 196-202
DOI 10.1016/j.ejmg.2012.01.003, PubMed 22306853

Squadrito ML, Pucci F, Magri L, Moi D, Gilfillan GD, Ranghetti A, Casazza A, Mazzone M, Lyle R, Naldini L, De Palma M (2012)
miR-511-3p modulates genetic programs of tumor-associated macrophages
Cell Rep, 1 (2), 141-54
DOI 10.1016/j.celrep.2011.12.005, PubMed 22832163

Straub T, Zabel A, Gilfillan GD, Feller C, Becker PB (2012)
Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq
Genome Res, 23 (3), 473-85
DOI 10.1101/gr.146407.112, PubMed 23233545

Publications 2011

Gervin K, Hammerø M, Akselsen HE, Moe R, Nygård H, Brandt I, Gjessing HK, Harris JR, Undlien DE, Lyle R (2011)
Extensive variation and low heritability of DNA methylation identified in a twin study
Genome Res, 21 (11), 1813-21
DOI 10.1101/gr.119685.110, PubMed 21948560

Ratnamala U, Lyle R, Rawal R, Singh R, Vishnupriya S, Himabindu P, Rao V, Aggarwal S, Paluru P, Bartoloni L, Young TL, Paoloni-Giacobino A, Morris MA, Nath SK, Antonarakis SE, Radhakrishna U (2011)
Refinement of the X-linked nonsyndromic high-grade myopia locus MYP1 on Xq28 and exclusion of 13 known positional candidate genes by direct sequencing
Invest Ophthalmol Vis Sci, 52 (9), 6814-9
DOI 10.1167/iovs.10-6815, PubMed 21357393

Selmer KK, Gilfillan GD, Strømme P, Lyle R, Hughes T, Hjorthaug HS, Brandal K, Nakken S, Misceo D, Egeland T, Munthe LA, Braekken SK, Undlien DE (2011)
A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions
Eur J Hum Genet, 20 (1), 58-63
DOI 10.1038/ejhg.2011.126, PubMed 21712855

Skinningsrud B, Lie BA, Lavant E, Carlson JA, Erlich H, Akselsen HE, Gervin K, Wolff AB, Erichsen MM, Løvås K, Husebye ES, Undlien DE (2011)
Multiple loci in the HLA complex are associated with Addison's disease
J Clin Endocrinol Metab, 96 (10), E1703-8
DOI 10.1210/jc.2011-0645, PubMed 21816777

Stax MJ, Naarding MA, Tanck MW, Lindquist S, Hernell O, Lyle R, Brandtzaeg P, Eggesbø M, Pollakis G, Paxton WA (2011)
Binding of human milk to pathogen receptor DC-SIGN varies with bile salt-stimulated lipase (BSSL) gene polymorphism
PLoS One, 6 (2), e17316
DOI 10.1371/journal.pone.0017316, PubMed 21386960

Publications 2010

Kulseth MA, Lyle R, Rødningen OK, Sorte H, Prescott T (2010)
Exon trapping analysis of c.301-19G > A in intron 1 of the SHH gene in a patient with a microform of holoprosencephaly
Eur J Med Genet, 54 (2), 130-5
DOI 10.1016/j.ejmg.2010.10.011, PubMed 21044704

Munthe-Kaas MC, Torjussen TM, Gervin K, Lødrup Carlsen KC, Carlsen KH, Granum B, Hjorthaug HS, Undlien D, Lyle R (2010)
CD14 polymorphisms and serum CD14 levels through childhood: a role for gene methylation?
J Allergy Clin Immunol, 125 (6), 1361-8
DOI 10.1016/j.jaci.2010.02.010, PubMed 20398919

Publications 2009

Bartkuhn M, Straub T, Herold M, Herrmann M, Rathke C, Saumweber H, Gilfillan GD, Becker PB, Renkawitz R (2009)
Active promoters and insulators are marked by the centrosomal protein 190
EMBO J, 28 (7), 877-88
DOI 10.1038/emboj.2009.34, PubMed 19229299

Bjørnvold M, Munthe-Kaas MC, Egeland T, Joner G, Dahl-Jørgensen K, Njølstad PR, Akselsen HE, Gervin K, Carlsen KC, Carlsen KH, Undlien DE (2009)
A TLR2 polymorphism is associated with type 1 diabetes and allergic asthma
Genes Immun, 10 (2), 181-7
DOI 10.1038/gene.2008.100, PubMed 19148143

Moldrich RX, Dauphinot L, Laffaire J, Vitalis T, Hérault Y, Beart PM, Rossier J, Vivien D, Gehrig C, Antonarakis SE, Lyle R, Potier MC (2009)
Proliferation deficits and gene expression dysregulation in Down's syndrome (Ts1Cje) neural progenitor cells cultured from neurospheres
J Neurosci Res, 87 (14), 3143-52
DOI 10.1002/jnr.22131, PubMed 19472221

