Publications of the Comparative genomics group

2011 Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA.
FACIL: Fast and Accurate Genetic Code Inference and Logo.
Bioinformatics, Jul;27(14):1929-1933 Details

2011 Huigsloot M, Nijtmans LG, Szklarczyk R, Baars MJ, van den Brand MA, Hendriksfranssen MG, van den Heuvel LP, Smeitink JA, Huynen MA, Rodenburg RJ.
A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy.
Am J Hum Genet, Apr 8;88(4):488-493. Details

2011 van Dam TJ, Bos JL, Snel B.
Evolution of the Ras-like small GTPases and their regulators.
Small Gtpases, Jan;2(1):4-16. Details

2011 Jansen BJ, Sama IE, Eleveld-Trancikova D, van Hout-Kuijer MA, Jansen JH, Huynen MA, Adema GJ.
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters.
BMC Genomics, Jun 27;12(1):330. Details

2011 Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldon T.
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Brief Bioinform, Sep;12(5):442-448. Details

2011 de Graaf RM, Ricard G, van Alen TA, Duarte I, Dutilh BE, Burgtorf C, Kuiper JW, van der Staay GW, Tielens AG, Huynen MA, Hackstein JH.
The organellar genome and metabolic potential of the hydrogen- producing mitochondrion of Nyctotherus ovalis.
Mol Biol Evol, Aug;28(8):2379-2391. Details

2011 Minczuk M, He J, Duch AM, Ettema TJ, Chlebowski A, Dzionek K, Nijtmans LG, Huynen MA, Holt IJ.
TEFM (c17orf42) is necessary for transcription of human mtDNA.
Nucleic Acids Res, May 1;39(10):4284-4299. Details

2011 Kip N, Dutilh BE, Pan Y, Bodrossy L, Neveling K, Kwint MP, Jetten MSM and Op den Camp HJM.
Ultra-deep pyrosequencing of pmoA amplicons confirms prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog.
Environmental Microbiology Reports, Mar;3(6):667–673. Details

2011 Dutilh BE, Huynen MA, Gloerich J, Strous M.
Iterative read mapping and assembly allows the use of a more distant reference in metagenome assembly.
Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, Chapter 43:379-385. Details

2011 Emons J, Dutilh BE, Decker E, Pirzer H, Sticht C, Gretz N, Rappold G, Cameron ER, Neil JC, Stein GS, van Wijnen AJ, Wit JM, Post JN, Karperien M.
Genome wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation.
Journal of Endocrinology , May;209(2):245-254. Details

2011 Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H.
Towards the Human Colorectal Cancer Microbiome.
PLoS One, 6(5):e20447. Details

2011 de Bok FA, Janssen PW, Bayjanov JR, Sieuwerts S, Lommen A, van Hylckama Vlieg JE, Molenaar D.
Volatile compound fingerprinting of mixed-culture fermentations.
Appl Environ Microbiol, Sep;77(17):6233-6239. Details

2011 Jonckheere AI, Huigsloot M, Lammens M, Jansen J, van den Heuvel LP, Spiekerkoetter U, von Kleist-Retzow JC, Forkink M, Koopman WJ, Szklarczyk R, Huynen MA, Fransen JA, Smeitink JA, Rodenburg RJ.
Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology.
Mitochondrion, Nov;11(6):954-963. Details

2011 Thompson CC, Marin MA, Dias GM, Dutilh BE, Edwards RA, Iida T, Thompson FL, Vicente AC.
Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia.
J Bacteriol, 193(20):5877-5878. Details

2011 van Kessel MA, Dutilh BE, Neveling K, Kwint MP, Veltman JA, Flik G, Jetten MS, Klaren PH, Op den Camp HJ.
Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.).
AMB Express, Nov 18;1:41. Details

2011 van Dam TJ, Zwartkruis FJ, Bos JL, Snel B.
Evolution of the TOR Pathway.
J Mol Evol, Oct;73(3-4):209-220. Details

2011 Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG.
Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.
J Proteomics, Feb 16;75(5):1547-1562. Details

2011 Babu MM, van der Lee R, de Groot NS, Gsponer J.
Intrinsically disordered proteins: regulation and disease.
Curr Opin Struct Biol, Jun;21(3):432-440. Details

2011 Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA.
Analysis of genome-wide association study data using the protein knowledge base.
BMC Genet, Nov 13;12(1):98. Details

