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Erik Bongcam Rudloff

Erik Bongcam Rudloff

Presentation

My main interest is in solving Life Science problems using bioinformatics approaches. Developing and managing complex multidisciplinary networked projects.

Erik Bongcam-Rudloff on Twitter: "The B3Africa project was presented at ISBER, Toronto, Canada



Teaching

Development of Bioinformatics courses and platforms. 
eBioKit: www.ebiokit.eu

Research

ML4microbiome: Statistical and machine learning techniques in human microbiome studies.

B3Africa: The European-African Bioibanks initiative

DEANN: a Marie Curie EU-American continent NGS Action project

H3AfricaBionet: The Pan African Bioinformatics Network

Setaria Digitata Genome Sequencing and annotation

Coral Reef Metagenomics

Background

Education and degree

  • Dr. Medical Sciences, Uppsala University, 1995
  • Docent exam, Swedish University of Agricultural Sciences, 2004

Positions

  • Professor in Bioinformatics
    Head SLU-Global Bioinformatics Centre
    Head of SLU Bioinformatics Infrastructure (SLUBI)
  • Associate Professor Department of Animal Breeding and Genetics, Bioinformatics section 2008-2016
  • Associate Professor Linnaeus Centre for Bioinformatics 2004-2008
  • Assistant professor Linnaeus Centre for Bioinformatics 2000-2004

Supervision

Principal supervisor and co-supervisor of 20 Ph-thesis 

Selected publications

1: Hollmann S, Kremer A, Baebler Š, Trefois C, Gruden K, Rudnicki WR, Tong W,
Gruca A, Bongcam-Rudloff E, Evelo CT, Nechyporenko A, Frohme M, Šafránek D,
Regierer B, D'Elia D. The need for standardisation in life science research - an
approach to excellence and trust. F1000Res. 2020 Dec 4;9:1398. doi:
10.12688/f1000research.27500.1. PMID: 33604028; PMCID: PMC7863991.

2: Van Damme R, Hölzer M, Viehweger A, Müller B, Bongcam-Rudloff E, Brandt C.
Metagenomics workflow for hybrid assembly, differential coverage binning,
metatranscriptomics and pathway analysis (MUFFIN). PLoS Comput Biol. 2021 Feb
9;17(2):e1008716. doi: 10.1371/journal.pcbi.1008716. PMID: 33561126; PMCID:
PMC7899367.

3: Corduneanu A, Mihalca AD, Sándor AD, Hornok S, Malmberg M, Viso NP, Bongcam-
Rudloff E. The heart microbiome of insectivorous bats from Central and South
Eastern Europe. Comp Immunol Microbiol Infect Dis. 2021 Apr;75:101605. doi:
10.1016/j.cimid.2020.101605. Epub 2021 Jan 7. PMID: 33421678.

4: Rugumisa BT, Bongcam-Rudloff E, Lukumay MS, Lyantagaye SL. Factors associated
with risk of preterm delivery in Tanzania: A case-control study at Muhimbili
National Hospital. Int J Gynaecol Obstet. 2020 Dec 5. doi: 10.1002/ijgo.13520.
Epub ahead of print. PMID: 33277704.

5: Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B. High-
Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate
Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.
Front Microbiol. 2020 Aug 27;11:2066. doi: 10.3389/fmicb.2020.02066. PMID:
32983047; PMCID: PMC7481360.

6: Jhamat N, Niazi A, Guo Y, Chanrot M, Ivanova E, Kelsey G, Bongcam-Rudloff E,
Andersson G, Humblot P. LPS-treatment of bovine endometrial epithelial cells
causes differential DNA methylation of genes associated with inflammation and
endometrial function. BMC Genomics. 2020 Jun 3;21(1):385. doi:
10.1186/s12864-020-06777-7. PMID: 32493210; PMCID: PMC7268755.

7: Solé M, Lindgren G, Bongcam-Rudloff E, Jansson A. Benefits and risks of
barefoot harness racing in Standardbred trotters. Anim Sci J. 2020 Jan-
Dec;91(1):e13380. doi: 10.1111/asj.13380. PMID: 32363779.

