Publications referred in PubMed since 2002 for the Bioinformatics group at Department of Informatics and CBU.


Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes. Engelen E, Akinci U, Bryne JC, Hou J, Gontan C, Moen M, Szumska D, Kockx C, van Ijcken W, Dekkers DH, Demmers J, Rijkers EJ, Bhattacharya S, Philipsen S, Pevny LH, Grosveld FG, Rottier RJ, Lenhard B, Poot RA. Nat Genet. 2011 Jun;43(6):607-11.                                                                                                    

Making enhancers from spare parts of the genome. Fredman D, Dong X, Lenhard B.    Genome Biol. 2011 Dec 29;12(12):138.                                                                                                                                                                                                                      
Promoter architecture of mouse olfactory receptor genes. Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Succhelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P.    Genome Res. 2011 Dec 22.
The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ light chain locus. Ribeiro de Almeida C, Stadhouders R, de Bruijn MJ, Bergen IM, Thongjuea S, Lenhard B, van Ijcken W, Grosveld F, Galjart N, Soler E, Hendriks RW. Immunity. 2011 Oct 28;35(4):501-13.
Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. Royo JL, Hidalgo C, Roncero Y, Seda MA, Akalin A, Lenhard B, Casares F, G√≥mez-Skarmeta JL.    PLoS One. 2011;6(9):e24824.

Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, Stevens M, de Boer E, Kockx C, van der Sloot A, van den Hout M, van Ijcken W, Eick D, Lenhard B, Grosveld F, Soler E.    EMBO J. 2011 Dec 13.
A prioritization analysis of disease association by data-mining of functional annotation of human genes. Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T.    Genomics. 2011 Oct 14.

Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. Goncearenco A, Berezovsky IN.    Bioinformatics. 2011 Sep 1;27(17):2368-75.
Binding leverage as a molecular basis for allosteric regulation. Mitternacht S, Berezovsky IN.    PLoS Comput Biol. 2011 Sep;7(9):e1002148.

On the importance of amino acid sequence and spatial proximity of interacting residues for protein folding. Mitternacht S, Berezovsky IN.    J Biomol Struct Dyn. 2011 Feb;28(4):607-9;
Coherent conformational degrees of freedom as a structural basis for allosteric communication.       Mitternacht S, Berezovsky IN.    PLoS Comput Biol. 2011 Dec;7(12)
A geometry-based generic predictor for catalytic and allosteric sites.    Mitternacht S, Berezovsky IN.    Protein Eng Des Sel. 2011 Apr;24(4):405-9.
Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener's autoantigen, in RBL cells: implication for its pathogenic activity. Kantari C, Millet A, Gabillet J, Hajjar E, Broemstrup T, Pluta P, Reuter N, Witko-Sarsat V.    J Leukoc Biol. 2011 Nov;90(5):941-50.
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Skjaerven L, Martinez A, Reuter N.    Proteins. 2011 Jan;79(1):232-43.

Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach. Skjaerven L, Reuter N, Martinez A.    Future Med Chem. 2011 Dec;3(16):2079-100.
Modulation of transcriptional and inflammatory responses in murine macrophages by the Mycobacterium tuberculosis mammalian cell entry (Mce) 1 complex. Stavrum R, Stavrum AK, Valvatne H, Riley LW, Ulvestad E, Jonassen I, Assmus J, Doherty TM, Grewal HM.    PLoS One. 2011;6(10)
The genome sequence of Atlantic cod reveals a unique immune system. Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, et al.    Nature. 2011 Aug 10;477(7363):207-10.

Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. Hollup SM, Sadowski MI, Jonassen I, Taylor WR.    Comput Biol Chem. 2011 Jun;35(3):174-88.

Systematic exploration of error sources in pyrosequencing flowgram data. Balzer S, Malde K, Jonassen I.    Bioinformatics. 2011 Jul 1;27(13):i304-9.