2011 Oti M, Ballouz S, Wouters MA.
Web tools for the prioritization of candidate disease genes.
Methods Mol Biol, 760:189-206. Details

2011 Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GSS, Venugopal A, Sekhar NR, Kelkar DS, Nemade HN, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A.
A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.
Proteomics, [Epub ahead of print]

2011 Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A.
Proteogenomic Analysis of Candida glabrata using High Resolution Mass Spectrometry.
J Proteome Res, Jan 1;11(1):247-260. Details

2011 Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Pandey A.
Comprehensive proteomic analysis of human bile.
Proteomics, Dec;11(23):4443-4453. Details

2011 Kumar GS, Venugopal AK, Selvan LD, Marimuthu A, Keerthikumar S, Pathare S, Dikshit JB, Tata P, Hariharan R, Prasad TS, Harsha HC, Ramachandra YL, Mahadevan A, Chaerkady R, Shankar SK, Pandey A.
Gene Expression Profiling of Tuberculous Meningitis.
Journal of Proteomics and Bioinformatics, 4:98-105. Details

2011 Marimuthu A, Jacob HK, Jakharia A, Subbannayya Y, Keerthikumar S, Kashyap MK, Goel R, Balakrishnan L, Dwivedi S, Pathare S, Dikshit JB, Maharudraiah J, Singh S, Kumar GS, Vijayakumar M, Veerendra Kumar KV, Premalatha CS, Tata P, Hariharan R, Roa JC, Prasad TS, Chaerkady R, Kumar RV, Pandey A.
Gene Expression Profiling of Gastric Cancer.
J Proteomics Bioinform, 4:074-082. Details

2011 De Franceschi L, Tomelleri C, Matte A, Brunati AM, Bovee-Geurts PH, Bertoldi M, Lasonder E, Tibaldi E, Danek A, Walker RH, Jung HH, Bader B, Siciliano A, Ferru E, Mohandas N, Bosman GJ.
Erythrocyte membrane changes of chorea-acanthocytosis are the result of altered Lyn kinase activity.
Blood, Nov 17;118(20):5652-5663. Details

2011 Kartal B, Maalcke WJ, de Almeida NM, Cirpus I, Gloerich J, Geerts W, Op den Camp HJ, Harhangi HR, Janssen-Megens EM, Francoijs KJ, Stunnenberg HG, Keltjens JT, Jetten MS, Strous M.
Molecular mechanism of anaerobic ammonium oxidation.
Nature, Oct 2;479(7371):127-130. Details

2011 Laurentino EC, Taylor S, Mair GR, Lasonder E, Bartfai R, Stunnenberg HG, Kroeze H, Ramesar J, Franke-Fayard B, Khan SM, Janse CJ, Waters AP.
Experimentally controlled downregulation of the histone chaperone FACT in Plasmodium berghei reveals that it is critical to male gamete fertility.
Cell Microbiol, Dec;13(12):1956-1974. Details

2011 Szklarczyk R, Wanschers BF, Nabuurs SB, Nouws J, Nijtmans LG, Huynen MA.
NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I.
FEBS Lett, Mar 9;585(5):737-743. Details

2010 Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM, Novotný VM.
Comparative proteomics of erythrocyte aging in vivo and in vitro.
J Proteomics, Jan;73(3):396-402. Details

2010 Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D.
Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level.
J Proteome Res, Apr 5;9(4):1727-1737. Details

2010 van Diepen A, Brand HK, Sama I, Lambooy LH, van den Heuvel LP, van der Well L, Huynen M, Osterhaus AD, Andeweg AC, Hermans PW.
Quantitative proteome profiling of respiratory virus-infected lung epithelial cells.
J Proteomics, Aug 5;73(9):1680-1693. Details

2010 Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M.
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.
Nature, Mar 25;464(7288):543-548. Details

2010 Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE, Alonso ME, de la Calle-Mustienes E, Smeenk L, Rinne T, Parsaulian L, Bolat E, Jurgelenaite R, Huynen MA, Hoischen A, Veltman JA, Brunner HG, Roscioli T, Oates E, Wilson M, Manzanares M, Gómez-Skarmeta JL, Stunnenberg HG, Lohrum M, van Bokhoven H, Zhou H.
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
PLoSGenetics, 6:e1001065 Details

2010 Sama IE, Huynen MA.
Measuring the physical cohesiveness of proteins using Physical Interaction Enrichment (PIE).
Bioinformatics, Nov 1;26(21):2737-2743. Details

