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High throughput barcoding method for genome-scale phasing.

Redin D, Frick T, Aghelpasand H, Käller M, Borgström E, Olsen RA, Ahmadian A.

Sci Rep. 2019 Dec 2;9(1):18116. doi: 10.1038/s41598-019-54446-x.


Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.

Tiukova IA, Pettersson ME, Hoeppner MP, Olsen RA, Käller M, Nielsen J, Dainat J, Lantz H, Söderberg J, Passoth V.

PLoS One. 2019 May 1;14(5):e0215077. doi: 10.1371/journal.pone.0215077. eCollection 2019.


Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.

Eisfeldt J, Pettersson M, Vezzi F, Wincent J, Käller M, Gruselius J, Nilsson D, Syk Lundberg E, Carvalho CMB, Lindstrand A.

PLoS Genet. 2019 Feb 8;15(2):e1007858. doi: 10.1371/journal.pgen.1007858. eCollection 2019 Feb.


Contrast Agent Toxicity.

Kaller MO, An J.

StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan-.
2019 Dec 14.


Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.

Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Mäkitie O, Nordgren A, Vezzi F, Wirta V, Käller M, Hjortshøj TD, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Lundberg ES, Tümer Z, Lindstrand A.

PLoS Genet. 2018 Nov 12;14(11):e1007780. doi: 10.1371/journal.pgen.1007780. eCollection 2018 Nov.


Ap4 is rate limiting for intestinal tumor formation by controlling the homeostasis of intestinal stem cells.

Jaeckel S, Kaller M, Jackstadt R, Götz U, Müller S, Boos S, Horst D, Jung P, Hermeking H.

Nat Commun. 2018 Sep 3;9(1):3573. doi: 10.1038/s41467-018-06001-x.


Discovery of TRPM8 Antagonist ( S)-6-(((3-Fluoro-4-(trifluoromethoxy)phenyl)(3-fluoropyridin-2-yl)methyl)carbamoyl)nicotinic Acid (AMG 333), a Clinical Candidate for the Treatment of Migraine.

Horne DB, Biswas K, Brown J, Bartberger MD, Clarine J, Davis CD, Gore VK, Harried S, Horner M, Kaller MR, Lehto SG, Liu Q, Ma VV, Monenschein H, Nguyen TT, Yuan CC, Youngblood BD, Zhang M, Zhong W, Allen JR, Chen JJ, Gavva NR.

J Med Chem. 2018 Sep 27;61(18):8186-8201. doi: 10.1021/acs.jmedchem.8b00518. Epub 2018 Sep 10.


Combined Inactivation of TP53 and MIR34A Promotes Colorectal Cancer Development and Progression in Mice Via Increasing Levels of IL6R and PAI1.

Öner MG, Rokavec M, Kaller M, Bouznad N, Horst D, Kirchner T, Hermeking H.

Gastroenterology. 2018 Dec;155(6):1868-1882. doi: 10.1053/j.gastro.2018.08.011. Epub 2018 Aug 10.


Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, Johansson S, Logue JB, Huss M, Käller M, Lundeberg J, Fagerberg J, Andersson AF.

Sci Rep. 2018 Aug 9;8(1):11907. doi: 10.1038/s41598-018-29920-7.


Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.

Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN.

Nat Commun. 2018 Apr 16;9(1):1478. doi: 10.1038/s41467-018-03902-9.


PBX3 Is Part of an EMT Regulatory Network and Indicates Poor Outcome in Colorectal Cancer.

Lamprecht S, Kaller M, Schmidt EM, Blaj C, Schiergens TS, Engel J, Jung A, Hermeking H, Grünewald TGP, Kirchner T, Horst D.

Clin Cancer Res. 2018 Apr 15;24(8):1974-1986. doi: 10.1158/1078-0432.CCR-17-2572. Epub 2018 Feb 1.


Loss of p53-inducible long non-coding RNA LINC01021 increases chemosensitivity.

Kaller M, Götz U, Hermeking H.

Oncotarget. 2017 Nov 1;8(61):102783-102800. doi: 10.18632/oncotarget.22245. eCollection 2017 Nov 28.


Myelin plasticity and behaviour-connecting the dots.

Kaller MS, Lazari A, Blanco-Duque C, Sampaio-Baptista C, Johansen-Berg H.

Curr Opin Neurobiol. 2017 Dec;47:86-92. doi: 10.1016/j.conb.2017.09.014. Epub 2017 Oct 17. Review.


BET 2: Treatment of frostbite with iloprost.

Kaller M.

Emerg Med J. 2017 Oct;34(10):689-690. doi: 10.1136/emermed-2017-207129.2. Review.


Pan-cancer EMT-signature identifies RBM47 down-regulation during colorectal cancer progression.

Rokavec M, Kaller M, Horst D, Hermeking H.

Sci Rep. 2017 Jul 5;7(1):4687. doi: 10.1038/s41598-017-04234-2.


Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

Redin D, Borgström E, He M, Aghelpasand H, Käller M, Ahmadian A.

Nucleic Acids Res. 2017 Jul 27;45(13):e125. doi: 10.1093/nar/gkx436.


Cluster Flow: A user-friendly bioinformatics workflow tool.

Ewels P, Krueger F, Käller M, Andrews S.

Version 2. F1000Res. 2016 Dec 6 [revised 2017 Jan 1];5:2824. doi: 10.12688/f1000research.10335.2. eCollection 2016.


Co-cultures with stem cell-derived human sensory neurons reveal regulators of peripheral myelination.

Clark AJ, Kaller MS, Galino J, Willison HJ, Rinaldi S, Bennett DLH.

Brain. 2017 Apr 1;140(4):898-913. doi: 10.1093/brain/awx012.


Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.

Nilsson D, Pettersson M, Gustavsson P, Förster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Mäkitie O, Wirta V, Käller M, Vezzi F, Lupski JR, Nordenskjöld M, Lundberg ES, Carvalho CMB, Lindstrand A.

Hum Mutat. 2017 Feb;38(2):180-192. doi: 10.1002/humu.23146. Epub 2016 Dec 5.


Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.

Engström K, Wojdacz TK, Marabita F, Ewels P, Käller M, Vezzi F, Prezza N, Gruselius J, Vahter M, Broberg K.

Arch Toxicol. 2017 May;91(5):2067-2078. doi: 10.1007/s00204-016-1879-4. Epub 2016 Nov 12.


Interplay Between Transcription Factors and MicroRNAs Regulating Epithelial-Mesenchymal Transitions in Colorectal Cancer.

Kaller M, Hermeking H.

Adv Exp Med Biol. 2016;937:71-92. doi: 10.1007/978-3-319-42059-2_4. Review.


MultiQC: summarize analysis results for multiple tools and samples in a single report.

Ewels P, Magnusson M, Lundin S, Käller M.

Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16.


Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.

Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M.

Nucleic Acids Res. 2016 Aug 19;44(14):6756-69. doi: 10.1093/nar/gkw316. Epub 2016 Apr 29.


Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:69. doi: 10.1186/s12859-016-0910-3.


De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F.

Gigascience. 2015 Nov 26;4:56. doi: 10.1186/s13742-015-0094-1. eCollection 2015.


T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.

Grunewald J, Kaiser Y, Ostadkarampour M, Rivera NV, Vezzi F, Lötstedt B, Olsen RA, Sylwan L, Lundin S, Käller M, Sandalova T, Ahlgren KM, Wahlström J, Achour A, Ronninger M, Eklund A.

Eur Respir J. 2016 Mar;47(3):898-909. doi: 10.1183/13993003.01209-2015. Epub 2015 Nov 19.


p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses.

Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H.

Mol Cell Proteomics. 2015 Oct;14(10):2609-29. doi: 10.1074/mcp.M115.050237. Epub 2015 Jul 16.


Cardiac shock wave therapy and myocardial perfusion in severe coronary artery disease.

Kaller M, Faber L, Bogunovic N, Horstkotte D, Burchert W, Lindner O.

Clin Res Cardiol. 2015 Oct;104(10):843-9. doi: 10.1007/s00392-015-0853-0. Epub 2015 Apr 17.


Corrigendum. IL-6R/STAT3/miR-34a feedback loop promotes EMT-mediated colorectal cancer invasion and metastasis.

Rokavec M, Öner MG, Li H, Jackstadt R, Jiang L, Lodygin D, Kaller M, Horst D, Ziegler PK, Schwitalla S, Slotta-Huspenina J, Bader FG, Greten FR, Hermeking H.

J Clin Invest. 2015 Mar 2;125(3):1362. doi: 10.1172/JCI81340. Epub 2015 Mar 2. No abstract available.


Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, Foam N, Pettersson E, Käller M, Wirta V, Lexow P, Lundeberg J.

PLoS One. 2015 Jan 28;10(1):e0117059. doi: 10.1371/journal.pone.0117059. eCollection 2015.


Synthesis and preliminary biological evaluation of potent and selective 2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors with improved solubility.

Rzasa RM, Frohn MJ, Andrews KL, Chmait S, Chen N, Clarine JG, Davis C, Eastwood HA, Horne DB, Hu E, Jones AD, Kaller MR, Kunz RK, Miller S, Monenschein H, Nguyen T, Pickrell AJ, Porter A, Reichelt A, Zhao X, Treanor JJS, Allen JR.

Bioorg Med Chem. 2014 Dec 1;22(23):6570-6585. doi: 10.1016/j.bmc.2014.10.013.


Pushing steric bias in the Scholl reaction to access liquid crystalline crown ethers.

Wöhrle T, Kirres J, Kaller M, Mansueto M, Tussetschläger S, Laschat S.

J Org Chem. 2014 Nov 7;79(21):10143-52. doi: 10.1021/jo501790d. Epub 2014 Oct 15.


Identification of microRNA targets by pulsed SILAC.

Kaller M, Oeljeklaus S, Warscheid B, Hermeking H.

Methods Mol Biol. 2014;1188:327-49. doi: 10.1007/978-1-4939-1142-4_23.


Synthesis and structure-activity relationship of trisubstituted thiazoles as Cdc7 kinase inhibitors.

Reichelt A, Bailis JM, Bartberger MD, Yao G, Shu H, Kaller MR, Allen JG, Weidner MF, Keegan KS, Dao JH.

Eur J Med Chem. 2014 Jun 10;80:364-82. doi: 10.1016/j.ejmech.2014.04.013. Epub 2014 Apr 5.


Hematopoietic overexpression of FOG1 does not affect B-cells but reduces the number of circulating eosinophils.

Du Roure C, Versavel A, Doll T, Cao C, Pillonel V, Matthias G, Kaller M, Spetz JF, Kopp P, Kohler H, Müller M, Matthias P.

PLoS One. 2014 Apr 18;9(4):e92836. doi: 10.1371/journal.pone.0092836. eCollection 2014.


IL-6R/STAT3/miR-34a feedback loop promotes EMT-mediated colorectal cancer invasion and metastasis.

Rokavec M, Öner MG, Li H, Jackstadt R, Jiang L, Lodygin D, Kaller M, Horst D, Ziegler PK, Schwitalla S, Slotta-Huspenina J, Bader FG, Greten FR, Hermeking H.

J Clin Invest. 2014 Apr;124(4):1853-67. doi: 10.1172/JCI73531. Epub 2014 Mar 18. Erratum in: J Clin Invest. 2015 Mar 2;125(3):1362.


Optimization of potency and pharmacokinetic properties of tetrahydroisoquinoline transient receptor potential melastatin 8 (TRPM8) antagonists.

Horne DB, Tamayo NA, Bartberger MD, Bo Y, Clarine J, Davis CD, Gore VK, Kaller MR, Lehto SG, Ma VV, Nishimura N, Nguyen TT, Tang P, Wang W, Youngblood BD, Zhang M, Gavva NR, Monenschein H, Norman MH.

J Med Chem. 2014 Apr 10;57(7):2989-3004. doi: 10.1021/jm401955h. Epub 2014 Mar 19.


Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

Hasmats J, Gréen H, Orear C, Validire P, Huss M, Käller M, Lundeberg J.

PLoS One. 2014 Jan 7;9(1):e84785. doi: 10.1371/journal.pone.0084785. eCollection 2014.


Dispersant and salinity effects on weathering and acute toxicity of South Louisiana crude oil.

Kuhl AJ, Nyman JA, Kaller MD, Green CC.

Environ Toxicol Chem. 2013 Nov;32(11):2611-20.


The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Wiegand S, Meier D, Seehafer C, Malicki M, Hofmann P, Schmith A, Winckler T, Földesi B, Boesler B, Nellen W, Reimegård J, Käller M, Hällman J, Emanuelsson O, Avesson L, Söderbom F, Hammann C.

Nucleic Acids Res. 2014 Mar;42(5):3330-45. doi: 10.1093/nar/gkt1337. Epub 2013 Dec 24.


Chemical fragmentation for massively parallel sequencing library preparation.

Gyarmati P, Song Y, Hällman J, Käller M.

J Biotechnol. 2013 Oct 10;168(1):95-100. doi: 10.1016/j.jbiotec.2013.08.020. Epub 2013 Aug 27.


The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.


Identification and verification of microRNAs by high-throughput sequencing.

Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F.

Methods Mol Biol. 2013;983:125-38. doi: 10.1007/978-1-62703-302-2_7.


Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.

Lundin S, Gruselius J, Nystedt B, Lexow P, Käller M, Lundeberg J.

Sci Rep. 2013;3:1186. doi: 10.1038/srep01186.


The p53/microRNA network in cancer: experimental and bioinformatics approaches.

Hünten S, Siemens H, Kaller M, Hermeking H.

Adv Exp Med Biol. 2013;774:77-101. doi: 10.1007/978-94-007-5590-1_5. Review.


A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of β-Secretase.

Kaller MR, Harried SS, Albrecht B, Amarante P, Babu-Khan S, Bartberger MD, Brown J, Brown R, Chen K, Cheng Y, Citron M, Croghan MD, Graceffa R, Hickman D, Judd T, Kriemen C, La D, Li V, Lopez P, Luo Y, Masse C, Monenschein H, Nguyen T, Pennington LD, Miguel TS, Sickmier EA, Wahl RC, Weiss MM, Wen PH, Williamson T, Wood S, Xue M, Yang B, Zhang J, Patel V, Zhong W, Hitchcock S.

ACS Med Chem Lett. 2012 Mar 29;3(11):886-91. doi: 10.1021/ml3000148. eCollection 2012 Nov 8.


Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.

Solnestam BW, Stranneheim H, Hällman J, Käller M, Lundberg E, Lundeberg J, Akan P.

BMC Genomics. 2012 Oct 30;13:574. doi: 10.1186/1471-2164-13-574.


Establishing the relationship between in vitro potency, pharmacokinetic, and pharmacodynamic parameters in a series of orally available, hydroxyethylamine-derived β-secretase inhibitors.

Wood S, Wen PH, Zhang J, Zhu L, Luo Y, Babu-Khan S, Chen K, Pham R, Esmay J, Dineen TA, Kaller MR, Weiss MM, Hitchcock SA, Citron M, Zhong W, Hickman D, Williamson T.

J Pharmacol Exp Ther. 2012 Nov;343(2):460-7. doi: 10.1124/jpet.112.197954. Epub 2012 Aug 21.


Triphenylene silanes for direct surface anchoring in binary mixed self-assembled monolayers.

Mansueto M, Sauer S, Butschies M, Kaller M, Baro A, Woerner R, Hansen NH, Tovar G, Pflaum J, Laschat S.

Langmuir. 2012 Jun 5;28(22):8399-407. doi: 10.1021/la300775n. Epub 2012 May 23.


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