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. Lanzén A, Jørgensen SL, Bengtsson MM, Jonassen I, Øvreås L, Urich T.    FEMS Microbiol Ecol. 2011 Sep;77(3):577-89.

Gene expression patterns related to vascular invasion and aggressive features in endometrial cancer.    Mannelqvist M, Stefansson IM, Bredholt G, Hellem Bø T, Oyan AM, Jonassen I, Kalland KH, Salvesen HB, Akslen LA.    Am J Pathol. 2011 Feb;178(2):861-71.
Untangling the intracellular signalling network in cancer--a strategy for data integration in acute myeloid leukaemia. Jørgensen KM, Hjelle SM, Øye OK, Puntervoll P, Reikvam H, Skavland J, Anderssen E, Bruserud Ø, Gjertsen BT.    J Proteomics. 2011 Mar 1;74(3):269-81.

Brain proteome alterations of Atlantic cod (Gadus morhua) exposed to PCB 153. Berg K, Puntervoll P, Klungsøyr J, Goksøyr A.    Aquat Toxicol. 2011 Oct;105(3-4):206-17.
Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows. Sztromwasser P, Puntervoll P, Petersen K. J Integr Bioinform. 2011 Jul 26;8(2):163.
Polyploidization increases meiotic recombination frequency in Arabidopsis. Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid O.    BMC Biol. 2011 Apr 21;9:24.

High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm.    Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MT, Spillane C, Nordborg M, Rehmsmeier M, Köhler C.    PLoS Genet. 2011 Jun;7(6).

A global analysis of peptide fragmentation variability. Barsnes H, Eidhammer I, Martens L. Proteomics. 2011 Mar;11(6).

Submitting proteomics data to PRIDE using PRIDE Converter. Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L. Methods Mol Biol. 2011;694:237-53.


Arntzen, M. Ø., Koehler, C. J., Barsnes, H., Berven, F. S., Treumann, A. & Thiede, B. (2010). IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ and TMT. Journal of proteome research.

Balzer, S., Malde, K., Lanzen, A., Sharma, A. & Jonassen, I. (2010). Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim. Bioinformatics 26, i420-i425.                                                                                                                                                               
Barsnes, H., Côté, R. G., Eidhammer, I. & Martens, L. (2010). OLS dialog: an open-source front end to the ontology lookup service. BMC bioinformatics 11, 34.

Barsnes, H., Eidhammer, I. & Martens, L. (2010). FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics 10, 1087-1090.                                                            

Bartossek, R., Nicol, G. W., Lanzen, A., Klenk, H.-P. & Schleper, C. (2010). Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environmental microbiology 12, 1075-1088.

Berg, K., Puntervoll, P., Valdersnes, S. & Goksøyr, A. (2010). Responses in the brain proteome of Atlantic cod (Gadus morhua) exposed to methylmercury. Aquatic toxicology (Amsterdam, Netherlands) 100, 51-65.                                                                               

Berge, E. O., Knappskog, S., Geisler, S., Staalesen, V., Pacal, M., Børresen-Dale, A.-L., Puntervoll, P., Lillehaug, J. R. & Lønning, P. E. (2010). Identification and characterization of retinoblastoma gene mutations disturbing apoptosis in human breast cancers. Molecular cancer 9, 173.                              

Broemstrup, T. & Reuter, N. (2010). How does proteinase 3 interact with lipid bilayers? Physical chemistry chemical physics : PCCP 12, 7487-7496.                                                                               
Broemstrup, T. & Reuter, N. (2010). Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic Phospholipid Bilayers. Biophysical journal 99, 825-833.                                                                         

Côté, R., Reisinger, F., Martens, L., Barsnes, H., Vizcaino, J. A. & Hermjakob, H. (2010). The Ontology Lookup Service: bigger and better. Nucleic acids research 38 Suppl, W155-160.                                                                                                                                                               
Davidson, W. S., Koop, B. F., Jones, S. J., Iturra, P., Vidal, R., Maass, A., Jonassen, I., Lien, S. & Omholt, S. W. (2010). Sequencing the genome of the Atlantic salmon (Salmo salar). Genome biology 11, 403.                                                                               