2010 Szklarczyk R, Huynen MA.
Mosaic origin of the mitochondrial proteome.
Proteomics, Nov;10(22):4012-4024. Details

2010 Nouws J, Nijtmans L, Houten SM, van den Brand M, Huynen M, Venselaar H, Hoefs S, Gloerich J, Kronick J, Hutchin T, Willems P, Rodenburg R, Wanders R, van den Heuvel L, Smeitink J, Vogel RO.
Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I.
Cell Metab, Sep 8;12(3):283-294. Details

2010 Richter R, Rorbach J, Pajak A, Smith PM, Wessels HJ, Huynen MA, Smeitink JA, Lightowlers RN, Chrzanowska-Lightowlers ZM.
A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome.
EMBO J, Mar 17;29(6):1116-1125. Details

2010 Silvestrini F, Lasonder E, Olivieri A, Camarda G, van Schaijk B, Sanchez M, Younis Younis S, Sauerwein R, Alano P.
Protein export marks the early phase of gametocytogenesis of the human malaria parasite Plasmodium falciparum.
Mol Cell Proteomics, Jul;9(7):1437-1448. Details

2010 Mair GR, Lasonder E, Garver LS, Franke-Fayard BM, Carret CK, Wiegant JC, Dirks RW, Dimopoulos G, Janse CJ, Waters AP.
Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development.
PLoS Pathog, Feb 12;6(2):e1000767. Details

2010 van der Voort R, Verweij V, de Witte TM, Lasonder E, Adema GJ, Dolstra H.
An alternatively spliced CXCL16 isoform expressed by dendritic cells is a secreted chemoattractant for CXCR6+ cells.
J Leukoc Biol, Jun;87(6):1029-1039. Details

2010 Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O.
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
DNA Res, Jun;17(3):197-208. Details

2010 Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A.
NetPath: a public resource of curated signal transduction pathways.
Genome Biol, Jan 12;11(1):R3 Details

2010 Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A.
SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.
Cancer Biol Ther, Oct 15;10(8):796-810. Details

2010 Prasad TSK, Keerthikumar S, Chaerkady R, Kandasamy K, Renuse S, Marimuthu A, Venugopal AK, Thomas JK, Jacob HKC, et al.
Comparative Proteomic Analysis of Candida albicans and Candida glabrata.
Clinical Proteomics, 6(4):163-173. Details

2009 Dutilh BE, Huynen MA, Strous M.
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
Bioinformatics, Nov 1;25(21):2878-2881. Details

2009 Saada A, Vogel RO, Hoefs SJ, van den Brand MA, Wessels HJ, Willems PH, Venselaar H, Shaag A, Barghuti F, Reish O, Shohat M, Huynen MA, Smeitink JA, van den Heuvel LP, Nijtmans LG.
Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease.
Am J Hum Genet, Jun;84(6):718-727. Details

2009 Szklarczyk R, Huynen MA.
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.
Genome Biol, Nov 24;10(11):R135. Details

2009 Parmley JL, Huynen MA.
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation.
PLoS Genet, Jul;5(7):e1000548. Details

2009 de Graaf RM, van Alen TA, Dutilh BE, Kuiper JW, van Zoggel HJ, Huynh MB, Görtz HD, Huynen MA, Hackstein JH.
The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.
BMC Genomics, Nov 6;10:514. Details

2009 Huynen MA, de Hollander M, Szklarczyk R.
Mitochondrial proteome evolution and genetic disease.
Biochim Biophys Acta, Dec;1792(12):1122-1129. Details

2009 Jurgelenaite R, Dijkstra TMH, Kocken CHM, Heskes T.
Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum.
Bioinformatics, 25(12):1484-1491. Details

2009 Doerig C, Baker D, Billker O, Blackman MJ, Chitnis C, Dhar Kumar S, Heussler V, Holder AA, Kocken C, Krishna S, Langsley G, Lasonder E, Menard R, Meissner M, Pradel G, Ranford-Cartwright L, Sharma A, Sharma P, Tardieux T, Tatu U, Alano P.
Signalling in malaria parasites. The MALSIG consortium.
Parasite, Sep;16(3):169-182. Details

2009 Middelbeek J, Clark K, Venselaar H, Huynen MA, Van Leeuwen FN.
The alpha-kinase family: an exceptional branch on the protein kinase tree.
Cellular and Molecular Life Sciences, Mar;67(6):875-890. Details

2009 Oti M, Huynen MA, Brunner HG.
The biological coherence of human phenome databases.
Am J Hum Genet, Dec;85(6):801-808. Details

2009 de Graaf RM, Duarte I, van Alen TA, Kuiper JW, Schotanus K, Rosenberg J, Huynen MA, Hackstein JH.
The hydrogenosomes of Psalteriomonas lanterna.
BMC Evol Biol, Dec 9;9:287. Details

2008 Kensche PR, van Noort V, Dutilh BE, Huynen MA.
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
J R Soc Interface, 5(19):151-170. Details

2008 Dutilh BE, Snel B, Ettema TJG, Huynen MA.
Signature genes as a phylogenomic tool.
Molecular Biology and Evolution, Aug;25(8):1659-1667. Details

2008 Dutilh BE, He Y, Hekkelman ML, Huynen MA.
Signature, a web server for taxonomic characterization of sequence samples using signature genes.
Nucleic Acids Research, Jul 1;36(Web Server issue):W470-474. Details

2008 Kensche PR, Oti M, Dutilh BE, Huynen MA.
Conservation of divergent transcription in fungi.
Trends in Genetics, May;24(5):207-211. Details

2008 Franck E, Hulsen T, Huynen MA, de Jong WW, Lubsen NH, Madsen O.
Evolution of closely linked gene pairs in vertebrate genomes.
Mol Biol Evol, Sep;25(9):1909-1921. Details

2008 Oti M, van Reeuwijk J, Huynen MA, Brunner HG.
Co-expression for candidate disease gene prioritization.
BMC Bioinformatics, Apr 23;9:208. Details

2008 Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Di Cunto F.
Prediction of human disease genes by human-mouse conserved coexpression analysis.
PLoS Comput Biol, Mar 28;4(3):e1000043. Details

2008 Oti M, Huynen MA, Brunner HG.
Phenome connections.
Trends Genet, Mar;24(3):103-106. Details

2008 Kensche, PR, van Noort V, Dutilh BE, Huynen MA.
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
J R Soc Interface, Feb 6;5(19):151-170. Details

2008 Bych K, Kerscher S, Netz DJ, Pierik AJ, Zwicker K, Huynen MA, Lill R, Brandt U, Balk J.
The iron-sulphur protein Ind1 is required for effective complex I assembly.
EMBO J, 27(12):1736-1746. Details

2008 Schoeber JP, Topala CN, Lee KP, Lambers TT, Ricard G, van der Kemp AW, Huynen MA, Hoenderop JG, Bindels RJ.
Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity.
Pflugers Arch, 457(1):91-101. Details

2008 Lasonder E, Janse CJ, van Gemert GJ, Mair GR, Vermunt AM, Douradinha BG, van Noort V, Huynen MA, Luty AJ, Kroeze H, Khan SM, Sauerwein RW, Waters AP, Mann M, Stunnenberg HG.
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.
PLoS Pathog, 4(10):e1000195. Details

2008 Warnecke T, JL Parmley, Hurst LD.
Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes.
Genome Biol, 9(2):R29. Details

2008 Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA.
Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns.
BMC Genomics, Dec 5;9:587. Details

2008 Szklarczyk R, Huynen MA, Snel B.
Complex fate of paralogs.
BMC Evol Biol, Dec 18;8:337. Details

2008 Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG.
Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells.
Mol Cell Biol, Apr;28(8):2732-2744. Details

2008 Clark K, Middelbeek J, Dorovkov MV, Figdor CG, Ryazanov AG, Lasonder E, van Leeuwen FN.
The alpha-kinases TRPM6 and TRPM7, but not eEF-2 kinase, phosphorylate the assembly domain of myosin IIA, IIB and IIC.
FEBS , Lett. 582:2993-29977. Details

2008 Clark K, Middelbeek J, Lasonder E, Dulyaninova N, Morrice NA, Ryazanov AG, Bresnick AR, Figdor CG, van Leeuwen FN.
Trpm7 regulates myosin IIA filament stability and protein localization by heavy chain phosphorylation.
J Mol Biol , May 9;378(4):790-803. Details

2008 Clark K, Middelbeek J, Morrice N. Figdor CG, Lasonder E, van Leeuwen FN.
Massive Autophosphorylation of the Ser/Thr-Rich Domain Controls Protein Kinase Activity of TRPM6 and TRPM7.
PLoS ONE 3 , Mar 26;3(3):e1876. Details