Roxrud I, Raiborg C, Gilfillan GD, Strømme P, Stenmark H (2009)
Dual degradation mechanisms ensure disposal of NHE6 mutant protein associated with neurological disease
Exp Cell Res, 315 (17), 3014-27
DOI 10.1016/j.yexcr.2009.07.012, PubMed 19619532

Skinningsrud B, Husebye ES, Gilfillan GD, Frengen E, Erichsen A, Gervin K, Ormerod E, Egeland T, Undlien DE (2009)
X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene
J Clin Endocrinol Metab, 94 (10), 4086-93
DOI 10.1210/jc.2009-0923, PubMed 19773398

Publications 2008

Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A, Lee K, Dorschner M, Dermitzakis ET, Antonarakis SE, Stamatoyannopoulos JA (2008)
Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells
Genome Biol, 9 (12), R168
DOI 10.1186/gb-2008-9-12-r168, PubMed 19055709

Bjørnvold M, Undlien DE, Joner G, Dahl-Jørgensen K, Njølstad PR, Akselsen HE, Gervin K, Rønningen KS, Stene LC (2008)
Joint effects of HLA, INS, PTPN22 and CTLA4 genes on the risk of type 1 diabetes
Diabetologia, 51 (4), 589-96
DOI 10.1007/s00125-008-0932-0, PubMed 18292987

Canzonetta C, Mulligan C, Deutsch S, Ruf S, O'Doherty A, Lyle R, Borel C, Lin-Marq N, Delom F, Groet J, Schnappauf F, De Vita S, Averill S, Priestley JV, Martin JE, Shipley J, Denyer G, Epstein CJ, Fillat C, Estivill X, Tybulewicz VL, Fisher EM, Antonarakis SE, Nizetic D (2008)
DYRK1A-dosage imbalance perturbs NRSF/REST levels, deregulating pluripotency and embryonic stem cell fate in Down syndrome
Am J Hum Genet, 83 (3), 388-400
DOI 10.1016/j.ajhg.2008.08.012, PubMed 18771760

Dahoun S, Gagos S, Gagnebin M, Gehrig C, Burgi C, Simon F, Vieux C, Extermann P, Lyle R, Morris MA, Antonarakis SE, Béna F, Blouin JL (2008)
Monozygotic twins discordant for trisomy 21 and maternal 21q inheritance: a complex series of events
Am J Med Genet A, 146A (16), 2086-93
DOI 10.1002/ajmg.a.32431, PubMed 18627064

Fokstuen S, Lyle R, Munoz A, Gehrig C, Lerch R, Perrot A, Osterziel KJ, Geier C, Beghetti M, Mach F, Sztajzel J, Sigwart U, Antonarakis SE, Blouin JL (2008)
A DNA resequencing array for pathogenic mutation detection in hypertrophic cardiomyopathy
Hum Mutat, 29 (6), 879-85
DOI 10.1002/humu.20749, PubMed 18409188

Friedli M, Nikolaev S, Lyle R, Arcangeli M, Duboule D, Spitz F, Antonarakis SE (2008)
Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3
Mamm Genome, 19 (4), 272-8
DOI 10.1007/s00335-008-9106-0, PubMed 18392654

Gilfillan GD, Selmer KK, Roxrud I, Smith R, Kyllerman M, Eiklid K, Kroken M, Mattingsdal M, Egeland T, Stenmark H, Sjøholm H, Server A, Samuelsson L, Christianson A, Tarpey P, Whibley A, Stratton MR, Futreal PA, Teague J, Edkins S, Gecz J, Turner G, Raymond FL, Schwartz C, Stevenson RE et al. (2008)
SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome
Am J Hum Genet, 82 (4), 1003-10
DOI 10.1016/j.ajhg.2008.01.013, PubMed 18342287

Lyle R, Béna F, Gagos S, Gehrig C, Lopez G, Schinzel A, Lespinasse J, Bottani A, Dahoun S, Taine L, Doco-Fenzy M, Cornillet-Lefèbvre P, Pelet A, Lyonnet S, Toutain A, Colleaux L, Horst J, Kennerknecht I, Wakamatsu N, Descartes M, Franklin JC, Florentin-Arar L, Kitsiou S, Aït Yahya-Graison E, Costantine M et al. (2008)
Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21
Eur J Hum Genet, 17 (4), 454-66
DOI 10.1038/ejhg.2008.214, PubMed 19002211