Denoeud, F., Henriet, S., Mungpakdee, S., …, Danks, G., …, Aasland, R., …, Lenhard, B., Roest Crollius, H., Wincker, P., Chourrout, D. (2010). Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science. 330: 1381-5.                                                                                                                                                               
Dong, X., Akalin, A., Sharma, Y. & Lenhard, B. (2010). Translog, a web browser for studying the expression divergence of homologous genes. BMC bioinformatics 11 Suppl 1, S59.                                                                                                                                                              
Dong, X., Navratilova, P., Fredman, D., Drivenes, Ø., Becker, T. S. & Lenhard, B. (2010). Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic acids research 38, 1071-1085.                                                                               

Gould, C. M., Diella, F., Via, A. Puntervoll, P. & other authors (2010). ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic acids research 38, D167-180.                                                                                                                                                               
Hajjar, E., Broemstrup, T., Kantari, C., Witko-Sarsat, V. & Reuter, N. (2010). Structures of human proteinase 3 and neutrophil elastase--so similar yet so different. The FEBS journal 277, 2238-2254.                                                                                                                                                              
Helsens, K., Colaert, N., Barsnes, H. & other authors (2010). ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics 10, 1261-1264.                                                                                                                                                               
Jørgensen, K. M., Hjelle, S. M., Oye, O. K., Puntervoll, P., Reikvam, H., Skavland, J., Anderssen, E., Bruserud, O. & Gjertsen, B. T. (2010). Untangling the intracellular signalling network in cancer - a strategy for data integration in acute myeloid leukaemia. Journal of proteomics.                                                                                                                                                               
Kalas, M., Puntervoll, P., Joseph, A., …., Jonassen, I. (2010). BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics (Oxford, England) 26, i540-546.                                                                                                                                                               
Muth, T., Vaudel, M., Barsnes, H., Martens, L. & Sickmann, A. (2010). XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics 10, 1522-1524.                                                                                                                                                               
Navratilova, P., Fredman, D., Lenhard, B. & Becker, T. S. (2010). Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Molecular genetics and genomics : MGG 283, 171-184.                                                                                                                                                               
Pettifer, S., Ison, J., Kalas, M. …, Jonassen I, Liaquat A, …, Vriend G. (2010). The EMBRACE web service collection. Nucleic acids research 38 Suppl, W683-688.                                                             

Portales-Casamar, E., Thongjuea, S., Kwon, A. T., …, Lenhard B, Wasserman WW, Sandelin A. (2010). JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic acids research 38, D105-110.                                                                               

Ragvin, A., Moro, E., Fredman, D. …, Engström, P.G., …, Lenhard B, Becker TS. (2010). Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proceedings of the National Academy of Sciences of the United States of America 107, 775-780.                                                                                                                                                               
Ravasi, T., Suzuki, H., Cannistraci, C. V., … Akalin A, …, Lenhard B, …, Hayashizaki Y. (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140, 744-752.                                                                                                                                                               
Skjærven, L., Martinez, A. & Reuter, N. (2010). Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins: Structure, Function, and Bioinformatics, n/a-n/a.                                                                               

Soler, E., Andrieu-Soler, C., de Boer, E., Bryne J.C., Thongjuea S, …, Lenhard, B., Grosveld, F. (2010). The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes & development 24, 277-289.                                                                               
Subramanian, S., Puntervoll, P. & Sztromwasser, P. (2010). Optimizing the Data-Traffic of Centrally Coordinated Scientific Workflow Systems: IEEE.                                                                               

Taxt, A., Aasland, R., Sommerfelt, H., Nataro, J. & Puntervoll, P. (2010). Heat-stable enterotoxin of enterotoxigenic Escherichia coli as a vaccine target. Infection and immunity 78, 1824-1831.               

Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H. & Martens, L. (2010). The Proteomics Identifications database: 2010 update. Nucleic acids research 38, D736-742.                                                                              

Witko-Sarsat, V., Mocek, J., Bouayad, D.,…, Reuter, N.,… , Cassatella MA. (2010). Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival. The Journal of experimental medicine.                                                                               
Witko-Sarsat, V., Reuter, N. & Mouthon, L. (2010). Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener's granulomatosis. Current opinion in rheumatology 22, 1-7. 


OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results

Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L.

Proteomics. 2009 Jul;9(14):3772-4

Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods.

Leversen NA, de Souza GA, Målen H, Prasad S, Jonassen I, Wiker HG.

Microbiology. 2009 Jul;155(Pt 7):2375-83. Epub 2009 Apr 23.

Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia.

Øyan AM, Anensen N, Bø TH, Stordrange L, Jonassen I, Bruserud Ø, Kalland KH, Gjertsen BT.

BMC Cancer. 2009 Mar 5;9:77.


Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis.

Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen I, Petersen K, Goldfinger N, Rotter V, Akslen LA, Oyan AM, Kalland KH.

PLoS One. 2009;4(3):e4687. Epub 2009 Mar 5.

Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis.

Pendino F, Nguyen E, Jonassen I, Dysvik B, Azouz A, Lanotte M, Ségal-Bendirdjian E, Lillehaug JR.

Blood. 2009 Apr 2;113(14):3172-81. Epub 2009 Jan 30

PRIDE Converter: making proteomics data-sharing easy

Barsnes H, Vizcaíno JA, Eidhammer I, Martens L.

Nat Biotechnol. 2009 Jul;27(7):598-9.

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.

Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C.

Proteomics. 2009 Jul;9(14):3626-9.

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.

Proteomics. 2009 Aug;9(15):3928-33.

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.

Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C.

Proteomics. 2009 Jan;9(2):218-22.


Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases

Barsnes H, Mikalsen SO, Eidhammer I.

BMC Res Notes. 2008 Dec 19;1:130

Protease-dependent fractional mass and peptide properties

Barsnes H, Eidhammer I, Cruciani V, Mikalsen SO.

Eur J Mass Spectrom (Chichester, Eng). 2008;14(5):311-7

MassSorter: peptide mass fingerprinting data analysis

Eidhammer I, Barsnes H, Mikalsen SO.

Methods Mol Biol. 2008;484:345-59

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG.

BMC Genomics. 2008 Jul 2;9:316.

Analysis of gene-expression data using J-Express.

Stavrum AK, Petersen K, Jonassen I, Dysvik B.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 7:Unit 7.3.

Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar.

Stavrum R, Valvatne H, Bø TH, Jonassen I, Hinds J, Butcher PD, Grewal HM.

PLoS One. 2008 Apr 9;3(4):e1973.

Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis.

Eichner C, Frost P, Dysvik B, Jonassen I, Kristiansen B, Nilsen F.

BMC Genomics. 2008 Mar 10;9:126


Implementation and application of a versatile clustering tool for tandem mass spectrometry data

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L.

Proteomics. 2007 Sep;7(18):3245-58

Using hydropathy features for function prediction of membrane protein

Pánek J, Eidhammer I, Aasland R.

Mol Membr Biol. 2007 Jul-Aug;24(4):304-12

Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users.

Suhr ML, Dysvik B, Bruland O, Warnakulasuriya S, Amaratunga AN, Jonassen I, Vasstrand EN, Ibrahim SO.

Oncol Rep. 2007 Nov;18(5):1061-75.

Characterization of early stages of human B cell development by gene expression profiling.

Hystad ME, Myklebust JH, Bø TH, Sivertsen EA, Rian E, Forfang L, Munthe E, Rosenwald A, Chiorazzi M, Jonassen I, Staudt LM, Smeland EB.