2008 Bosman GJCGM, Lasonder E, Luten M, Roerdinkholder-Stoelwinder B, Novotny VMJ, Bos H, De Grip WJ.
The proteome of erythrocyte membranes and vesicles during storage in blood bank conditions.
Transfusion, May;48(5):827-835. Details

2008 Pandithage R, Lilischkis R, Harting K, Wolf A, Jedamzik B, Lüscher_Firzlaff J, Vervoorts J, Lasonder E, Kremmer E, Knöll B, Lüscher B.
The regulation of SIRT2 function by cyclin-dependent kinases affects cell motility.
J Cell Biol, Mar 10;180(5):915-929. Details

2008 Cao G, Thébault S, van der Wijst J, van der Kemp A, Lasonder E, Bindels RJ, Hoenderop JG.
RACK1 inhibits TRPM6 Activity via Phosphorylation of the Fused alpha-Kinase Domain.
Curr Biol, Feb 12;18(3):168-176. Details

2007 van der Heijden RT, Snel B, van Noort V, Huynen MA.
Orthology prediction at Scalable Resolution by phylogenetic Tree analysis.
BMC Bioinformatics, 8(1):83. Details

2007 Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA.
Assessment of phylogenomic and orthology approaches for phylogenetic inference.
Bioinformatics, Apr 1;23(7):815-824. Details

2007 van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools, HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg, R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H.Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP.
Genome sequencing and analysis of the versatile cell actory Aspergillus niger CBS 513.88.
Nat Biotechnol, 25(2):221-231. Details

2007 Boxma B, Ricard G, van Hoek AH, Severing E, Moon-van der Staay SY, van der Staay GW, van Alen TA, de Graaf RM, Cremers G, Kwantes M, McEwan NR, Newbold CJ, Jouany JP, Michalowski T, Pristas P, Huynen MA, Hackstein JH.
The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.
BMC Evol Biol , Nov 16;7:230. Details

2007 Datson NA, Morsink MC, Atanasova S, Armstrong VW, Zischler H, Schlumbohm C, Dutilh BE, Huynen MA, Waegele B, Ruepp A, de Kloet ER, Fuchs E.
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate.
BMC Genomics, Jun 25;8:190. Details

2007 Gabaldón T, Huynen MA.
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism.
PLoS Comput Biol, Nov;3(11):e219. Details

2007 Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P.
Optimized design and assessment of whole genome tiling arrays.
Bioinformatics, Jul 1;23(13):i195-204. Details

2007 Kirchberger S, Leroch M, Huynen MA, Wahl M, Neuhaus HE, Tjaden J.
Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays.
J Biol Chem , Aug 3;282(31):22481-22491. Details

2007 Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ.
Reconstructing the evolution of the mitochondrial ribosomal proteome.
Nucleic Acids Res, 35(14):4686-4703. Details

2007 van Noort V, Snel B, Huynen MA.
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.
Genome Biol, 8(9):R197. Details

2007 Datson NA, Morsink MC, Atanasova S, Armstrong VW, Zischler H, Schlumbohm C, Dutilh BE, Huynen MA, Waegele B, Ruepp A, de Kloet ER, Fuchs E.
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate.
BMC Genomics, Jun 25;8:190. Details

2006 Dutilh BE, Huynen MA, Snel B.
A global definition of expression context is conserved between orthologs but does not correlate with sequence conservation.
BMC Genomics, Jan 19;7:10. Details

2006 Ettema TJ, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, van der Oost J.
Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2.
Microbiology , Jul;152(Pt 7):1969-1979. Details

2006 Oti M, Snel B, Huynen MA, Brunner HG.
Predicting disease genes using protein-protein interactions.
J Med Genet, Aug;43(8):691-698. Details

2006 Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W.
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.
Nucleic Acids Res, Jun 6;34(10):3067-3081. Details

2006 Ricard G, McEwan NR, Dutilh BE, Jouany J-P, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T., Nagamine T, Nelson N, Newbold ChJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA.
Horizontal Gene Transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic carbohydrates, rich-environment.
BMC Genomics , Feb 10;7:22. Details

2006 Strous M, Pelletier E, Mangenot S, Rattei Th, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift Ch, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes H-W, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D.
Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
Nature, Apr 6;440(7085):790-794. Details

2006 von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B.
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Res, Jan 1;31(1):258-261. Details

2006 Hackstein JH, Tjaden J, Huynen M.
Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering!
Curr Genet., Oct;50(4):225-245. Details

2006 Pastore C, Adinolfi S, Huynen MA, Rybin V, Martin S, Mayer M, Bukau B, Pastore A.
YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein?
Structure, May;14(5):857-867. Details

2006 Oti M, Snel B, Huynen MA, Brunner HG.
Predicting disease genes using protein-protein interactions.
J Med Genet., Aug;43(8):691-698. Details

2006 Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA.
Origin and evolution of the peroxisomal proteome.
Biol Direct, Mar 23;1:8. Details

2006 van Noort V, Huynen MA.
Combinatorial gene regulation in Plasmodium falciparum.
Trends Genet, Feb;22(2):73-78. Details

2006 Kuramae EE, Robert V, Snel B, Boekhout T.
Conflicting phylogenetic position of Schizosaccharomyces pombe.
Genomics, Oct;88(4):387-393. Details

2006 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P.
Toward automatic reconstruction of a highly resolved tree of life.
Science, Mar 3;311(5765):1283-1287. Details

2006 Tabak HF, Hoepfner D, Zand AV, Geuze HJ, Braakman I, Huynen MA.
Formation of peroxisomes: Present and past.
Biochim Biophys Acta, Dec;1763(12):1647-1654. Details

2006 Tjalsma H, Scholler-Guinard M, Lasonder E, Ruers TJ, Willems HL, Swinkels DW.
Profiling the humoral immune response in colon cancer patients: diagnostic antigens from Streptococcus bovis.
Int J Cancer, Nov 1;119(9):2127-2135. Details

2006 Vermeulen M, Walter W, Le Guezennec X, Kim J, Edayathumangalam RS, Lasonder E, Luger K, Roeder RG, Logie C, Berger SL, Stunnenberg HG.
A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin.
Mol Cell Biol, Jul;26(14):5226-5236. Details

2006 Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, Lasonder E, Stunnenberg HG.
MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties.
Mol Cell Biol, Feb;26(3):843-851. Details

2005 Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B.
The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation.
Biochem J, Sep 1;390(Pt 2):529-540. Details

2005 Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, Gabaldón T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, Tielens AG, Friedrich T, Veenhuis M, Huynen MA, Hackstein JH.
An anaerobic mitochondrion that produces hydrogen.
Nature, Mar 3;434(7029):74-79. Details

2005 Ettema TJ, de Vos WM, van der Oost J.
Discovering novel biology by in silico archaeology.
Nat Rev Microbiol, Nov;3(11):859-869. Details

2005 Gabaldón T, Huynen MA.
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
Bioinformatics, Sep 1;21 Suppl 2:ii144-150. Details

2005 Gabaldón T, Rainey D, Huynen MA.
Tracing the evolution of a large protein complex in the eukaryotes, NADH: ubiquinone oxidoreductase (Complex I).
J Mol Biol, May 13;348(4):857-870. Details

2005 Huynen MA, Gabaldón T, Snel B.
Variation and evolution of biomolecular systems: searching for functional relevance.
FEBS Lett, Mar 21;579(8):1839-1845. Details

2005 Huynen MA, Spronk CA, Gabaldon T, Snel B.
Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin.
FEBS Lett, Jan 31;579(3):591-596. Details

2005 Kaper T, Talik B, Ettema TJ, Bos H, van der Maarel MJ, Dijkhuizen L.
Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels.
Appl Environ Microbiol, Sep;71(9):5098-5106. Details

2005 Kunin V, Teichmann SA, Huynen MA, Ouzounis CA.
The properties of protein family space depend on experimental design.
Bioinformatics, Jun 1;21(11):2618-2622. Details

2005 von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res, Jan 1;33(Database issue):D433-437. Details

2005 Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.
Correlation between sequence conservation and the genomic context after gene duplication .
Nucleic Acids Res, Oct 27;33(19):6164-6171. Details

2005 van Reeuwijk J, Janssen M, van den Elzen C, Beltran-Valero de Bernabé D, Sabatelli P, Merlini L, Boon M, Scheffer H, Brockington M, Muntoni F, Huynen MA, Verrips A, Walsh CA, Barth PG, Brunner HG, van Bokhoven H.
POMT2 mutations cause {alpha}-dystroglycan hypoglycosylation and Walker-Warburg syndrome.
J Med Genet, Dec;42(12):907-912. Details