8: Senanayake KS, Söderberg J, Põlajev A, Malmberg M, Karunanayake EH, Tennekoon
KH, Samarakoon SR, Bongcam-Rudloff E, Niazi A. The Genome of Setaria digitata: A
Cattle Nematode Closely Related to Human Filarial Parasites. Genome Biol Evol.
2020 Feb 1;12(2):3971-3976. doi: 10.1093/gbe/evaa017. PMID: 32022853; PMCID:
PMC7061230.

9: Guo Y, van Schaik T, Jhamat N, Niazi A, Chanrot M, Charpigny G, Valarcher JF,
Bongcam-Rudloff E, Andersson G, Humblot P. Differential gene expression in
bovine endometrial epithelial cells after challenge with LPS; specific
implications for genes involved in embryo maternal interactions. PLoS One. 2019
Sep 5;14(9):e0222081. doi: 10.1371/journal.pone.0222081. PMID: 31487323; PMCID:
PMC6728075.

10: Papakonstantinou E, Bacopoulou F, Brouzas D, Megalooikonomou V, D'Elia D,
Bongcam-Rudloff E, Vlachakis D. NOTCH3 and CADASIL syndrome: a genetic and
structural overview. EMBnet J. 2019;24:e921. doi: 10.14806/ej.24.0.921. Epub
2019 May 22. PMID: 31218211; PMCID: PMC6583802.

11: Gourlé H, Karlsson-Lindsjö O, Hayer J, Bongcam-Rudloff E. Simulating
Illumina metagenomic data with InSilicoSeq. Bioinformatics. 2019 Feb
1;35(3):521-522. doi: 10.1093/bioinformatics/bty630. PMID: 30016412; PMCID:
PMC6361232.

12: Cárdenas CA, González-Aravena M, Font A, Hestetun JT, Hajdu E, Trefault N,
Malmberg M, Bongcam-Rudloff E. High similarity in the microbiota of cold-water
sponges of the Genus <i>Mycale</i> from two different geographical areas. PeerJ.
2018 Jun 7;6:e4935. doi: 10.7717/peerj.4935. PMID: 29892508; PMCID: PMC5994334.

13: Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Genome-Guided Analysis
of Clostridium ultunense and Comparative Genomics Reveal Different Strategies
for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising
Bacteria. Genes (Basel). 2018 Apr 23;9(4):225. doi: 10.3390/genes9040225. PMID:
29690652; PMCID: PMC5924567.

14: Hernández-de-Diego R, de Villiers EP, Klingström T, Gourlé H, Conesa A,
Bongcam-Rudloff E. The eBioKit, a stand-alone educational platform for
bioinformatics. PLoS Comput Biol. 2017 Sep 14;13(9):e1005616. doi:
10.1371/journal.pcbi.1005616. PMID: 28910280; PMCID: PMC5598936.

15: Klingstrom T, Bongcam-Rudloff E, Reichel J. Legal & ethical compliance when
sharing biospecimen. Brief Funct Genomics. 2018 Jan 1;17(1):1-7. doi:
10.1093/bfgp/elx008. PMID: 28460118; PMCID: PMC5859993.

16: Loftsdóttir H, Söderlund R, Jinnerot T, Eriksson E, Bongcam-Rudloff E, Aspán
A. Dynamics of insertion sequence element IS629 inactivation of verotoxin 2
genes in Escherichia coli O157:H7. FEMS Microbiol Lett. 2017 Apr 1;364(8). doi:
10.1093/femsle/fnx074. PMID: 28402463.

17: Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B. Genome-Guided Analysis
and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising
Bacterium Syntrophaceticus schinkii. PLoS One. 2016 Nov 16;11(11):e0166520. doi:
10.1371/journal.pone.0166520. PMID: 27851830; PMCID: PMC5113046.

18: Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Complete genome sequence
of <i>Methanoculleus bourgensis</i> strain MAB1, the syntrophic partner of
mesophilic acetate-oxidising bacteria (SAOB). Stand Genomic Sci. 2016 Oct
12;11:80. doi: 10.1186/s40793-016-0199-x. PMID: 27777650; PMCID: PMC5062929.

19: Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J.
MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral
Metagenomics Studies. PLoS One. 2016 Aug 1;11(8):e0160334. doi:
10.1371/journal.pone.0160334. PMID: 27479078; PMCID: PMC4968819.

