Susanne Bornelöv "sblab"

bioinformatics, (epi)genomics, machine learning, piRNAs, codon usage


All papers are also listed on Google Scholar.

# = equal contribution, § = corresponding author, orange = key publication


A code within the genetic code [Journal Club]
Bornelöv S§
Nature Reviews Molecular Cell Biology [final version]
A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci
Akkouche A#, Kneuss E#, Bornelöv S#, Renaud Y, Eastwood EL, van Lopik J, Gueguen N, Jiang M, Creixell P, Maupetit-Mehouas S, Czech Nicholson B§, Brasset E§, Hannon GJ§
bioRxiv 2024.01.11.575256 [preprint]


Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus
van Lopik J#, Alizada A, Trapotsi M-A, Hannon GJ, Bornelöv S#,§, Czech Nicholson B§
Nature Communications 14:7337 [final version] [preprint]
Evaluation and optimization of sequence-based gene regulatory deep learning models
Rafi AM§, Penzar D, Nogina D, Lee D, Vaishnav ED, Lee D, Kim N, Kim S, Meshcheryakov G, Lando A, Yadollahpour P, Zinkevich A, Kim D, Shin Y, Kwak I-Y, Kim B-C, Lee J, Random Promoter DREAM Challenge Consortium (72 members, including Bornelöv S and Trapotsi M-A), Kim S, Regev A, Albrecht J, Gong W, Kulakovskiy IV, Meyer P, de Boer C§
bioRxiv 2023.04.26.538471 [preprint]


Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma
Rebbeck CA#,§, Xian J#, Bornelöv S, Geradts J, Hobeika A, Geiger H, Franco Alvarez J, Rozhkova E, Nicholls A, Robine N, Lyerly HK§, Hannon GJ§
Nature Communications 13:3399 [final version] [preprint]
An evolutionarily conserved stop codon enrichment at the 5’ ends of mammalian piRNAs
Bornelöv S§, Czech B, Hannon GJ§
Nature Communications 13:2118 [final version] [preprint]
Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells
Lawrence M#, Shahsavari A#, Bornelöv S#, Moreau T, Kania K, Paramor M, McDonald R, Baye J, Perrin M, Steindel M, Jimenez-Gomez P, Penfold C, Mohorianu I§, Ghevaert C§
Science Advances 8:7:eabj8618 [final version] [preprint]


Pluripotent stem cells related to embryonic disc exhibit common self-renewal requirements in diverse livestock species
Kinoshita M, Kobayashi T, Planells B, Klisch D, Spindlow D, Masaki H, Bornelöv S, Stirparo GG, Matsunari H, Uchikura A, Lamas-Toranzo I, Nichols J, Nakauchi H, Nagashima H, Alberio R§, Smith A§
Development 148:23 [final version] [research highlight]
Rn7sk small nuclear RNA controls bidirectional transcription of highly expressed gene pairs in skin
Bandiera R, Wagner R, Britto-Borges T, Dieterich C, Dietmann S, Bornelöv S§ and Frye M§
Nature Communications 12:5864 [final version]
Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis
Gong C#, Krupka J#, Gao J, Grigoropoulos NF, Screen M, Usheva Z, Cucco F, Barrans S, Painter D, Mohammed M, Haupl B, Bornelöv S, Mozos I, Meng W, Zhou P, Blain A, Forde S, Matthews J, Tan MGK, Burke GA, Siu N, Beer P, Burton C, Campbell PJ, Rand V, Turner S, Ule J, Roman E, Tooze R, Oellerich T, Turner M, Du M-Q, Samarajiwa S§ and Hodson D§
Molecular Cell 81:19:4059-4075 [final version] [preprint]
Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Munafò M, Lawless VR, Passera A, MacMillan S, Bornelöv S, Haussmann IU, Soller M, Hannon GJ§, Czech B§
Elife 10:e66321 [final version]
The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus
Schwochow D, Bornelöv S, Jiang T, Li J, Gourichon D, Bed’Hom B, Dorshorst B, Chuong C-M, Tixier-Boichard M and Andersson L§
Pigment Cell & Melanoma Research 34:6:1015-1028 [final version]
R.ROSETTA: an interpretable machine learning framework
Garbulowski M, Diamanti K#, Smolińska K#, Baltzer N, Stoll P, Bornelöv S, Øhrn A, Feuk L and Komorowski J§
BMC Bioinformatics 22:110 [final version] [preprint]
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila
Eastwood EL, Jara KA#, Bornelöv S#, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B§ and Hannon GJ§
Elife 10:e65557 [final version] [preprint]
Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6
Selmi T#, Hussain S#, Dietmann S, Heiß M, Borland K, Flad S, Carter J-M, Dennison R, Huang Y-L, Kellner S, Bornelöv S§ and Frye M§
Nucleic Acids Research 49:2:1006-1022 [final version] [preprint]
CONCUR: quick and robust calculation of codon usage from ribosome profiling data
Frye M and Bornelöv S§
Bioinformatics 13:3399 [final version]