Skinningsrud B, Husebye ES, Gervin K, Løvås K, Blomhoff A, Wolff AB, Kemp EH, Egeland T, Undlien DE (2008)
Mutation screening of PTPN22: association of the 1858T-allele with Addison's disease
Eur J Hum Genet, 16 (8), 977-82
DOI 10.1038/ejhg.2008.33, PubMed 18301444

Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB (2008)
The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex
PLoS Genet, 4 (12), e1000302
DOI 10.1371/journal.pgen.1000302, PubMed 19079572

Publications 2007

Gilfillan GD, König C, Dahlsveen IK, Prakoura N, Straub T, Lamm R, Fauth T, Becker PB (2007)
Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex
Nucleic Acids Res, 35 (11), 3561-72
DOI 10.1093/nar/gkm282, PubMed 17483514

Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, Dahoun S, She X, Bena F, Wang SY, Van Broeckhoven C, Eichler EE, Guigo R, Rogers J, de Jong PJ, Reymond A et al. (2007)
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
Genome Res, 17 (11), 1690-6
DOI 10.1101/gr.6675307, PubMed 17895424

Munthe-Kaas MC, Carlsen KH, Håland G, Devulapalli CS, Gervin K, Egeland T, Carlsen KL, Undlien D (2007)
T cell-specific T-box transcription factor haplotype is associated with allergic asthma in children
J Allergy Clin Immunol, 121 (1), 51-6
DOI 10.1016/j.jaci.2007.07.068, PubMed 17949803

Prandini P, Deutsch S, Lyle R, Gagnebin M, Delucinge Vivier C, Delorenzi M, Gehrig C, Descombes P, Sherman S, Dagna Bricarelli F, Baldo C, Novelli A, Dallapiccola B, Antonarakis SE (2007)
Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance
Am J Hum Genet, 81 (2), 252-63
DOI 10.1086/519248, PubMed 17668376

Publications 2006

Dahlsveen IK, Gilfillan GD, Shelest VI, Lamm R, Becker PB (2006)
Targeting determinants of dosage compensation in Drosophila
PLoS Genet, 2 (2), e5
DOI 10.1371/journal.pgen.0020005, PubMed 16462942

Everman DB, Morgan CT, Lyle R, Laughridge ME, Bamshad MJ, Clarkson KB, Colby R, Gurrieri F, Innes AM, Roberson J, Schrander-Stumpel C, van Bokhoven H, Antonarakis SE, Schwartz CE (2006)
Frequency of genomic rearrangements involving the SHFM3 locus at chromosome 10q24 in syndromic and non-syndromic split-hand/foot malformation
Am J Med Genet A, 140 (13), 1375-83
DOI 10.1002/ajmg.a.31246, PubMed 16761290

Gilfillan GD, Straub T, de Wit E, Greil F, Lamm R, van Steensel B, Becker PB (2006)
Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex
Genes Dev, 20 (7), 858-70
DOI 10.1101/gad.1399406, PubMed 16547172

Lyle R, Radhakrishna U, Blouin JL, Gagos S, Everman DB, Gehrig C, Delozier-Blanchet C, Solanki JV, Patel UC, Nath SK, Gurrieri F, Neri G, Schwartz CE, Antonarakis SE (2006)
Split-hand/split-foot malformation 3 (SHFM3) at 10q24, development of rapid diagnostic methods and gene expression from the region
Am J Med Genet A, 140 (13), 1384-95
DOI 10.1002/ajmg.a.31247, PubMed 16691619

Merla G, Howald C, Henrichsen CN, Lyle R, Wyss C, Zabot MT, Antonarakis SE, Reymond A (2006)
Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes
Am J Hum Genet, 79 (2), 332-41
DOI 10.1086/506371, PubMed 16826523

Tjeldhorn L, Rand-Hendriksen S, Gervin K, Brandal K, Inderhaug E, Geiran O, Paus B (2006)
Rapid and efficient FBN1 mutation detection using automated sample preparation and direct sequencing as the primary strategy
Genet Test, 10 (4), 258-64
DOI 10.1089/gte.2006.258-264, PubMed 17253931

Publications 2005

Deutsch S, Lyle R, Dermitzakis ET, Attar H, Subrahmanyan L, Gehrig C, Parand L, Gagnebin M, Rougemont J, Jongeneel CV, Antonarakis SE (2005)
Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes
Hum Mol Genet, 14 (23), 3741-9
DOI 10.1093/hmg/ddi404, PubMed 16251198

Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P, Dermitzakis ET (2005)
Genome-wide associations of gene expression variation in humans
PLoS Genet, 1 (6), e78
DOI 10.1371/journal.pgen.0010078, PubMed 16362079