20: Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi
F, Korpelainen E. Recommendations on e-infrastructures for next-generation
sequencing. Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. PMID:
27267963; PMCID: PMC4897895.

21: Mushtaq M, Bongcam-Rudloff E, Loftsdottir H, Pringle M, Segerman B, Zuerner
R, Rosander A. Genetic analysis of a Treponema phagedenis locus encoding
antigenic lipoproteins with potential for antigenic variation. Vet Microbiol.
2016 Jun 30;189:91-8. doi: 10.1016/j.vetmic.2016.04.027. Epub 2016 May 6. PMID:
27259832.

22: 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. 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. PLoS Genet. 2016 May
12;12(5):e1006000. doi: 10.1371/journal.pgen.1006000. PMID: 27171399; PMCID:
PMC4865040.

23: Söderlund R, Hurel J, Jinnerot T, Sekse C, Aspán A, Eriksson E, Bongcam-
Rudloff E. 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. Infect Ecol Epidemiol. 2016 Feb
16;6:30246. doi: 10.3402/iee.v6.30246. PMID: 26895282; PMCID: PMC4759829.

24: 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.
Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1,
isolated from a Kenyan dromedary camel. Stand Genomic Sci. 2015 Nov 20;10:109.
doi: 10.1186/s40793-015-0098-6. PMID: 26594310; PMCID: PMC4654806.

25: Manzoor S, Müller B, Niazi A, Schnürer A, Bongcam-Rudloff E. Working draft
genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus
schinkii strain Sp3. Stand Genomic Sci. 2015 Nov 11;10:99. doi:
10.1186/s40793-015-0092-z. PMID: 26566424; PMCID: PMC4642661.

26: Mushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson DS. Brachyspira
suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from
pigs and mallards: genomic and phenotypic characteristics. BMC Microbiol. 2015
Oct 12;15:208. doi: 10.1186/s12866-015-0537-y. PMID: 26458507; PMCID:
PMC4603578.

27: 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. The
genomes of three stocks comprising the most widely utilized live sporozoite
Theileria parva vaccine exhibit very different degrees and patterns of sequence
divergence. BMC Genomics. 2015 Sep 24;16:729. doi: 10.1186/s12864-015-1910-9.
PMID: 26403690; PMCID: PMC4583173.

28: Dahlö M, Haziza F, Kallio A, Korpelainen E, Bongcam-Rudloff E, Spjuth O.
BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences. Bioinform
Biol Insights. 2015 Sep 10;9:125-8. doi: 10.4137/BBI.S28636. PMID: 26401099;
PMCID: PMC4567039.

29: Mushtaq M, Manzoor S, Pringle M, Rosander A, Bongcam-Rudloff E. Draft genome
sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital
dermatitis. Stand Genomic Sci. 2015 Sep 21;10:67. doi:
10.1186/s40793-015-0059-0. PMID: 26392840; PMCID: PMC4576374.

30: 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. Experiences with
workflows for automating data-intensive bioinformatics. Biol Direct. 2015 Aug
19;10:43. doi: 10.1186/s13062-015-0071-8. PMID: 26282399; PMCID: PMC4539931.

31: Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F,
Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium. Correction:
GOBLET: The Global Organisation for Bioinformatics Learning, Education and
Training. PLoS Comput Biol. 2015 May 14;11(5):e1004281. doi:
10.1371/journal.pcbi.1004281. Erratum for: PLoS Comput Biol. 2015
Apr;11(4):e1004143. Atwood, Teresa K [corrected to Attwood, Teresa K]. PMID:
25974841; PMCID: PMC4431671.

32: Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F,
Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium. GOBLET: the
Global Organisation for Bioinformatics Learning, Education and Training. PLoS
Comput Biol. 2015 Apr 9;11(4):e1004143. doi: 10.1371/journal.pcbi.1004143.
Erratum in: PLoS Comput Biol. 2015 May;11(5):e1004281. Atwood, Teresa K
[corrected to Attwood, Teresa K]. PMID: 25856076; PMCID: PMC4391932.

33: Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A. Genome-guided
analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides
insights into environmental adaptations and syntrophic acetate oxidation. PLoS
One. 2015 Mar 26;10(3):e0121237. doi: 10.1371/journal.pone.0121237. PMID:
25811859; PMCID: PMC4374699.

34: Johansson AH, Bejai S, Niazi A, Manzoor S, Bongcam-Rudloff E, Meijer J.
Studies of plant colonisation by closely related Bacillus amyloliquefaciens
biocontrol agents using strain specific quantitative PCR assays. Antonie Van
Leeuwenhoek. 2014 Dec;106(6):1247-57. doi: 10.1007/s10482-014-0295-0. Epub 2014
Oct 8. PMID: 25294724.

35: Niazi A, Manzoor S, Bejai S, Meijer J, Bongcam-Rudloff E. Complete genome
sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp.
plantarum UCMB5033. Stand Genomic Sci. 2014 Feb 15;9(3):718-25. doi:
10.4056/sigs.4758653. PMID: 25197456; PMCID: PMC4148973.

36: 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. The GOBLET
training portal: a global repository of bioinformatics training materials,
courses and trainers. Bioinformatics. 2015 Jan 1;31(1):140-2. doi:
10.1093/bioinformatics/btu601. Epub 2014 Sep 4. PMID: 25189782; PMCID:
PMC4271145.

37: Söderlund R, Jernberg C, Ivarsson S, Hedenström I, Eriksson E, Bongcam-
Rudloff E, Aspán A. Molecular typing of Escherichia coli O157:H7 isolates from
Swedish cattle and human cases: population dynamics and virulence. J Clin
Microbiol. 2014 Nov;52(11):3906-12. doi: 10.1128/JCM.01877-14. Epub 2014 Aug 20.
PMID: 25143581; PMCID: PMC4313222.

38: Niazi A, Manzoor S, Asari S, Bejai S, Meijer J, Bongcam-Rudloff E. Genome
analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a
rhizobacterium that improves plant growth and stress management. PLoS One. 2014
Aug 13;9(8):e104651. doi: 10.1371/journal.pone.0104651. PMID: 25119988; PMCID:
PMC4138018.

39: Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M,
Gisel A, Ballestar E, Bongcam-Rudloff E, Conesa A, Tegnér J. Data integration in
the era of omics: current and future challenges. BMC Syst Biol. 2014;8 Suppl
2(Suppl 2):I1. doi: 10.1186/1752-0509-8-S2-I1. Epub 2014 Mar 13. PMID: 25032990;
PMCID: PMC4101704.

40: 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. Relationship between genome and
epigenome--challenges and requirements for future research. BMC Genomics. 2014
Jun 18;15(1):487. doi: 10.1186/1471-2164-15-487. PMID: 24942464; PMCID:
PMC4073504.

41: Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek
F, Romano P. Integrated Bio-Search: challenges and trends for the integration,
search and comprehensive processing of biological information. BMC
Bioinformatics. 2014;15 Suppl 1(Suppl 1):S2. doi: 10.1186/1471-2105-15-S1-S2.
Epub 2014 Jan 10. PMID: 24564249; PMCID: PMC4015876.

42: Steinhauf D, Rodriguez A, Vlachakis D, Virgo G, Maksimov V, Kristell C,
Olsson I, Linder T, Kossida S, Bongcam-Rudloff E, Bjerling P. Silencing motifs
in the Clr2 protein from fission yeast, Schizosaccharomyces pombe. PLoS One.
2014 Jan 27;9(1):e86948. doi: 10.1371/journal.pone.0086948. PMID: 24475199;
PMCID: PMC3903592.

43: 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.
Camel Streptococcus agalactiae populations are associated with specific disease
complexes and acquired the tetracycline resistance gene tetM via a Tn916-like
element. Vet Res. 2013 Oct 1;44(1):86. doi: 10.1186/1297-9716-44-86. PMID:
24083845; PMCID: PMC3850529.

44: Zubair S, de Villiers EP, Younan M, Andersson G, Tettelin H, Riley DR, Jores
J, Bongcam-Rudloff E, Bishop RP. Genome Sequences of Two Pathogenic
Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.
Genome Announc. 2013 Jul 18;1(4):e00515-13. doi: 10.1128/genomeA.00515-13. PMID:
23868134; PMCID: PMC3715676.

45: Zubair S, de Villiers EP, Fuxelius HH, Andersson G, Johansson KE, Bishop RP,
Bongcam-Rudloff E. Genome Sequence of Streptococcus agalactiae Strain
09mas018883, Isolated from a Swedish Cow. Genome Announc. 2013 Jul
11;1(4):e00456-13. doi: 10.1128/genomeA.00456-13. PMID: 23846269; PMCID:
PMC3709146.

46: 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. Best practices
in bioinformatics training for life scientists. Brief Bioinform. 2013
Sep;14(5):528-37. doi: 10.1093/bib/bbt043. Epub 2013 Jun 25. PMID: 23803301;
PMCID: PMC3771230.

47: Manzoor S, Müller B, Niazi A, Bongcam-Rudloff E, Schnürer A. Draft Genome
Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing
Bacterium. Genome Announc. 2013 Mar 28;1(2):e0010713. doi:
10.1128/genomeA.00107-13. PMID: 23538905; PMCID: PMC3622961.

48: Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E. Genome Sequence of
a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036. Genome
Announc. 2013 Mar 21;1(2):e0011113. doi: 10.1128/genomeA.00111-13. PMID:
23516223; PMCID: PMC3622975.

49: Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B. First Genome Sequence of
a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain
Re1. Genome Announc. 2013 Jan;1(1):e00213-12. doi: 10.1128/genomeA.00213-12.
Epub 2013 Feb 21. PMID: 23469343; PMCID: PMC3587937.

50: Benachenhou F, Sperber GO, Bongcam-Rudloff E, Andersson G, Boeke JD,
Blomberg J. Conserved structure and inferred evolutionary history of long
terminal repeats (LTRs). Mob DNA. 2013 Feb 1;4(1):5. doi: 10.1186/1759-8753-4-5.
PMID: 23369192; PMCID: PMC3601003.

51: Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock
DD, Höglund J. Transcriptome sequencing of black grouse (Tetrao tetrix) for
immune gene discovery and microsatellite development. Open Biol. 2012
Apr;2(4):120054. doi: 10.1098/rsob.120054. PMID: 22724064; PMCID: PMC3376728.

52: 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. Workshop on
laboratory protocol standards for the Molecular Methods Database. N Biotechnol.
2013 Jan 25;30(2):109-13. doi: 10.1016/j.nbt.2012.05.019. Epub 2012 Jun 2. PMID:
22687389.

53: Fischer A, Shapiro B, Muriuki C, Heller M, Schnee C, Bongcam-Rudloff E,
Vilei EM, Frey J, Jores J. The origin of the 'Mycoplasma mycoides cluster'
coincides with domestication of ruminants. PLoS One. 2012;7(4):e36150. doi:
10.1371/journal.pone.0036150. Epub 2012 Apr 27. PMID: 22558362; PMCID:
PMC3338596.

54: 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. Implementation of proteomic biomarkers:
making it work. Eur J Clin Invest. 2012 Sep;42(9):1027-36. doi:
10.1111/j.1365-2362.2012.02674.x. Epub 2012 Apr 21. PMID: 22519700; PMCID:
PMC3464367.

55: Barrio ÁM, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff
E, Blomberg J, Andersson G. The first sequenced carnivore genome shows complex
host-endogenous retrovirus relationships. PLoS One. 2011 May 12;6(5):e19832.
doi: 10.1371/journal.pone.0019832. PMID: 21589882; PMCID: PMC3093408.

56: 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. A novel unstable
duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and
a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS Genet. 2011
Mar;7(3):e1001332. doi: 10.1371/journal.pgen.1001332. Epub 2011 Mar 17. PMID:
21437276; PMCID: PMC3060080.

57: 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.
Contributions of the EMERALD project to assessing and improving microarray data
quality. Biotechniques. 2011 Jan;50(1):27-31. doi: 10.2144/000113591. PMID:
21231919.

58: Mischak H, Kolch W, Aivaliotis M, Bouyssié D, Court M, Dihazi H, Dihazi GH,
Franke J, Garin J, Gonzalez de Peredo A, Iphöfer A, Jänsch L, Lacroix C,
Makridakis M, Masselon C, Metzger J, Monsarrat B, Mrug M, Norling M, Novak J,
Pich A, Pitt A, Bongcam-Rudloff E, Siwy J, Suzuki H, Thongboonkerd V, Wang LS,
Zoidakis J, Zürbig P, Schanstra JP, Vlahou A. Comprehensive human urine
standards for comparability and standardization in clinical proteome analysis.
Proteomics Clin Appl. 2010 Apr;4(4):464-78. doi: 10.1002/prca.200900189. Epub
2010 Feb 3. PMID: 21137064; PMCID: PMC3064949.

59: Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett
SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF,
Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J,
Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP,
Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina
F, Monsarrat B, Novak J, Peter K, Rossing P, Sánchez-Carbayo M, Schanstra JP,
Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra
TD, Weissinger E, Yamamoto T, Vlahou A. Recommendations for biomarker
identification and qualification in clinical proteomics. Sci Transl Med. 2010
Aug 25;2(46):46ps42. doi: 10.1126/scitranslmed.3001249. PMID: 20739680.

60: Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R,
Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig
J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon
AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M,
Thorisson GA, Zouberakis M, Hancock JM. Finding and sharing: new approaches to
registries of databases and services for the biomedical sciences. Database
(Oxford). 2010 Jul 6;2010:baq014. doi: 10.1093/database/baq014. PMID: 20627863;
PMCID: PMC2911849.

61: Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A,
Fernández JM, Rodriguez JM; INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice
P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB,
Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G. The
EMBRACE web service collection. Nucleic Acids Res. 2010 Jul;38(Web Server
issue):W683-8. doi: 10.1093/nar/gkq297. Epub 2010 May 12. PMID: 20462862; PMCID:
PMC2896104.

62: Klint M, Thollesson M, Bongcam-Rudloff E, Birkelund S, Nilsson A, Herrmann
B. Mosaic structure of intragenic repetitive elements in histone H1-like protein
Hc2 varies within serovars of Chlamydia trachomatis. BMC Microbiol. 2010 Mar
17;10:81. doi: 10.1186/1471-2180-10-81. PMID: 20236532; PMCID: PMC2848022.

63: Bannasch D, Young A, Myers J, Truvé K, Dickinson P, Gregg J, Davis R,
Bongcam-Rudloff E, Webster MT, Lindblad-Toh K, Pedersen N. Localization of
canine brachycephaly using an across breed mapping approach. PLoS One. 2010 Mar
10;5(3):e9632. doi: 10.1371/journal.pone.0009632. PMID: 20224736; PMCID:
PMC2835769.

64: Vlahou A, Allmaier G, Attwood T, Bongcam-Rudloff E, Charonis A, Frokiaer J,
Mischak H, Schanstra J, Spasovski G. 2nd Combined Working Group and Management
Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009,
Nafplio, Greece. Proteomics Clin Appl. 2009 Sep;3(9):1017-22. doi:
10.1002/prca.200900087. Epub 2009 Aug 4. PMID: 21137004.

65: Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E,
Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R,
Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl
M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H,
Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van
der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. A community
standard format for the representation of protein affinity reagents. Mol Cell
Proteomics. 2010 Jan;9(1):1-10. doi: 10.1074/mcp.M900185-MCP200. Epub 2009 Aug
11. PMID: 19674966; PMCID: PMC2808255.

66: Martinez Barrio A, Eriksson O, Badhai J, Fröjmark AS, Bongcam-Rudloff E,
Dahl N, Schuster J. Targeted resequencing and analysis of the Diamond-Blackfan
anemia disease locus RPS19. PLoS One. 2009 Jul 9;4(7):e6172. doi:
10.1371/journal.pone.0006172. PMID: 19587786; PMCID: PMC2703794.

67: Barrio AM, Lagercrantz E, Sperber GO, Blomberg J, Bongcam-Rudloff E.
Annotation and visualization of endogenous retroviral sequences using the
Distributed Annotation System (DAS) and eBioX. BMC Bioinformatics. 2009 Jun
16;10 Suppl 6(Suppl 6):S18. doi: 10.1186/1471-2105-10-S6-S18. PMID: 19534743;
PMCID: PMC2697641.

68: D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L, Bongcam-
Rudloff E. The 20th anniversary of EMBnet: 20 years of bioinformatics for the
Life Sciences community. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6(Suppl 6):S1.
doi: 10.1186/1471-2105-10-S6-S1. PMID: 19534734; PMCID: PMC2697632.

69: Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C,
Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R,
Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K,
Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G. PDB_REDO: automated re-
refinement of X-ray structure models in the PDB. J Appl Crystallogr. 2009 Jun
1;42(Pt 3):376-384. doi: 10.1107/S0021889809008784. Epub 2009 Apr 3. PMID:
22477769; PMCID: PMC3246819.

70: Singh U, Bongcam-Rudloff E, Westermark B. A DNA sequence directed mutual
transcription regulation of HSF1 and NFIX involves novel heat sensitive protein
interactions. PLoS One. 2009;4(4):e5050. doi: 10.1371/journal.pone.0005050. Epub
2009 Apr 1. PMID: 19337383; PMCID: PMC2660424.

71: Lee C, Bongcam-Rudloff E, Sollner C, Jahnen-Dechent W, Claesson-Welsh L.
Type 3 cystatins; fetuins, kininogen and histidine-rich glycoprotein. Front
Biosci (Landmark Ed). 2009 Jan 1;14:2911-22. doi: 10.2741/3422. PMID: 19273244.

72: Vlahou A, Schanstra J, Frokiaer J, El Nahas M, Spasovski G, Mischak H, Domon
B, Allmaier G, Bongcam-Rudloff E, Attwood T; European Kidney and Urine
Proteomics Network. Establishment of a European Network for Urine and Kidney
Proteomics. J Proteomics. 2008 Oct 7;71(4):490-2. doi:
10.1016/j.jprot.2008.06.009. Epub 2008 Jun 22. PMID: 18620085.

73: Rising A, Johansson J, Larson G, Bongcam-Rudloff E, Engström W, Hjälm G.
Major ampullate spidroins from Euprosthenops australis: multiplicity at protein,
mRNA and gene levels. Insect Mol Biol. 2007 Oct;16(5):551-61. doi:
10.1111/j.1365-2583.2007.00749.x. Epub 2007 Aug 4. PMID: 17680798.

74: Martinez Barrio A, Soeria-Atmadja D, Nistér A, Gustafsson MG, Hammerling U,
Bongcam-Rudloff E. EVALLER: a web server for in silico assessment of potential
protein allergenicity. Nucleic Acids Res. 2007 Jul;35(Web Server
issue):W694-700. doi: 10.1093/nar/gkm370. Epub 2007 May 30. PMID: 17537818;
PMCID: PMC1933222.

75: Stenshamn K, Bongcam-Rudloff E, Salmon Hillbertz N, Nødtvedt A, Bergvall K,
Hedhammar A, Andersson G. Evaluation of kallikrein 7 as a disease-causing gene
for canine atopic dermatitis using microsatellite-based association mapping.
Anim Genet. 2006 Dec;37(6):601-3. doi: 10.1111/j.1365-2052.2006.01537.x. PMID:
17121614.

76: Giuffra E, Törnsten A, Marklund S, Bongcam-Rudloff E, Chardon P, Kijas JM,
Anderson SI, Archibald AL, Andersson L. A large duplication associated with
dominant white color in pigs originated by homologous recombination between LINE
elements flanking KIT. Mamm Genome. 2002 Oct;13(10):569-77. doi:
10.1007/s00335-002-2184-5. PMID: 12420135.

77: Lopez-Egido J, Cunningham J, Berg M, Oberg K, Bongcam-Rudloff E, Gobl A.
Menin's interaction with glial fibrillary acidic protein and vimentin suggests a
role for the intermediate filament network in regulating menin activity. Exp
Cell Res. 2002 Aug 15;278(2):175-83. doi: 10.1006/excr.2002.5575. PMID:
12169273.

78: Andrae J, Bongcam-Rudloff E, Hansson I, Lendahl U, Westermark B, Nistér M. A
1.8kb GFAP-promoter fragment is active in specific regions of the embryonic CNS.
Mech Dev. 2001 Sep;107(1-2):181-5. doi: 10.1016/s0925-4773(01)00460-9. PMID:
11520676.

79: Jeon JT, Amarger V, Rogel-Gaillard C, Robic A, Bongcam-Rudloff E, Paul S,
Looft C, Milan D, Chardon P, Andersson L. Comparative analysis of a BAC contig
of the porcine RN region and the human transcript map: implications for the
cloning of trait loci. Genomics. 2001 Mar 15;72(3):297-303. doi:
10.1006/geno.2000.6495. PMID: 11401445.