Cytosine-5 RNA methylation links protein synthesis to cell metabolism
Gkatza NA, Castro C, Harvey RF, Heiß M, Popis MC, Blanco S, Bornelöv S, Sajini AA, Gleeson JG, Griffin JL, West JA, Kellner S, Willis AE, Dietmann S and Frye M§
PLOS Biology 17:6:e3000297 [final version]
Codon usage optimization in pluripotent embryonic stem cells
Bornelöv S#, Selmi T#, Flad S, Dietmann S and Frye M§
Genome Biology 20:1:119 [final version]
Loss of 5-methylcytosine alters the biogenesis of Vault-derived small RNAs to coordinate epidermal differentiation
Sajini A, Choudhury NR, Wagner R, Bornelöv S, Selmi T, Spanos C, Dietmann S, Rappsilber J, Michlewski G§ and Frye M§
Nature Communications 10:1-13 [final version]
Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Kalkan T§, Bornelöv S#, Mulas C#, Diamanti E, Lohoff T, Ralser M, Middlekamp S, Lombard P, Nichols J and Smith A§
Cell Stem Cell 24:5:785-801 [final version]


The nucleosome remodeling and deacetylation complex modulates chromatin structure at sites of active transcription to fine-tune gene expression
Bornelöv S#, Reynolds N#, Xenophontos M, Gharbi S, Johnstone E, Floyd R, Ralser M, Signolet J, Loos R, Dietmann S, Bertone P§ and Hendrich B§
Molecular Cell 71:1:56-72 [final version] [preprint] [news coverage]
Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Bornelöv S#, Seroussi E#, Yosefi S, Benjamini S, Miyara S, Ruzal M, Grabherr M, Rafati N, Molin A-M, Pendavis K, Burgess SC, Andersson L and Friedman-Einat M§
BMC Genomics 19:1:295 [final version]


Mapping of leptin and its syntenic genes to chicken chromosome 1p
Seroussi E§, Pitel F, Leroux S, Morisson M, Bornelöv S, Miyara S, Yosefi S, Cogburn LA, Burt DW, Andersson L and Friedman-Einat M§
BMC Genetics 18:1:77 [final version]
Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost
Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, Friedman-Einat M§ and Andersson L§
Genome Biology 18:1:112 [final version]


Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination
Lee MO, Bornelöv S, Andersson L, Lamont SJ, Chen J and Womack JE§
PNAS 113:48:13815-13820 [final version]
Selection of Significant Features Using Monte Carlo Feature Selection [book chapter]
Bornelöv S and Komorowski J§
Challenges in Computational Statistics and Data Mining 605 of Studies in Computational Intelligence, 25-38, Springer-Verlag [final version]


Identification of the long-sought leptin in chicken and duck: expression pattern of the highly GC-rich avian leptin fits an autocrine/paracrine rather than endocrine function
Seroussi E, Cinnamon Y, Yosefi S, Genin O, Smith JG, Rafati N, Bornelöv S, Andersson L and Friedman-Einat M§
Endocrinology 157:2:737-751 [final version]
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription
Bornelöv S, Komorowski J§ and Wadelius C§
BMC Genomics 16:1:300 [final version]
'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements
Dąbrowski MJ§, Bornelöv S, Kruczyk M, Baltzer N and Komorowski J
Molecular Ecology Resources 15:3:477-488 [final version]


Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
Bornelöv S, Marillet S and Komorowski J§
BMC Bioinformatics 15:1:139 [final version]


ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer
Bysani M, Wallerman O, Bornelöv S, Zatloukal K, Komorowski J and Wadelius C§
BMC Medical Genomics 6:50 [final version]
Rule-based models of the interplay between genetic and environmental factors in childhood allergy
Bornelöv S#, Sääf A#, Melén E, Bergström A, Torabi Moghadam B, Pulkkinen V, Acevedo N, Orsmark Pietras C, Ege M, Braun-Fahrländer C, Riedler J, Doekes G, Kabesch M, van Hage M, Kere J, Scheynius A, Söderhäll C, Pershagen G§ and Komorowski J
PLOS ONE 8:11:e80080 [final version]


Combinations of histone modifications mark exon inclusion levels
Enroth S#, Bornelöv S#, Wadelius C§ and Komorowski J§
PLOS ONE 7:1:e29911 [final version]
Visualization of rules in rule-based classifiers [conference paper]
Bornelöv S, Enroth S and Komorowski J§
In Watada J, Watanabe T, Phillips-Wren G, Howlett R, Jain L (eds) Intelligent Decision Technologies 15 of Smart Innovation, Systems and Technologies, 329-338 Springer, Berlin, Heidelberg [final version]

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