SBC Publications


2012



1	Moruz, L., Staes, A., Foster, J.M., Hatzou, M., Timmerman, E., Martens, L. and Kall, L. (2012) Chromatographic retention time prediction for posttranslationally modified peptides. Proteomics 12 (8) : 1151-1159.	Link to article	PubMed

2	Henrion, U., Renhorn, J., Borjesson, S.I., Nelson, E.M., Schwaiger, C.S., Bjelkmar, P., Wallner, B., Lindahl, E. and Elinder, F. (Epub 2012) Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci U S A (Epub ahead of print)	Link to article	PubMed

3	Liberles, D.A., Teichmann, S.A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L.J., de Koning, A.P., Dokholyan, N.V., Echave, J., Elofsson, A., Gerloff, D.L., Goldstein, R.A., Grahnen, J.A., Holder, M.T., Lakner, C., Lartillot, N., Lovell, S.C., Naylor, G., Perica, T., Pollock, D.D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjolander, K., Sunyaev, S., Teufel, A.I., Thorne, J.L., Thornton, J.W., Weinreich, D.M. and Whelan, S. (Epub 2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (Epub ahead of print)	Link to article	PubMed

4	Wacker, S.J., Jurkowski, W., Simmons, K.J., Fishwick, C.W., Johnson, A.P., Madge, D., Lindahl, E., Rolland, J.F. and de Groot, B.L. (Epub 2012) Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2((3)) by High-Throughput Virtual Screening and Automated Patch Clamp. ChemMedChem (Epub ahead of print)	Link to article	PubMed

5	Linden, M., Sens, P. and Phillips, R. (2012) Entropic tension in crowded membranes. PLoS Comput Biol 8 (3) : e1002431.	Link to article	PubMed

6	Galian, C., Bjorkholm, P., Bulleid, N. and von Heijne, G. (Epub 2012) Efficient glycosylphosphatidylinositol (GPI) modification of membrane proteins requires a C-terminal anchoring signal of marginal hydrophobicity. J Biol Chem (Epub ahead of print)	Link to article	PubMed

7	Light, S., Sagit, R., Ithychanda, S.S., Qin, J. and Elofsson, A. (Epub 2012) The evolution of filamin - A protein domain repeat perspective. J Struct Biol (Epub ahead of print)	Link to article	PubMed

8	Forslund, K. and Sonnhammer, E.L. (2012) Evolution of protein domain architectures. Methods Mol Biol 856: 187-216.	Link to article	PubMed

9	Dessimoz, C., Gabaldon, T., Roos, D.S., Sonnhammer, E.L., Herrero, J. and {the Quest for Orthologs Consortium (2012) Toward community standards in the quest for orthologs. Bioinformatics 28 (6) : 900-904.	Link to article	PubMed

10	Ostlund, G. and Sonnhammer, E.L. (2012) Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation. Gene 497 (2) : 228-236.	Link to article	PubMed

11	Ojemalm, K., Halling, K.K., Nilsson, I. and von Heijne, G. (2012) Orientational Preferences of Neighboring Helices Can Drive ER Insertion of a Marginally Hydrophobic Transmembrane Helix. Mol Cell 45 (4) : 529-540.	Link to article	PubMed

12	Hayat, S. and Elofsson, A. (2012) BOCTOPUS: improved topology prediction of transmembrane beta barrel proteins. Bioinformatics 28 (4) : 516-522.	Link to article	PubMed

13	Contreras, F.X., Ernst, A.M., Haberkant, P., Bjorkholm, P., Lindahl, E., Gonen, B., Tischer, C., Elofsson, A., von Heijne, G., Thiele, C., Pepperkok, R., Wieland, F. and Brugger, B. (2012) Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature 481 (7382) : 525-529.	Link to article	PubMed

14	Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E.L., Eddy, S.R., Bateman, A. and Finn, R.D. (2012) The Pfam protein families database. Nucleic Acids Res 40 (D1) : D290-D301.	Link to article	PubMed

15	Alexeyenko, A., Schmitt, T., Tjarnberg, A., Guala, D., Frings, O. and Sonnhammer, E.L. (2012) Comparative interactomics with Funcoup 2.0. Nucleic Acids Res 40 (1) : D821-8.	Link to article	PubMed

16	Skoog, K., Soderstrom, B., Widengren, J., von Heijne, G. and Daley, D.O. (2012) Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli. J Bacteriol 194 (3) : 584-586.	Link to article	PubMed

17	Norholm, M.H., Light, S., Virkki, M.T., Elofsson, A., von Heijne, G. and Daley, D.O. (Epub 2012) Manipulating the genetic code for membrane protein production: What have we learnt so far? Biochim Biophys Acta (Epub ahead of print) 1818 (4) : 1091-1096.	Link to article	PubMed


2011



18	Petersen, T.N., Brunak, S., von Heijne, G. and Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8 (10) : 785-786.	Link to article	PubMed

19	Forslund, K., Pekkari, I. and Sonnhammer, E.L. (2011) Domain architecture conservation in orthologs. BMC Bioinformatics 12 (1) : 326.	Link to article	PubMed

20	Hedin, L.E., Illergard, K. and Elofsson, A. (2011) An Introduction to Membrane Proteins (dagger). J Proteome Res 10 (8) : 3324-3331.	Link to article	PubMed

21	Basmarke-Wehelie, R., Sjolinder, H., Jurkowski, W., Elofsson, A., Arnqvist, A., Engstrand, L., Hagner, M., Wallin, E., Guan, N., Kuranasekera, H., Aro, H. and Jonsson, A.B. (2011) The Complement Regulator CD46 Is Bactericidal to Helicobacter pylori and Blocks Urease Activity. Gastroenterology 141 (3) : 918-928.	Link to article	PubMed

22	von Heijne, G. (2011) Introduction to theme "membrane protein folding and insertion". Annu Rev Biochem 80: 157-160.	Link to article	PubMed

23	Schmitt, T., Messina, D.N., Schreiber, F. and Sonnhammer, E.L. (2011) Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform 12 (5) : 485-488.	Link to article	PubMed

24	Norholm, M.H., Shulga, Y.V., Aoki, S., Epand, R.M. and von Heijne, G. (2011) Flanking residues help determine whether a hydrophobic segment adopts a monotopic or bitopic topology in the endoplasmic reticulum membrane. J Biol Chem 286 (28) : 25284-25290.	Link to article	PubMed

25	Ojemalm, K., Higuchi, T., Jiang, Y., Langel, U., Nilsson, I., White, S.H., Suga, H. and von Heijne, G. (2011) Apolar surface area determines the efficiency of translocon-mediated membrane-protein integration into the endoplasmic reticulum. Proc Natl Acad Sci U S A 108 (31) : E359-64.	Link to article	PubMed

26	von Heijne, G. (2011) Membrane proteins: from bench to bits. Biochem Soc Trans 39 (3) : 747-750.	Link to article	PubMed

27	Forslund, K., Schreiber, F., Thanintorn, N. and Sonnhammer, E.L. (2011) OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform 12 (5) : 463-473.	Link to article	PubMed

28	Shu, N. and Elofsson, A. (2011) KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics 27 (12) : 1702-1703.	Link to article	PubMed

29	Hennerdal, A. and Elofsson, A. (2011) Rapid membrane protein topology prediction. Bioinformatics 27 (9) : 1322-1323.	Link to article	PubMed

30	Osterberg, M., Calado Botelho, S., von Heijne, G. and Kim, H. (2011) Charged flanking residues control the efficiency of membrane insertion of the first transmembrane segment in yeast mitochondrial Mgm1p. FEBS Lett 585 (8) : 1238-1242.	Link to article	PubMed

31	Granholm, V., Noble, W.S. and Kall, L. (2011) On Using Samples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics. J Proteome Res 10 (5) : 2671-2678.	Link to article	PubMed

32	Linder, M., Britton, T. and Sennblad, B. (2011) Evaluation of Bayesian models of substitution rate evolution--parental guidance versus mutual independence. Syst Biol 60 (3) : 329-342.	Link to article	PubMed

33	Granholm, V. and Kall, L. (2011) Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 11 (6) : 1086-1093.	Link to article	PubMed

34	Kasson, P.M., Lindahl, E. and Pande, V.S. (2011) Water ordering at membrane interfaces controls fusion dynamics. J Am Chem Soc 133 (11) : 3812-3815.	Link to article	PubMed

35	Botelho, S.C., Osterberg, M., Reichert, A.S., Yamano, K., Bjorkholm, P., Endo, T., von Heijne, G. and Kim, H. (2011) TIM23-mediated insertion of transmembrane alpha-helices into the mitochondrial inner membrane. EMBO J 30 (6) : 1003-1011.	Link to article	PubMed

36	Norholm, M.H., Cunningham, F., Deber, C.M. and von Heijne, G. (2011) Converting a marginally hydrophobic soluble protein into a membrane protein. J Mol Biol 407 (1) : 171-179.	Link to article	PubMed

37	Larsson, P., Skwark, M.J., Wallner, B. and Elofsson, A. (2011) Improved predictions by Pcons.net using multiple templates. Bioinformatics 27 (3) : 426-427.	Link to article	PubMed

38	Illergard, K., Kauko, A. and Elofsson, A. (2011) Why are polar residues within the membrane core evolutionary conserved? Proteins 79 (1) : 79-91.	Link to article	PubMed


2010



39	Bertaccini, E.J., Wallner, B., Trudell, J.R. and Lindahl, E. (2010) Modeling Anesthetic Binding Sites within the Glycine Alpha One Receptor Based on Prokaryotic Ion Channel Templates: The Problem with TM4. J Chem Inf Model 50 (12) : 2248-2255.	Link to article	PubMed

40	Lima, M.F., Eloy, N.B., Pegoraro, C., Sagit, R., Rojas, C., Bretz, T., Vargas, L., Elofsson, A., Oliveira, A.C., Hemerly, A.S. and Ferreira, P.C. (2010) Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol 10 (1) : 254.	Link to article	PubMed

41	Ray, A., Lindahl, E. and Wallner, B. (2010) Model quality assessment for membrane proteins. Bioinformatics 26 (24) : 3067-3074.	Link to article	PubMed

42	Hennerdal, A., Falk, J., Lindahl, E. and Elofsson, A. (2010) Internal duplications in alpha-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci 19 (12) : 2305-2318.	Link to article	PubMed

43	Kall, L. (2010) Prediction of transmembrane topology and signal peptide given a protein's amino acid sequence. Methods Mol Biol 673: 53-62.	Link to article	PubMed

44	Runesson, J., Sollenberg, U.E., Jurkowski, W., Yazdi, S., Eriksson, E.E., Elofsson, A. and Langel, U. (2010) Determining receptor-ligand interaction of human galanin receptor type 3. Neurochem Int 57 (7) : 804-811.	Link to article	PubMed

45	Larsson, P. and Lindahl, E. (2010) A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. J Comput Chem 31 (14) : 2593-2600.	Link to article	PubMed

46	Lind, J., Lindahl, E., Peralvarez-Marin, A., Holmlund, A., Jornvall, H. and Maler, L. (2010) Structural features of proinsulin C-peptide oligomeric and amyloid states. FEBS J 277 (18) : 3759-3768.	Link to article	PubMed

47	Moruz, L., Tomazela, D. and Kall, L. (2010) Training, Selection, and Robust Calibration of Retention Time Models for Targeted Proteomics. J Proteome Res 9 (10) : 5209-5216.	Link to article	PubMed

48	Bjorklund, A.K., Light, S., Sagit, R. and Elofsson, A. (2010) Nebulin: A Study of Protein Repeat Evolution. J Mol Biol 402 (1) : 38-51.	Link to article	PubMed

49	Henricson, A., Forslund, K. and Sonnhammer, E.L. (2010) Orthology confers intron position conservation. BMC Genomics 11 (1) : 412.	Link to article	PubMed

50	Kasson, P.M., Lindahl, E. and Pande, V.S. (2010) Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput Biol 6 (6) : e1000829.	Link to article	PubMed

51	Illergard, K., Callegari, S. and Elofsson, A. (2010) MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinformatics 11 (1) : 333.	Link to article	PubMed

52	Frygelius, J., Arvestad, L., Wedell, A. and Tohonen, V. (2010) Evolution and human tissue expression of the Cres/Testatin subgroup genes, a reproductive tissue specific subgroup of the type 2 cystatins. Evol Dev 12 (3) : 329-342.	Link to article	PubMed

53	Seppala, S., Slusky, J.S., Lloris-Garcera, P., Rapp, M. and von Heijne, G. (2010) Control of membrane protein topology by a single C-terminal residue. Science 328 (5986) : 1698-1700.	Link to article	PubMed

54	Stranneheim, H., Kaller, M., Allander, T., Andersson, B., Arvestad, L. and Lundeberg, J. (2010) Classification of DNA sequences using Bloom filters. Bioinformatics 26 (13) : 1595-1600.	Link to article	PubMed

55	Niemela, P.S., Miettinen, M.S., Monticelli, L., Hammaren, H., Bjelkmar, P., Murtola, T., Lindahl, E. and Vattulainen, I. (2010) Membrane proteins diffuse as dynamic complexes with lipids. J Am Chem Soc 132 (22) : 7574-7575.	Link to article	PubMed

56	Alexeyenko, A., Wassenberg, D.M., Lobenhofer, E.K., Yen, J., Linney, E., Sonnhammer, E.L. and Meyer, J.N. (2010) Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PLoS One 5 (5) : e10465.	Link to article	PubMed

57	Fagerberg, L., Jonasson, K., von Heijne, G., Uhlen, M. and Berglund, L. (2010) Prediction of the human membrane proteome. Proteomics 10 (6) : 1141-1149.	Link to article	PubMed

58	Stromqvist, J., Skoog, K., Daley, D.O., Widengren, J. and von Heijne, G. (2010) Estimating Z-ring radius and contraction in dividing Escherichia coli. Mol Microbiol 76 (1) : 151-158.	Link to article	PubMed

59	Sehat, B., Tofigh, A., Lin, Y., Trocme, E., Liljedahl, U., Lagergren, J. and Larsson, O. (2010) SUMOylation Mediates the Nuclear Translocation and Signaling of the IGF-1 Receptor. Sci Signal 3 (108) : ra10.	Link to article	PubMed

60	Kauko, A., Hedin, L.E., Thebaud, E., Cristobal, S., Elofsson, A. and von Heijne, G. (2010) Repositioning of Transmembrane alpha-Helices during Membrane Protein Folding. J Mol Biol 397 (1) : 190-201.	Link to article	PubMed

61	Enstero, M., Akerborg, O., Lundin, D., Wang, B., Furey, T.S., Ohman, M. and Lagergren, J. (2010) A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinformatics 11 (1) : 6.	Link to article	PubMed

62	Jornvall, H., Lindahl, E., Astorga-Wells, J., Lind, J., Holmlund, A., Melles, E., Alvelius, G., Nerelius, C., Maler, L. and Johansson, J. (2010) Oligomerization and insulin interactions of proinsulin C-peptide: Threefold relationships to properties of insulin. Biochem Biophys Res Commun 391 (3) : 1561-1566.	Link to article	PubMed

63	Sakata, S., Kurokawa, T., Norholm, M.H., Takagi, M., Okochi, Y., von Heijne, G. and Okamura, Y. (2010) Functionality of the voltage-gated proton channel truncated in S4. Proc Natl Acad Sci U S A 107 (5) : 2313-2318.	Link to article	PubMed

64	Ostlund, G., Lindskog, M. and Sonnhammer, E.L. (2010) Network-based Identification of Novel Cancer Genes. Mol Cell Proteomics 9 (4) : 648-655.	Link to article	PubMed

65	Ekman, D. and Elofsson, A. (2010) Identifying and Quantifying Orphan Protein Sequences in Fungi. J Mol Biol 396 (2) : 396-405.	Link to article	PubMed

66	Daniels, R., Mellroth, P., Bernsel, A., Neiers, F., Normark, S., von Heijne, G. and Henriques-Normark, B. (2010) Disulfide Bond Formation and Cysteine Exclusion in Gram-positive Bacteria. J Biol Chem 285 (5) : 3300-3309.	Link to article	PubMed

67	Hedin, L.E., Ojemalm, K., Bernsel, A., Hennerdal, A., Illergard, K., Enquist, K., Kauko, A., Cristobal, S., von Heijne, G., Lerch-Bader, M., Nilsson, I. and Elofsson, A. (2010) Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context. J Mol Biol 396 (1) : 221-229.	Link to article	PubMed

68	Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E.L., Eddy, S.R. and Bateman, A. (2010) The Pfam protein families database. Nucleic Acids Res 38 (Database issue) : D211-22.	Link to article	PubMed

69	Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D.N., Roopra, S., Frings, O. and Sonnhammer, E.L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 38 (Database issue) : D196-203.	Link to article	PubMed


2009



70	Sennblad, B. and Lagergren, J. (2009) Probabilistic Orthology Analysis. Syst Biol 58 (4) : 411-424.	Link to article	PubMed

71	Johansson, A.C. and Lindahl, E. (2009) Protein contents in biological membranes can explain abnormal solvation of charged and polar residues. Proc Natl Acad Sci U S A 106 (37) : 15684-15689.	Link to article	PubMed

72	Klammer, M., Messina, D.N., Schmitt, T. and Sonnhammer, E.L. (2009) MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics 10: 314.	Link to article	PubMed

73	Gabaldon, T., Dessimoz, C., Huxley-Jones, J., Vilella, A.J., Sonnhammer, E.L. and Lewis, S. (2009) Joining forces in the quest for orthologs. Genome Biol 10 (9) : 403.	Link to article	PubMed

74	Bjorkholm, P. and Sonnhammer, E.L. (2009) Comparative analysis and unification of domain-domain interaction networks. Bioinformatics 25 (22) : 3020-3025.	Link to article	PubMed

75	Forslund, K. and Sonnhammer, E.L. (2009) Benchmarking homology detection procedures with low complexity filters. Bioinformatics 25 (19) : 2500-2505.	Link to article	PubMed

76	Fugelstad, J., Bouzenzana, J., Djerbi, S., Guerriero, G., Ezcurra, I., Teeri, T.T., Arvestad, L. and Bulone, V. (2009) Identification of the cellulose synthase genes from the Oomycete Saprolegnia monoica and effect of cellulose synthesis inhibitors on gene expression and enzyme activity. Fungal Genet Biol 46 (10) : 759-767.	Link to article	PubMed

77	Jaud, S., Fernandez-Vidal, M., Nilsson, I., Meindl-Beinker, N.M., Hubner, N.C., Tobias, D.J., von Heijne, G. and White, S.H. (2009) Insertion of short transmembrane helices by the Sec61 translocon. Proc Natl Acad Sci U S A 106 (28) : 11588-11593.	Link to article	PubMed

78	Larsson, P., Skwark, M.J., Wallner, B. and Elofsson, A. (2009) Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins 77 (S9) : 167-172.	Link to article	PubMed

79	Illergard, K., Ardell, D.H. and Elofsson, A. (2009) Structure is three to ten times more conserved than sequence-A study of structural response in protein cores. Proteins 77 (3) : 499-508.	Link to article	PubMed

80	Michino, M., Abola, E., Brooks, 3rd, C.L., Dixon, J.S., Moult, J. and Stevens, R.C. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 8 (6) : 455-463.	Link to article	PubMed

81	Hessa, T., Reithinger, J.H., von Heijne, G. and Kim, H. (2009) Analysis of transmembrane helix integration in the endoplasmic reticulum in S. cerevisiae. J Mol Biol 386 (5) : 1222-1228.		PubMed

82	Johansson, A.C. and Lindahl, E. (2009) The role of lipid composition for insertion and stabilization of amino acids in membranes. J Chem Phys 130 (18) : 185101.	Link to article	PubMed

83	Bernsel, A., Viklund, H., Hennerdal, A. and Elofsson, A. (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 37 (Web Server issue) : W465-8.	Link to article	PubMed

84	Spivak, M., Weston, J., Bottou, L., Kall, L. and Noble, W.S. (2009) Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets. J Proteome Res 8 (7) : 3737-3745.	Link to article	PubMed

85	Akerborg, O., Sennblad, B., Arvestad, L. and Lagergren, J. (2009) Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A 106 (14) : 5714-5719.	Link to article	PubMed

86	Messina, D.N. and Sonnhammer, E.L. (2009) DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics 25 (10) : 1333-1334.	Link to article	PubMed

87	Ollila, O.H., Risselada, H.J., Louhivuori, M., Lindahl, E., Vattulainen, I. and Marrink, S.J. (2009) 3D pressure field in lipid membranes and membrane-protein complexes. Phys Rev Lett 102 (7) : 078101.	Link to article	PubMed

88	Alexeyenko, A. and Sonnhammer, E.L. (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res 19 (6) : 1107-1116.	Link to article	PubMed

89	Enquist, K., Fransson, M., Boekel, C., Bengtsson, I., Geiger, K., Lang, L., Pettersson, A., Johansson, S., von Heijne, G. and Nilsson, I. (2009) Membrane-integration characteristics of two ABC transporters, CFTR and P-glycoprotein. J Mol Biol 387 (5) : 1153-1164.	Link to article	PubMed

90	Bjelkmar, P., Niemela, P.S., Vattulainen, I. and Lindahl, E. (2009) Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. PLoS Comput Biol 5 (2) : e1000289.	Link to article	PubMed

91	Juncker, A.S., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. and Brunak, S. (2009) Sequence-based feature prediction and annotation of proteins. Genome Biol 10 (2) : 206.	Link to article	PubMed

92	Kall, L., Storey, J.D. and Noble, W.S. (2009) QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics 25 (7) : 964-966.	Link to article	PubMed

93	Barth, P., Wallner, B. and Baker, D. (2009) Prediction of membrane protein structures with complex topologies using limited constraints. Proc Natl Acad Sci U S A 106 (5) : 1409-1414.	Link to article	PubMed

94	Johansson, A.C. and Lindahl, E. (2009) Titratable amino Acid solvation in lipid membranes as a function of protonation state. J Phys Chem B 113 (1) : 245-253.		PubMed

95	Lassmann, T., Frings, O. and Sonnhammer, E.L. (2009) Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res 37 (3) : 858-865.	Link to article	PubMed

96	Arvestad, L., Lagergren, J., Sennblad, B. (2009) The gene evolution model and computing its associated probabilities J ACM 56: 1-44.	Link to article

97	Sennblad, B., Lagergren, J. (2009) Probabilistic Orthology Analysis Syst Biol 58: 411-424.	Link to article

98	Hessa, T., Reithinger, J.H., von Heijne, G. and Kim, H. (2009) Quantitative analysis of transmembrane helix integration in the endoplasmic reticulum in S. cerevisiae J Mol Biol 386 (5) : 1222-1228.	Link to article


2008



99	Lage, K., Hansen, N.T., Karlberg, E.O., Eklund, A.C., Roque, F.S., Donahoe, P.K., Szallasi, Z., Jensen, T.S. and Brunak, S. (2008) A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A 105 (52) : 20870-20875.	Link to article	PubMed

100	Yosef, N. and Kall, L. (2008) From sequence to structure to networks. Genome Biol 9 (11) : 326.	Link to article	PubMed

101	Reynolds, S.M., Kall, L., Riffle, M.E., Bilmes, J.A. and Noble, W.S. (2008) Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol 4 (11) : e1000213.	Link to article	PubMed

102	Viklund, H., Bernsel, A., Skwark, M. and Elofsson, A. (2008) SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24 (24) : 2928-2929.	Link to article	PubMed

103	Bjorklund, A.K., Light, S., Hedin, L. and Elofsson, A. (2008) Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics 8 (22) : 4657-4667.	Link to article	PubMed

104	Lundin, C., Kim, H., Nilsson, I., White, S.H. and von Heijne, G. (2008) Molecular code for protein insertion in the endoplasmic reticulum membrane is similar for N(in)-C(out) and N(out)-C(in) transmembrane helices. Proc Natl Acad Sci U S A 105 (41) : 15702-15707.	Link to article	PubMed

105	Daub, C.O. and Sonnhammer, E.L. (2008) Employing conservation of co-expression to improve functional inference. BMC Syst Biol 2 (1) : 81.	Link to article	PubMed

106	Rajangam, A.S., Kumar, M., Aspeborg, H., Guerriero, G., Arvestad, L., Pansri, P., Brown, C.J., Hober, S., Blomqvist, K., Divne, C., Ezcurra, I., Mellerowicz, E., Sundberg, B., Bulone, V. and Teeri, T.T. (2008) MAP20, a microtubule-associated protein in the secondary cell walls of hybrid aspen, is a target of the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile. Plant Physiol 148 (3) : 1283-1294.	Link to article	PubMed

107	Kall, L., Storey, J.D. and Noble, W.S. (2008) Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics 24 (16) : i42-8.	Link to article	PubMed

108	Moore, A.D., Bjorklund, A.K., Ekman, D., Bornberg-Bauer, E. and Elofsson, A. (2008) Arrangements in the modular evolution of proteins. Trends Biochem Sci 33 (9) : 444-451.	Link to article	PubMed

109	Merrihew, G.E., Davis, C., Ewing, B., Williams, G., Kall, L., Frewen, B.E., Noble, W.S., Green, P., Thomas, J.H. and MacCoss, M.J. (2008) Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 18 (10) : 1660-1669.	Link to article	PubMed

110	von Heijne, G. and Rees, D. (2008) Membranes: reading between the lines. Curr Opin Struct Biol 18 (4) : 403-405.	Link to article	PubMed

111	Forslund, K. and Sonnhammer, E.L. (2008) Predicting protein function from domain content. Bioinformatics 24 (15) : 1681-1687.	Link to article	PubMed

112	Cassel, M., Seppala, S. and von Heijne, G. (2008) Confronting fusion protein-based membrane protein topology mapping with reality: the Escherichia coli ClcA H+/Cl- exchange transporter. J Mol Biol 381 (4) : 860-866.	Link to article	PubMed

113	White, S.H. and von Heijne, G. (2008) How translocons select transmembrane helices. Annu Rev Biophys 37: 23-42.	Link to article	PubMed

114	Kauko, A., Illergard, K. and Elofsson, A. (2008) Coils in the membrane core are conserved and functionally important. J Mol Biol 380 (1) : 170-180.	Link to article	PubMed

115	Park, C.Y., Klammer, A.A., Kall, L., MacCoss, M.J. and Noble, W.S. (2008) Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 7 (7) : 3022-3027.	Link to article	PubMed

116	Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G. and Elofsson, A. (2008) Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A 105 (20) : 7177-7181.	Link to article	PubMed

117	Viklund, H. and Elofsson, A. (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 24 (15) : 1662-1668.	Link to article	PubMed

118	Drew, D., Newstead, S., Sonoda, Y., Kim, H., von Heijne, G. and Iwata, S. (2008) GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc 3 (5) : 784-798.	Link to article	PubMed

119	Lindahl, E.R. (2008) Molecular dynamics simulations. Methods Mol Biol 443: 3-23.	Link to article	PubMed

120	Klammer, M., Roopra, S. and Sonnhammer, E.L. (2008) jSquid: a Java applet for graphical on-line network exploration. Bioinformatics 24 (12) : 1467-1468.	Link to article	PubMed

121	Larsson, P., Wallner, B., Lindahl, E. and Elofsson, A. (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci 17 (6) : 990-1002.	Link to article	PubMed

122	Lindahl, E. and Sansom, M.S. (2008) Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol 18 (4) : 425-431.	Link to article	PubMed

123	Chalk, A.M. and Sonnhammer, E.L. (2008) siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics 24 (10) : 1316-1317.	Link to article	PubMed

124	Bertaccini, E.J., Lindahl, E., Sixma, T. and Trudell, J.R. (2008) Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. J Chem Inf Model 48 (4) : 855-860.	Link to article	PubMed

125	Lerch-Bader, M., Lundin, C., Kim, H., Nilsson, I. and von Heijne, G. (2008) Contribution of positively charged flanking residues to the insertion of transmembrane helices into the endoplasmic reticulum. Proc Natl Acad Sci U S A 105 (11) : 4127-4132.	Link to article	PubMed

126	Akerborg, O., Sennblad, B. and Lagergren, J. (2008) Birth-death prior on phylogeny and speed dating. BMC Evol Biol 8: 77.	Link to article	PubMed

127	Hong, J., Wei, N., Chalk, A., Wang, J., Song, Y., Yi, F., Qiao, R.P., Sonnhammer, E.L., Wahlestedt, C., Liang, Z. and Du, Q. (2008) Focusing on RISC assembly in mammalian cells. Biochem Biophys Res Commun 368 (3) : 703-708.	Link to article	PubMed

128	Joannin, N., Abhiman, S., Sonnhammer, E.L. and Wahlgren, M. (2008) Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family. BMC Genomics 9: 19.	Link to article	PubMed

129	Johansson, A.C. and Lindahl, E. (Epub 2008) Correction to the article "Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations" Proteins (Epub ahead of print) 70 (4) : 1655-1656.	Link to article	PubMed

130	Papaloukas, C., Granseth, E., Viklund, H. and Elofsson, A. (2008) Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci 17 (2) : 271-278.	Link to article	PubMed

131	Bernsel, A., Viklund, H. and Elofsson, A. (2008) Remote homology detection of integral membrane proteins using conserved sequence features. Proteins 71 (3) : 1387-1399.	Link to article	PubMed

132	Kall, L., Storey, J.D., MacCoss, M.J. and Noble, W.S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 7 (1) : 29-34.	Link to article	PubMed

133	Berglund, A.C., Sjolund, E., Ostlund, G. and Sonnhammer, E.L. (2008) InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res 36 (Database issue) : D263-6.	Link to article	PubMed

134	Kall, L., Storey, J.D., MacCoss, M.J. and Noble, W.S. (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res 7 (1) : 40-44.	Link to article	PubMed

135	Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2008) The Pfam protein families database. Nucleic Acids Res 36 (Database issue) : D281-8.	Link to article	PubMed

136	Forslund, K., Henricson, A., Hollich, V. and Sonnhammer, E.L. (2008) Domain tree-based analysis of protein architecture evolution. Mol Biol Evol 25 (2) : 254-264.	Link to article	PubMed

137	Johansson, A.C. and Lindahl, E. (2008) Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 70 (4) : 1332-1344.	Link to article	PubMed

138	Wallner, B., and Elofsson, A. (2008) Prediction of global and local model qualities using MQAPs Eds Bujnicki 1: 1-1.	Link to article


2007



139	Hessa, T., Meindl-Beinker, N.M., Bernsel, A., Kim, H., Sato, Y., Lerch-Bader, M., Nilsson, I., White, S.H. and von Heijne, G. (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450 (7172) : 1026-1030.	Link to article	PubMed

140	Xie, K., Hessa, T., Seppala, S., Rapp, M., Heijne, G. and Dalbey, R.E. (2007) Features of transmembrane segments that promote the lateral release from the translocase into the lipid phase. Biochemistry 46 (51) : 15153-15161.	Link to article	PubMed

141	Lundin, C., Kall, L., Kreher, S.A., Kapp, K., Sonnhammer, E.L., Carlson, J.R., Heijne, G. and Nilsson, I. (2007) Membrane topology of the Drosophila OR83b odorant receptor. FEBS Lett 581 (29) : 5601-5604.	Link to article	PubMed

142	Hollich, V. and Sonnhammer, E.L. (2007) PfamAlyzer: domain-centric homology search. Bioinformatics 23 (24) : 3382-3383.	Link to article	PubMed

143	Kall, L., Canterbury, J.D., Weston, J., Noble, W.S. and MacCoss, M.J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4 (11) : 923-925.	Link to article	PubMed

144	Wallner, B. and Elofsson, A. (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69 (S8) : 184-193.	Link to article	PubMed

145	Granseth, E., Seppala, S., Rapp, M., Daley, D.O. and Von Heijne, G. (2007) Membrane protein structural biology - How far can the bugs take us? (Review). Mol Membr Biol 24 (5) : 329-332.	Link to article	PubMed

146	Newstead, S., Kim, H., von Heijne, G., Iwata, S. and Drew, D. (2007) High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 104 (35) : 13936-13941.	Link to article	PubMed

147	Ekman, D., Bjorklund, A.K. and Elofsson, A. (2007) Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol 372 (5) : 1337-1348.	Link to article	PubMed

148	Andersson, S.A. and Lagergren, J. (2007) Motif yggdrasil: sampling sequence motifs from a tree mixture model. J Comput Biol 14 (5) : 682-697.	Link to article	PubMed

149	Lundin, C., Johansson, S., Johnson, A.E., Naslund, J., von Heijne, G. and Nilsson, I. (2007) Stable insertion of Alzheimer Abeta peptide into the ER membrane strongly correlates with its length. FEBS Lett 581 (20) : 3809-3813.	Link to article	PubMed

150	Bertaccini, E.J., Trudell, J.R. and Lindahl, E. (2007) Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. J Chem Inf Model 47 (4) : 1572-1579.	Link to article	PubMed

151	Wallner, B., Larsson, P. and Elofsson, A. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35 (suppl_2) : W369-W374.	Link to article	PubMed

152	Stenberg, F., von Heijne, G. and Daley, D.O. (2007) Assembly of the Cytochrome bo(3) Complex. J Mol Biol 371 (3) : 765-773.	Link to article	PubMed

153	Elofsson, A. and von Heijne, G. (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140.	Link to article	PubMed

154	Lassmann, T. and Sonnhammer, E.L. (2007) Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinformatics 8 Suppl 5: S9.	Link to article	PubMed

155	von Heijne, G. (2007) Membrane proteins up for grabs. Nat Biotechnol 25 (6) : 646-647.	Link to article	PubMed

156	von Heijne, G. (2007) The membrane protein universe: what's out there and why bother? J Intern Med 261 (6) : 543-557.	Link to article	PubMed

157	Hughes, T., Ekman, D., Ardawatia, H., Elofsson, A. and Liberles, D.A. (2007) Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol 8 (5) : 213.	Link to article	PubMed

158	Julenius, K. (2007) NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology 17 (8) : 868-876.	Link to article	PubMed

159	Zhang, L., Sato, Y., Hessa, T., von Heijne, G., Lee, J.K., Kodama, I., Sakaguchi, M. and Uozumi, N. (2007) Contribution of hydrophobic and electrostatic interactions to the membrane integration of the Shaker K+ channel voltage sensor domain. Proc Natl Acad Sci U S A 104 (20) : 8263-8268.	Link to article	PubMed

160	Kall, L., Krogh, A. and Sonnhammer, E.L. (2007) Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res 35 (suppl_2) : W429-W432.	Link to article	PubMed

161	Vogt, G., Vogt, B., Chuzhanova, N., Julenius, K., Cooper, D.N. and Casanova, J.L. (2007) Gain-of-glycosylation mutations. Curr Opin Genet Dev 17 (3) : 245-251.	Link to article	PubMed

162	Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2 (4) : 953-971.	Link to article	PubMed

163	von Heijne, G. (2007) Formation of Transmembrane Helices In Vivo--Is Hydrophobicity All that Matters? J Gen Physiol 129 (5) : 353-356.	Link to article	PubMed

164	Kutzner, C., Van Der Spoel, D., Fechner, M., Lindahl, E., Schmitt, U.W., De Groot, B.L. and Grubmuller, H. (2007) Speeding up parallel GROMACS on high-latency networks. J Comput Chem 28 (12) : 2075-2084.	Link to article	PubMed

165	Wang, H., Julenius, K., Hryhorenko, J. and Hagen, F.K. (2007) Systematic Analysis of proteoglycan modification sites in Caenorhabditis elegans by scanning mutagenesis. J Biol Chem 282 (19) : 14586-14597.	Link to article	PubMed

166	Elias, I. and Lagergren, J. (2007) Fast computation of distance estimators. BMC Bioinformatics 8: 89.	Link to article	PubMed

167	Rapp, M., Seppala, S., Granseth, E. and von Heijne, G. (2007) Emulating membrane protein evolution by rational design. Science 315 (5816) : 1282-1284.	Link to article	PubMed

168	Andersson, A., Biverstahl, H., Nordin, J., Danielsson, J., Lindahl, E. and Maler, L. (2007) The membrane-induced structure of melittin is correlated with the fluidity of the lipids. Biochim Biophys Acta 1768 (1) : 115-121.	Link to article	PubMed

169	Roth, C., Rastogi, S., Arvestad, L., Dittmar, K., Light, S., Ekman, D. and Liberles, D.A. (2007) Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J Exp Zoolog B Mol Dev Evol 308 (1) : 58-73.	Link to article	PubMed

170	Lindahl, E. (2007) Molecular dynamics Simulations Molecular Modeling of Proteins : 1-24.


2006



171	von Heijne, G. (2006) Membrane-protein topology. Nat Rev Mol Cell Biol 7 (12) : 909-918.	Link to article	PubMed

172	Johansson, A.C. and Lindahl, E. (2006) Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophys J 91 (12) : 4450-4463.	Link to article	PubMed

173	Meindl-Beinker, N.M., Lundin, C., Nilsson, I., White, S.H. and von Heijne, G. (2006) Asn- and Asp-mediated interactions between transmembrane helices during translocon-mediated membrane protein assembly. EMBO Rep 7 (11) : 1111-1116.	Link to article	PubMed

174	Alexeyenko, A., Millar, A.H., Whelan, J. and Sonnhammer, E.L. (2006) Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis. Trends Genet 22 (11) : 589-593.	Link to article	PubMed

175	Bjorklund, A.K., Ekman, D. and Elofsson, A. (2006) Expansion of Protein Domain Repeats. PLoS Comput Biol 2 (8) : e114.	Link to article	PubMed

176	Julenius, K. and Pedersen, A.G. (2006) Protein evolution is faster outside the cell. Mol Biol Evol 23 (11) : 2039-2048.	Link to article	PubMed

177	Alexeyenko, A., Tamas, I., Liu, G. and Sonnhammer, E.L. (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22 (14) : e9-15.	Link to article	PubMed

178	Granseth, E., Viklund, H. and Elofsson, A. (2006) ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics 22 (14) : e191-6.	Link to article	PubMed

179	Ohlson, T., Aggarwal, V., Elofsson, A. and MacCallum, R.M. (2006) Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinformatics 7: 357.	Link to article	PubMed

180	Viklund, H., Granseth, E. and Elofsson, A. (2006) Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 361 (3) : 591-603.	Link to article	PubMed

181	Kim, H., Melen, K., Osterberg, M. and von Heijne, G. (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci U S A 103 (30) : 11142-11147.	Link to article	PubMed

182	Osterberg, M., Kim, H., Warringer, J., Melen, K., Blomberg, A. and von Heijne, G. (2006) Phenotypic effects of membrane protein overexpression in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 103 (30) : 11148-11153.	Link to article	PubMed

183	Lassmann, T. and Sonnhammer, E.L. (2006) Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res 34 (Web Server issue) : W596-9.	Link to article	PubMed

184	Lindahl, E., Azuara, C., Koehl, P. and Delarue, M. (2006) NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res 34 (Web Server issue) : W52-6.	Link to article	PubMed

185	Azuara, C., Lindahl, E., Koehl, P., Orland, H. and Delarue, M. (2006) PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res 34 (Web Server issue) : W38-42.	Link to article	PubMed

186	Amico, M., Finelli, M., Rossi, I., Zauli, A., Elofsson, A., Viklund, H., von Heijne, G., Jones, D., Krogh, A., Fariselli, P., Luigi Martelli, P. and Casadio, R. (2006) PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res 34 (Web Server issue) : W169-72.	Link to article	PubMed

187	Mackinnon, R. and von Heijne, G. (2006) Membranes. Curr Opin Struct Biol 16 (4) : 431.	Link to article	PubMed

188	Ekman, D., Light, S., Bjorklund, A.K. and Elofsson, A. (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol 7 (6) : R45.	Link to article	PubMed

189	Hjelm, M., Hoglund, M. and Lagergren, J. (2006) New probabilistic network models and algorithms for oncogenesis. J Comput Biol 13 (4) : 853-865.	Link to article	PubMed

190	Svensson, O., Arvestad, L. and Lagergren, J. (2006) Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2 (5) : e46.	Link to article	PubMed

191	Abhiman, S., Daub, C.O. and Sonnhammer, E.L. (2006) Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Mol Biol Evol 23 (7) : 1406-1413.	Link to article	PubMed

192	Lundin, C., Nordstrom, R., Wagner, K., Windpassinger, C., Andersson, H., von Heijne, G. and Nilsson, I. (2006) Membrane topology of the human seipin protein. FEBS Lett 580 (9) : 2281-2284.	Link to article	PubMed

193	Kemmer, D., Podowski, R.M., Arenillas, D., Lim, J., Hodges, E., Roth, P., Sonnhammer, E.L., Hoog, C. and Wasserman, W.W. (2006) NovelFam3000--uncharacterized human protein domains conserved across model organisms. BMC Genomics 7: 48.	Link to article	PubMed

194	Marani, P., Wagner, S., Baars, L., Genevaux, P., de Gier, J.W., Nilsson, I., Casadio, R. and von Heijne, G. (2006) New Escherichia coli outer membrane proteins identified through prediction and experimental verification. Protein Sci 15 (4) : 884-889.	Link to article	PubMed

195	Wallner, B. and Elofsson, A. (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 15 (4) : 900-913.	Link to article	PubMed

196	Wistrand, M., Kall, L. and Sonnhammer, E.L. (2006) A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci 15 (3) : 509-521.	Link to article	PubMed

197	Rapp, M., Granseth, E., Seppala, S. and von Heijne, G. (2006) Identification and evolution of dual-topology membrane proteins. Nat Struct Mol Biol 13 (2) : 112-116.	Link to article	PubMed

198	Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34 (Database issue) : D247-51.	Link to article	PubMed

199	Asa Bjorklund, Anna Thoren, Gunnar von Heijne and Arne Elofsson (2006) The use of Phylogenetic profils for Gene Predictions Revisited Current Genomics 7 (2) : 79-86.	Link to article

200	Bryant, D. and Lagergren, J. (2006) Compatibility of unrooted phylogenetic trees is FPT. Theo Comp Sci 351: 296-302.

201	Andersson, S.A. and Lagergren, J. (2006) Motif Yggdrasil: Sampling from a Tree Mixture Model Tenth Annual International Conference on Research in Computational Molecular Biology : 458-472.

202	Lindberg, J., Alexeyenko, A., Perez-Bercoff, A. and Sonnhammer, E. (2006) Overview and comparison of ortholog databases Drug Discovery Today: Technologies 3: 137-143.


2005



203	Lassmann, T. and Sonnhammer, E.L. (2005) Automatic assessment of alignment quality. Nucleic Acids Res 33 (22) : 7120-7128.	Link to article	PubMed

204	Lassmann, T. and Sonnhammer, E.L. (2005) Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298.	Link to article	PubMed

205	Villarejo, A., Buren, S., