Papers
All papers are also listed on Google Scholar.
# = equal contribution, § = corresponding author, orange = key publication
2024 | |
| SRSF2 transcriptional function maintains genome integrity during cell division Wagner RE, Arnetzl L, Britto-Borges T, Heit-Mondrzyk A, Bakr A, Sollier E, Gkatza NA, Panten J, Delaunay S, Sohn D, Schmezer P, Odom DT, Müller-Decker K, Plass C, Dieterich C, Lutsik P, Bornelöv S, Frye M§ Cell Reports 43:11 [final version] [preprint] | |
| A community effort to optimize sequence-based deep learning models of gene regulation Rafi AM§, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Shin Y, Kwek I-Y, Meshcheryakov G, Lando A, Zinkevich A, Kim B-C, Lee J, Kang T, Vaishnav ED, Yadollahpour P, Random Promoter DREAM Challenge Consortium (72 members, including Bornelöv S and Trapotsi M-A), Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer CG§ Nature Biotechnology s41587-024-02414-w [final version] [preprint] | |
| FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models Trapotsi M-A, van Lopik J, Hannon G J, Czech Nicholson B§, Bornelöv S§ NAR Genomics and Bioinformatics 6:3:lqae119 [final version] [preprint] | |
| A code within the genetic code [Journal Club] Bornelöv S§ Nature Reviews Molecular Cell Biology 25:423 [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] | |
2023 | |
| 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] | |
2022 | |
| 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] | |
2021 | |
| 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] | |
2019 | |
| 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] | |
2018 | |
| 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] | |
2017 | |
| 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] | |
2016 | |
| 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] | |
2015 | |
| 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] | |
2014 | |
| 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] | |
2013 | |
| 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] | |
2012 | |
| 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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