Straub T, Gilfillan GD, Maier VK, Becker PB (2005)
The Drosophila MSL complex activates the transcription of target genes
Genes Dev, 19 (19), 2284-8
DOI 10.1101/gad.1343105, PubMed 16204179

Wattenhofer M, Reymond A, Falciola V, Charollais A, Caille D, Borel C, Lyle R, Estivill X, Petersen MB, Meda P, Antonarakis SE (2005)
Different mechanisms preclude mutant CLDN14 proteins from forming tight junctions in vitro
Hum Mutat, 25 (6), 543-9
DOI 10.1002/humu.20172, PubMed 15880785

Webster KE, O'Bryan MK, Fletcher S, Crewther PE, Aapola U, Craig J, Harrison DK, Aung H, Phutikanit N, Lyle R, Meachem SJ, Antonarakis SE, de Kretser DM, Hedger MP, Peterson P, Carroll BJ, Scott HS (2005)
Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis
Proc Natl Acad Sci U S A, 102 (11), 4068-73
DOI 10.1073/pnas.0500702102, PubMed 15753313

Publications 2004

Antonarakis SE, Lyle R, Dermitzakis ET, Reymond A, Deutsch S (2004)
Chromosome 21 and down syndrome: from genomics to pathophysiology
Nat Rev Genet, 5 (10), 725-38
DOI 10.1038/nrg1448, PubMed 15510164

Gilfillan GD, Dahlsveen IK, Becker PB (2004)
Lifting a chromosome: dosage compensation in Drosophila melanogaster
FEBS Lett, 567 (1), 8-14
DOI 10.1016/j.febslet.2004.03.110, PubMed 15165886

Lyle R, Gehrig C, Neergaard-Henrichsen C, Deutsch S, Antonarakis SE (2004)
Gene expression from the aneuploid chromosome in a trisomy mouse model of down syndrome
Genome Res, 14 (7), 1268-74
DOI 10.1101/gr.2090904, PubMed 15231743

Publications 2003

de Mollerat XJ, Gurrieri F, Morgan CT, Sangiorgi E, Everman DB, Gaspari P, Amiel J, Bamshad MJ, Lyle R, Blouin JL, Allanson JE, Le Marec B, Wilson M, Braverman NE, Radhakrishna U, Delozier-Blanchet C, Abbott A, Elghouzzi V, Antonarakis S, Stevenson RE, Munnich A, Neri G, Schwartz CE (2003)
A genomic rearrangement resulting in a tandem duplication is associated with split hand-split foot malformation 3 (SHFM3) at 10q24
Hum Mol Genet, 12 (16), 1959-71
DOI 10.1093/hmg/ddg212, PubMed 12913067

Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR (2003)
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
Proc Natl Acad Sci U S A, 100 (3), 1140-5
DOI 10.1073/pnas.0337561100, PubMed 12552088

Tapparel C, Reymond A, Girardet C, Guillou L, Lyle R, Lamon C, Hutter P, Antonarakis SE (2003)
The TPTE gene family: cellular expression, subcellular localization and alternative splicing
Gene, 323, 189-99
DOI 10.1016/j.gene.2003.09.038, PubMed 14659893

Publications 2002

Antonarakis SE, Lyle R, Deutsch S, Reymond A (2002)
Chromosome 21: a small land of fascinating disorders with unknown pathophysiology
Int J Dev Biol, 46 (1), 89-96
PubMed 11902692

Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, Deutsch S, Stevenson BJ, Flegel V, Bucher P, Jongeneel CV, Antonarakis SE (2002)
Numerous potentially functional but non-genic conserved sequences on human chromosome 21
Nature, 420 (6915), 578-82
DOI 10.1038/nature01251, PubMed 12466853

Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M, de Souza S, Iseli C, Jongeneel CV, Bucher P, Simpson AJ, Antonarakis SE (2002)
Nineteen additional unpredicted transcripts from human chromosome 21
Genomics, 79 (6), 824-32
DOI 10.1006/geno.2002.6781, PubMed 12036297

Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, Scamuffa N, Caccioppoli C, Dermitzakis ET, Lyle R, Banfi S, Eichele G, Antonarakis SE, Ballabio A (2002)
Human chromosome 21 gene expression atlas in the mouse
Nature, 420 (6915), 582-6
DOI 10.1038/nature01178, PubMed 12466854

Publications 2001

Kageyama Y, Mengus G, Gilfillan G, Kennedy HG, Stuckenholz C, Kelley RL, Becker PB, Kuroda MI (2001)
Association and spreading of the Drosophila dosage compensation complex from a discrete roX1 chromatin entry site
EMBO J, 20 (9), 2236-45
DOI 10.1093/emboj/20.9.2236, PubMed 11331589