2005 Snel B, Huynen MA, Dutilh BE.
Genome trees and the nature of genome evolution.
Annu Rev Microbiol, 59:191-209. Details

2004 van Bakel H, Huynen M, Wijmenga C.
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
Bioinformatics, Nov 1;20(16):2644-2655. Details

2004 Boxma B, Voncken F, Jannink S, van Alen T, Akhmanova A, van Weelden SW, van Hellemond JJ, Ricard G, Huynen M, Tielens AG, Hackstein JH.
The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E.
Mol Microbiol, Mar;51(5):1389-1399. Details

2004 Dutilh BE, Huynen MA, Bruno WJ, Snel B.
The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise.
J Mol Evol, May;58(5):527-539. Details

2004 Ettema TJ, Makarova KS, Jellema GL, Gierman HJ, Koonin EV, Huynen MA, de Vos WM, van der Oost J.
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.
J Bacteriol, Nov;186(22):7754-7762. Details

2004 Franck E, Madsen O, van Rheede T, Ricard G, Huynen MA, de Jong WW.
Evolutionary diversity of vertebrate small heat shock proteins.
J Mol Evol, Dec;59(6):792-805. Details

2004 Gabaldón T, Huynen MA.
Prediction of protein function and pathways in the genome era.
Cell Mol Life Sci, Apr;61(7-8):930-944. Details

2004 Gabaldón T, Huynen MA.
Shaping the mitochondrial proteome.
Biochim Biophys Acta, Dec 6;1659(2-3):212-220. Details

2004 Huynen MA, Snel B, van Noort V.
Comparative Genomics for reliable protein-function prediction from genomic data.
Trends Genet , Aug;20(8):340-344. Details

2004 Van Noort V, Snel B, Huynen MA.
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.
EMBO Rep, Mar;5(3):280-284. Details

2004 Snel B, Huynen MA.
Quantifying modularity in the evolution of biomolecular systems.
Genome Res , Mar;14(3):391-397. Details

2004 Snel B, van Noort V, Huynen MA.
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.
Nucleic Acids Res, Sep 7;32(16):4725-4731. Details

2004 Tjaden J, Haferkamp I, Boxma B, Tielens AG, Huynen M, Hackstein JH.
A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles.
Mol Microbiol , Mar;51(5):1439-1446. Details

2003 Dutilh BE, de Boer RJ.
Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells.
J Theor Biol , Oct 7;224(3):351-358. Details

2003 Gabaldon T, Huynen MA.
Reconstruction of the proto-mitochondrial metabolism.
Science, Aug 1;301(5633):609. Details

2003 Ettema TJ, Huynen MA, de Vos WM, van der Oost J.
TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance.
Trends Biochem Sci, Apr;28(4):170-173. Details

2003 Huynen MA, Snel B.
Exploiting the variations in the genomic associations of genes to predict pathways and reconstruct their evolution.
Frontiers in Computational Genomics, Caister Academic Press:145-166.

2003 Huynen MA, Snel B, von Mering C, Bork P.
Function prediction and protein networks.
Curr Opin Cell Biol, Apr;15(2):191-198. Details

2003 Kesmir C, Van Noort V, De Boer RJ, Hogeweg P.
Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome.
Immunogenetics, Oct;55(7):437-449. Details

2003 van Noort V, Snel B, Huynen MA.
Predicting gene function by conserved co-expression.
Trends in Genetic , May;19(5):238-242. Details

2003 van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR.
Strand misalingments lead to quasipalindrome correction.
Trends in Genetics , Jul;19(7):365-369. Details

2003 Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P.
Systematic discovery of analogous enzymes in thiamin biosynthesis.
Nat. Biotechnol, Jul;21(7):790-795. Details

2002 Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P.
Comparative Genome Analysis of the Mollicutes.
Molecular Biology and Pathogenity of Mycoplasmas , Edited by Razin and Herrmann, Kluwer Academic/Plenum Publishers, New York, 255-278. Details

2002 Hackstein JH, van Hoek AH, Leunissen JA, Huynen M.
Anaerobic ciliates and their methanogenic endosymbionts.
Symbiosis: Mechanisms and Model Systems, Edited by J. Seckbach, Kluwer, Dordrecht, The Netherlands, 451-464. Details

2002 Kappé G, Leunissen JA, de Jong WW.
Evolution and diversity of prokaryotic small heat shock proteins.
Prog Mol Subcell Biol, 28:1-17. Details

2002 Korbel J, Snel B, Huynen MA, Bork P.
SHOT: a web server for the construction of genome phylogenies.
Trends in Genetics, Mar;18(3):158-162. Details

2002 von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.
Comparative assessment of large-scale data sets of protein-protein interactions.
Nature, May 23;417(6887):399-403. Details

2002 van der Oost J, Huynen MA, Verhees CH.
Molecular characterization of phosphoglycerate mutase in archaea.
FEMS Microbiol Lett , Jun 18;212(1):111-120. Details

2002 Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F.
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Proc Natl Acad Sci U S A, Oct 29;99(22):14422-14427. Details

2002 Snel B, Bork P, Huynen MA.
Conservation of gene co-regulation in prokaryotes and eukaryotes.
Trends Biotechnol, Oct 1;20(10):410. Details

2002 Snel B, Bork P, Huynen MA.
The identification of functional modules from the genomic association of genes.
Proc Natl Acad Sci U S A, Apr 30;99(9):5890-5895. Details

2002 Snel B, Bork P, Huynen MA.
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
Genome Research , Jan;12(1):17-25. Details

2002 Voncken FG, Boxma B, van Hoek AH, Akhmanova AS, Vogels GD, Huynen M, Veenhuis M, Hackstein JH.
A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2.
Gene, Feb 6;284(1-2):103-112. Details

2002 Voncken F, Boxma B, Tjaden J, Akhmanova A, Huynen M, Verbeek F, Tielens AG, Haferkamp I, Neuhaus HE, Vogels G, Veenhuis M, Hackstein JH.
Multiple origins of hydrogenosomes: A mitochondrial-type ADP/ATP carrier from the hydrogenosomes of the anaerobic chytrid Neocallimastix sp. L2.
Molecular Microbiology, Jun;44(6):1441-1454. Details

2001 Ettema T, van der Oost J, Huynen M.
Modularity in the gain and loss of genes: applications for function prediction.
Trends in Genetics , Sep;17(9):485-487. Details

2001 Hackstein JH, Akhmanova A, Voncken F, van Hoek A, van Alen T, Boxma B, Moon-van der Staay SY, van der Staay G, Leunissen J, Huynen M, Rosenberg J, Veenhuis M.
Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments.
Zoology , 104(3-4):290-302. Details

2001 Huynen MA.
Using comparative genome analysis to find interaction partners for frataxin.
Proceedings of ESF Cardiovascular Genomics: New Pathophysiological Concepts, Edited by Doevendans PA, Kääb S. Issue 4.

2001 Huynen MA, Snel B, Bork P.
Inversions and the dynamics of eukaryotic gene order.
Trends in Genetics , Jun;17(6):304-306. Details

2001 Huynen MA, Snel B, Bork P, Gibson TJ.
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Human Molecular Genetics, Oct 1;10(21):2463-2468. Details

2001 Verhees CH, Huynen MA, Ward DE, Schiltz E, de Vos WM, van der Oost J.
The Phosphoglucose Isomerase from the Hyperthermophilic Archaeon Pyrococcus furiosus Is a Unique Glycolytic Enzyme That Belongs to the Cupin Superfamily.
Journal of Biological Chemistry , Nov 2;276(44):40926-40932. Details

2000 van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, Hackstein JH.
Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates.
Mol Biol Evol, Feb;17(2):251-258. Details

2000 van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M.
AGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.
Bioinformatics, Oct;16(10):899-905. Details

2000 Kersten MASH, van der Drift C, Op den Camp HJM, Baars JJP, van Griensven LJLD, Schaap PJ, Müller Y, Visser J, Leunissen JAM
The glutamine synthetase from the edible mushroom Agaricus bisporus.
Science and clutivation of edible fungi - Proceedings of the 15th international congress, Edited by van Griensven LJLD. Balkema Publishers, Rotterdam/Brookfield, pp 71-78.

2000 Leunissen JAM.
De Gene Machine vindt al uw genen.
BioNieuws, Interview by Rinze Benedictus, July.

1999 Wang J, Bakkers JM, Galama JM, Bruins Slot HJ, Pilipenko EV, Agol VI, Melchers WJ.
Structural requirements of the higher order RNA kissing element in the enteroviral 3'UTR.
Nucleic Acids Res, Jan 15;27(2):485-490. Details