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The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites.

Senanayake KS, Söderberg J, Põlajev A, Malmberg M, Karunanayake EH, Tennekoon KH, Samarakoon SR, Bongcam-Rudloff E, Niazi A.

Genome Biol Evol. 2020 Feb 1;12(2):3971-3976. doi: 10.1093/gbe/evaa017.


Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.

Guo Y, van Schaik T, Jhamat N, Niazi A, Chanrot M, Charpigny G, Valarcher JF, Bongcam-Rudloff E, Andersson G, Humblot P.

PLoS One. 2019 Sep 5;14(9):e0222081. doi: 10.1371/journal.pone.0222081. eCollection 2019.


NOTCH3 and CADASIL syndrome: a genetic and structural overview.

Papakonstantinou E, Bacopoulou F, Brouzas D, Megalooikonomou V, D'Elia D, Bongcam-Rudloff E, Vlachakis D.

EMBnet J. 2019;24. pii: e921. doi: 10.14806/ej.24.0.921. Epub 2019 May 22.


Simulating Illumina metagenomic data with InSilicoSeq.

Gourlé H, Karlsson-Lindsjö O, Hayer J, Bongcam-Rudloff E.

Bioinformatics. 2019 Feb 1;35(3):521-522. doi: 10.1093/bioinformatics/bty630.


High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas.

Cárdenas CA, González-Aravena M, Font A, Hestetun JT, Hajdu E, Trefault N, Malmberg M, Bongcam-Rudloff E.

PeerJ. 2018 Jun 7;6:e4935. doi: 10.7717/peerj.4935. eCollection 2018.


The eBioKit, a stand-alone educational platform for bioinformatics.

Hernández-de-Diego R, de Villiers EP, Klingström T, Gourlé H, Conesa A, Bongcam-Rudloff E.

PLoS Comput Biol. 2017 Sep 14;13(9):e1005616. doi: 10.1371/journal.pcbi.1005616. eCollection 2017 Sep.


Legal & ethical compliance when sharing biospecimen.

Klingstrom T, Bongcam-Rudloff E, Reichel J.

Brief Funct Genomics. 2018 Jan 1;17(1):1-7. doi: 10.1093/bfgp/elx008.


Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H7.

Loftsdóttir H, Söderlund R, Jinnerot T, Eriksson E, Bongcam-Rudloff E, Aspán A.

FEMS Microbiol Lett. 2017 Apr 1;364(8). doi: 10.1093/femsle/fnx074.


Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii.

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B.

PLoS One. 2016 Nov 16;11(11):e0166520. doi: 10.1371/journal.pone.0166520. eCollection 2016.


Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B.

Stand Genomic Sci. 2016 Oct 12;11:80. eCollection 2016.


MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J.

PLoS One. 2016 Aug 1;11(8):e0160334. doi: 10.1371/journal.pone.0160334. eCollection 2016.


Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E.

Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. Review.


Genetic analysis of a Treponema phagedenis locus encoding antigenic lipoproteins with potential for antigenic variation.

Mushtaq M, Bongcam-Rudloff E, Loftsdottir H, Pringle M, Segerman B, Zuerner R, Rosander A.

Vet Microbiol. 2016 Jun 30;189:91-8. doi: 10.1016/j.vetmic.2016.04.027. Epub 2016 May 6.


Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

Truvé K, Dickinson P, Xiong A, York D, Jayashankar K, Pielberg G, Koltookian M, Murén E, Fuxelius HH, Weishaupt H, Swartling FJ, Andersson G, Hedhammar Å, Bongcam-Rudloff E, Forsberg-Nilsson K, Bannasch D, Lindblad-Toh K.

PLoS Genet. 2016 May 12;12(5):e1006000. doi: 10.1371/journal.pgen.1006000. eCollection 2016 May.


Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs.

Söderlund R, Hurel J, Jinnerot T, Sekse C, Aspán A, Eriksson E, Bongcam-Rudloff E.

Infect Ecol Epidemiol. 2016 Feb 16;6:30246. doi: 10.3402/iee.v6.30246. eCollection 2016.


Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.

Zubair S, Fischer A, Liljander A, Meens J, Hegerman J, Gourlé H, Bishop RP, Roebbelen I, Younan M, Mustafa MI, Mushtaq M, Bongcam-Rudloff E, Jores J.

Stand Genomic Sci. 2015 Nov 20;10:109. doi: 10.1186/s40793-015-0098-6. eCollection 2015.


Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.

Manzoor S, Müller B, Niazi A, Schnürer A, Bongcam-Rudloff E.

Stand Genomic Sci. 2015 Nov 11;10:99. doi: 10.1186/s40793-015-0092-z. eCollection 2015.


Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.

Mushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson DS.

BMC Microbiol. 2015 Oct 12;15:208. doi: 10.1186/s12866-015-0537-y.


The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Norling M, Bishop RP, Pelle R, Qi W, Henson S, Drábek EF, Tretina K, Odongo D, Mwaura S, Njoroge T, Bongcam-Rudloff E, Daubenberger CA, Silva JC.

BMC Genomics. 2015 Sep 24;16:729. doi: 10.1186/s12864-015-1910-9.

21. A Catalog of Virtual Machine Images for the Life Sciences.

Dahlö M, Haziza F, Kallio A, Korpelainen E, Bongcam-Rudloff E, Spjuth O.

Bioinform Biol Insights. 2015 Sep 10;9:125-8. doi: 10.4137/BBI.S28636. eCollection 2015.


Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.

Mushtaq M, Manzoor S, Pringle M, Rosander A, Bongcam-Rudloff E.

Stand Genomic Sci. 2015 Sep 21;10:67. doi: 10.1186/s40793-015-0059-0. eCollection 2015.


Experiences with workflows for automating data-intensive bioinformatics.

Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.


Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training.

Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium.

PLoS Comput Biol. 2015 May 14;11(5):e1004281. doi: 10.1371/journal.pcbi.1004281. eCollection 2015 May. No abstract available.


GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium.

PLoS Comput Biol. 2015 Apr 9;11(4):e1004143. doi: 10.1371/journal.pcbi.1004143. eCollection 2015 Apr. Erratum in: PLoS Comput Biol. 2015 May;11(5):e1004281. Atwood, Teresa K [corrected to Attwood, Teresa K].


Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation.

Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A.

PLoS One. 2015 Mar 26;10(3):e0121237. doi: 10.1371/journal.pone.0121237. eCollection 2015.


Studies of plant colonisation by closely related Bacillus amyloliquefaciens biocontrol agents using strain specific quantitative PCR assays.

Johansson AH, Bejai S, Niazi A, Manzoor S, Bongcam-Rudloff E, Meijer J.

Antonie Van Leeuwenhoek. 2014 Dec;106(6):1247-57. doi: 10.1007/s10482-014-0295-0. Epub 2014 Oct 8.


Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.

Niazi A, Manzoor S, Bejai S, Meijer J, Bongcam-Rudloff E.

Stand Genomic Sci. 2014 Feb 15;9(3):718-25. doi: 10.4056/sigs.4758653. eCollection 2014 Jun 15.


The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Corpas M, Jimenez RC, Bongcam-Rudloff E, Budd A, Brazas MD, Fernandes PL, Gaeta B, van Gelder C, Korpelainen E, Lewitter F, McGrath A, MacLean D, Palagi PM, Rother K, Taylor J, Via A, Watson M, Schneider MV, Attwood TK.

Bioinformatics. 2015 Jan 1;31(1):140-2. doi: 10.1093/bioinformatics/btu601. Epub 2014 Sep 4.


Molecular typing of Escherichia coli O157:H7 isolates from Swedish cattle and human cases: population dynamics and virulence.

Söderlund R, Jernberg C, Ivarsson S, Hedenström I, Eriksson E, Bongcam-Rudloff E, Aspán A.

J Clin Microbiol. 2014 Nov;52(11):3906-12. doi: 10.1128/JCM.01877-14. Epub 2014 Aug 20.


Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.

Niazi A, Manzoor S, Asari S, Bejai S, Meijer J, Bongcam-Rudloff E.

PLoS One. 2014 Aug 13;9(8):e104651. doi: 10.1371/journal.pone.0104651. eCollection 2014.


Data integration in the era of omics: current and future challenges.

Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, Ballestar E, Bongcam-Rudloff E, Conesa A, Tegnér J.

BMC Syst Biol. 2014;8 Suppl 2:I1. doi: 10.1186/1752-0509-8-S2-I1. Epub 2014 Mar 13. Review.


Relationship between genome and epigenome--challenges and requirements for future research.

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.

BMC Genomics. 2014 Jun 18;15:487. doi: 10.1186/1471-2164-15-487.


Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information.

Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P.

BMC Bioinformatics. 2014;15 Suppl 1:S2. doi: 10.1186/1471-2105-15-S1-S2. Epub 2014 Jan 10. Review.


Silencing motifs in the Clr2 protein from fission yeast, Schizosaccharomyces pombe.

Steinhauf D, Rodriguez A, Vlachakis D, Virgo G, Maksimov V, Kristell C, Olsson I, Linder T, Kossida S, Bongcam-Rudloff E, Bjerling P.

PLoS One. 2014 Jan 27;9(1):e86948. doi: 10.1371/journal.pone.0086948. eCollection 2014.


Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element.

Fischer A, Liljander A, Kaspar H, Muriuki C, Fuxelius HH, Bongcam-Rudloff E, de Villiers EP, Huber CA, Frey J, Daubenberger C, Bishop R, Younan M, Jores J.

Vet Res. 2013 Oct 1;44:86. doi: 10.1186/1297-9716-44-86.


Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.

Zubair S, de Villiers EP, Younan M, Andersson G, Tettelin H, Riley DR, Jores J, Bongcam-Rudloff E, Bishop RP.

Genome Announc. 2013 Jul 18;1(4). pii: e00515-13. doi: 10.1128/genomeA.00515-13.


Genome Sequence of Streptococcus agalactiae Strain 09mas018883, Isolated from a Swedish Cow.

Zubair S, de Villiers EP, Fuxelius HH, Andersson G, Johansson KE, Bishop RP, Bongcam-Rudloff E.

Genome Announc. 2013 Jul 11;1(4). pii: e00456-13. doi: 10.1128/genomeA.00456-13.


Best practices in bioinformatics training for life scientists.

Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.

Brief Bioinform. 2013 Sep;14(5):528-37. doi: 10.1093/bib/bbt043. Epub 2013 Jun 25.


Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium.

Manzoor S, Müller B, Niazi A, Bongcam-Rudloff E, Schnürer A.

Genome Announc. 2013 Mar 28;1(2):e0010713. doi: 10.1128/genomeA.00107-13.


Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.

Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E.

Genome Announc. 2013 Mar 21;1(2):e0011113. doi: 10.1128/genomeA.00111-13.


First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B.

Genome Announc. 2013 Jan;1(1). pii: e00213-12. doi: 10.1128/genomeA.00213-12. Epub 2013 Feb 21.


Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).

Benachenhou F, Sperber GO, Bongcam-Rudloff E, Andersson G, Boeke JD, Blomberg J.

Mob DNA. 2013 Feb 1;4(1):5. doi: 10.1186/1759-8753-4-5.


Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J.

Open Biol. 2012 Apr;2(4):120054. doi: 10.1098/rsob.120054.


Workshop on laboratory protocol standards for the Molecular Methods Database.

Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E.

N Biotechnol. 2013 Jan 25;30(2):109-13. doi: 10.1016/j.nbt.2012.05.019. Epub 2012 Jun 2.


The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants.

Fischer A, Shapiro B, Muriuki C, Heller M, Schnee C, Bongcam-Rudloff E, Vilei EM, Frey J, Jores J.

PLoS One. 2012;7(4):e36150. doi: 10.1371/journal.pone.0036150. Epub 2012 Apr 27.


Implementation of proteomic biomarkers: making it work.

Mischak H, Ioannidis JP, Argiles A, Attwood TK, Bongcam-Rudloff E, Broenstrup M, Charonis A, Chrousos GP, Delles C, Dominiczak A, Dylag T, Ehrich J, Egido J, Findeisen P, Jankowski J, Johnson RW, Julien BA, Lankisch T, Leung HY, Maahs D, Magni F, Manns MP, Manolis E, Mayer G, Navis G, Novak J, Ortiz A, Persson F, Peter K, Riese HH, Rossing P, Sattar N, Spasovski G, Thongboonkerd V, Vanholder R, Schanstra JP, Vlahou A.

Eur J Clin Invest. 2012 Sep;42(9):1027-36. doi: 10.1111/j.1365-2362.2012.02674.x. Epub 2012 Apr 21.


The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships.

Barrio ÁM, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff E, Blomberg J, Andersson G.

PLoS One. 2011 May 12;6(5):e19832. doi: 10.1371/journal.pone.0019832.


A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.

Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K.

PLoS Genet. 2011 Mar;7(3):e1001332. doi: 10.1371/journal.pgen.1001332. Epub 2011 Mar 17.


Contributions of the EMERALD project to assessing and improving microarray data quality.

Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.

Biotechniques. 2011 Jan;50(1):27-31. doi: 10.2144/000113591.


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