80: Elobeid A, Bongcam-Rudloff E, Westermark B, Nistér M. Effects of inducible
glial fibrillary acidic protein on glioma cell motility and proliferation. J
Neurosci Res. 2000 Apr 15;60(2):245-56. doi:
10.1002/(SICI)1097-4547(20000415)60:2<245::AID-JNR14>3.0.CO;2-1. PMID: 10740230.

81: Enblad P, Hesselager G, Bongcam-Rudloff E, Hallin I, Westermark B, Nistér M.
Modulation of phenotype and induction of irregular vessels accompany high
tumorigenic potential of clonal human glioma cells xenografted to nude-rat
brain. Int J Cancer. 2000 Mar 15;85(6):819-28. doi:
10.1002/(sici)1097-0215(20000315)85:6<819::aid-ijc15>3.0.co;2-q. PMID: 10709103.

82: Hammerling U, Bongcam-Rudloff E, Setterblad N, Kroon R, Rehnström AK,
Viitanen E, Andersson G, Sjödin L. The beta-gal interferon assay: a new, precise
and sensitive method. J Interferon Cytokine Res. 1998 Jul;18(7):451-60. doi:
10.1089/jir.1998.18.451. PMID: 9712360.

83: Valgeirsdóttir S, Claesson-Welsh L, Bongcam-Rudloff E, Hellman U, Westermark
B, Heldin CH. PDGF induces reorganization of vimentin filaments. J Cell Sci.
1998 Jul 30;111 ( Pt 14):1973-80. PMID: 9645945.

84: Cervós-Navarro J, Sharma HS, Westman J, Bongcam-Rudloff E. Glial reactions
in the central nervous system following heat stress. Prog Brain Res.
1998;115:241-74. doi: 10.1016/s0079-6123(08)62039-7. PMID: 9632939.

85: El-Obeid A, Bongcam-Rudloff E, Sörby M, Ostman A, Nistér M, Westermark B.
Cell scattering and migration induced by autocrine transforming growth factor
alpha in human glioma cells in vitro. Cancer Res. 1997 Dec 15;57(24):5598-604.
PMID: 9407973.

86: Karlsson C, Stenman G, Vojta PJ, Bongcam-Rudloff E, Barrett JC, Westermark
B, Paulsson Y. Escape from senescence in hybrid cell clones involves deletions
of two regions located on human chromosome 1q. Cancer Res. 1996 Jan
15;56(2):241-5. PMID: 8542573.

87: Wang JL, Nistér M, Bongcam-Rudloff E, Pontén J, Westermark B. Suppression of
platelet-derived growth factor alpha- and beta-receptor mRNA levels in human
fibroblasts by SV40 T/t antigen. J Cell Physiol. 1996 Jan;166(1):12-21. doi:
10.1002/(SICI)1097-4652(199601)166:1<12::AID-JCP2>3.0.CO;2-J. PMID: 8557760.

88: Afink GB, Nistér M, Stassen BH, Joosten PH, Rademakers PJ, Bongcam-Rudloff
E, Van Zoelen EJ, Mosselman S. Molecular cloning and functional characterization
of the human platelet-derived growth factor alpha receptor gene promoter.
Oncogene. 1995 Apr 20;10(8):1667-72. PMID: 7731723.

89: Bongcam-Rudloff E, Nistér M, Betsholtz C, Wang JL, Stenman G, Huebner K,
Croce CM, Westermark B. Human glial fibrillary acidic protein: complementary DNA
cloning, chromosome localization, and messenger RNA expression in human glioma
cell lines of various phenotypes. Cancer Res. 1991 Mar 1;51(5):1553-60. PMID:
1847665.

90: Bywater M, Rorsman F, Bongcam-Rudloff E, Mark G, Hammacher A, Heldin CH,
Westermark B, Betsholtz C. Expression of recombinant platelet-derived growth
factor A- and B-chain homodimers in rat-1 cells and human fibroblasts reveals
differences in protein processing and autocrine effects. Mol Cell Biol. 1988
Jul;8(7):2753-62. doi: 10.1128/mcb.8.7.2753. PMID: 3405217; PMCID: PMC363492.

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