J Immunol. 2007 Sep 15;179(6):3662-71. Erratum in: J Immunol. 2009 May1;182(9):5882.

TMM@: a web application for the analysis of transmembrane helix mobility.

Skjaerven L, Jonassen I, Reuter N.

BMC Bioinformatics. 2007 Jul 2;8:232.

Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization.

Petersen K, Oyan AM, Rostad K, Olsen S, Bø TH, Salvesen HB, Gjertsen BT, Bruserud O, Halvorsen OJ, Akslen LA, Steen VM, Jonassen I, Kalland KH.

Anal Biochem. 2007 Jul 1;366(1):46-58. Epub 2007 Mar 18.

Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins.

Saelensminde G, Halskau Ø Jr, Helland R, Willassen NP, Jonassen I.

Extremophiles. 2007 Jul;11(4):585-96. Epub 2007 Apr 12.

Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation.

Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jørgensen HA, Jonassen I, Steen VM.

BMC Genomics. 2007 Apr 4;8:94.

Increased expression of SIM2-s protein is a novel marker of aggressive prostate cancer.

Halvorsen OJ, Rostad K, Øyan AM, Puntervoll H, Bø TH, Stordrange L, Olsen S, Haukaas SA, Hood L, Jonassen I, Kalland KH, Akslen LA.

Clin Cancer Res. 2007 Feb 1;13(3):892-7.

ERG upregulation and related ETS transcription factors in prostate cancer.

Rostad K, Mannelqvist M, Halvorsen OJ, Oyan AM, Bø TH, Stordrange L, Olsen S, Haukaas SA, Lin B, Hood L, Jonassen I, Akslen LA, Kalland KH.

Int J Oncol. 2007 Jan;30(1):19-32.


Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering

Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I.

Proteomics. 2006 Apr;6(7):2086-94

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences

Barsnes H, Mikalsen SO, Eidhammer I.

BMC Bioinformatics. 2006 Jan 26;7:4

Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools

Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, Lillehaug JR, Eidhammer I, Jensen HB

Arch Microbiol. 2006 Feb;184(6):362-77. Epub 2005 Nov 26

Angiogenesis-independent tumor growth mediated by stem-like cancer cells.

Sakariassen PØ, Prestegarden L, Wang J, Skaftnesmo KO, Mahesparan R, Molthoff C, Sminia P, Sundlisaeter E, Misra A, Tysnes BB, Chekenya M, Peters H, Lende G, Kalland KH, Øyan AM, Petersen K, Jonassen I, van der Kogel A, Feuerstein BG, Terzis AJ, Bjerkvig R, Enger PØ.

Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16466-71. Epub 2006 Oct 20.

Protein model refinement using structural fragment tessellation.

Jonassen I, Klose D, Taylor WR.

Comput Biol Chem. 2006 Oct;30(5):360-6. Epub 2006 Sep 18.

RBR: library-less repeat detection for ESTs.

Malde K, Schneeberger K, Coward E, Jonassen I.

Bioinformatics. 2006 Sep 15;22(18):2232-6. Epub 2006 Jul 12.

Dynamic domain threading.

Taylor WR, Lin K, Klose D, Fraternali F, Jonassen I.

Proteins. 2006 Aug 15;64(3):601-14.

cDNA microarray analysis of non-selected cases of acute myeloid leukemia demonstrates distinct clustering independent of cytogenetic aberrations and consistent with morphological signs of differentiation.

Øyan AM, Bø TH, Jonassen I, Gjertsen BT, Bruserud Ø, Kalland KH.

Int J Oncol. 2006 May;28(5):1065-80.


Gene expression profiles of head and neck carcinomas from Sudanese and Norwegian patients reveal common biological pathways regardless of race and lifestyle.

Dysvik B, Vasstrand EN, Løvlie R, Elgindi OA, Kross KW, Aarstad HJ, Johannessen AC, Jonassen I, Ibrahim SO.

Clin Cancer Res. 2006 Feb 15;12(4):1109-20


Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data

Rossnes R, Eidhammer I, Liberles DA.

BMC Bioinformatics. 2005 May 27;6:127

A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Pánek J, Eidhammer I, Aasland R.

Proteins. 2005 Mar 1;58(4):923-34

Gene expression profiling of minor salivary glands clearly distinguishes primary Sjögren's syndrome patients from healthy control subjects.

Hjelmervik TO, Petersen K, Jonassen I, Jonsson R, Bolstad AI.

Arthritis Rheum. 2005 May;52(5):1534-44.

Masking repeats while clustering ESTs.

Schneeberger K, Malde K, Coward E, Jonassen I.

Nucleic Acids Res. 2005 Apr 14;33(7):2176-80. Print 2005.

CD34 expression in native human acute myelogenous leukemia blasts: differences in CD34 membrane molecule expression are associated with different gene expression profiles.

Oyan AM, Bø TH, Jonassen I, Ulvestad E, Gjertsen BT, Kalland KH, Bruserud O.

Cytometry B Clin Cytom. 2005 Mar;64(1):18-27.

Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation.

Halvorsen OJ, Oyan AM, Bø TH, Olsen S, Rostad K, Haukaas SA, Bakke AM, Marzolf B, Dimitrov K, Stordrange L, Lin B, Jonassen I, Hood L, Akslen LA, Kalland KH.

Int J Oncol. 2005 Feb;26(2):329-36.

A graph based algorithm for generating EST consensus sequences.

Malde K, Coward E, Jonassen I.

Bioinformatics. 2005 Apr 15;21(8):1371-5. Epub 2004 Nov 30. Erratum in: Bioinformatics. 2005 Jul 1;21(13):3062


Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Ward N, Larsen Ø, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methé B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA.

PLoS Biol. 2004 Oct;2(10):e303. Epub 2004 Sep 21

BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria

Berven FS, Flikka K, Jensen HB, Eidhammer I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9

Structure motif discovery and mining the PDB

Jonassen I, Eidhammer I, Conklin D, Taylor WR.

Bioinformatics. 2002 Feb;18(2):362-7

XHM: a system for detection of potential cross hybridizations in DNA microarrays.

Flikka K, Yadetie F, Laegreid A, Jonassen I.

BMC Bioinformatics. 2004 Aug 27;5:117.


A structural pattern-based method for protein fold recognition.

Taylor WR, Jonassen I.

Proteins. 2004 Aug 1;56(2):222-34.

LSimpute: accurate estimation of missing values in microarray data with least squares methods.

Bø TH, Dysvik B, Jonassen I.

Nucleic Acids Res. 2004 Feb 20;32(3):e34.


Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data.

Wang J, Bø TH, Jonassen I, Myklebost O, Hovig E.

BMC Bioinformatics. 2003 Dec 2;4:60.

Fast sequence clustering using a suffix array algorithm.

Malde K, Coward E, Jonassen I.

Bioinformatics. 2003 Jul 1;19(10):1221-6.


Structure motif discovery and mining the PDB

Jonassen I, Eidhammer I, Conklin D, Taylor WR.

Bioinformatics. 2002 Feb;18(2):362-7

A fast top-down method for constructing reliable radiation hybrid frameworks

Bø TH, Jonassen I, Eidhammer I, Helgesen C.

Bioinformatics. 2002 Jan;18(1):11-8.

New feature subset selection procedures for classification of expression profiles.

Bø T, Jonassen I.

Genome Biol. 2002;3(4):RESEARCH0017. Epub 2002 Mar 14.

Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences.

Conklin D, Jonassen I, Aasland R, Taylor WR.

Bioinformatics. 2002 Jan;18(1):182-9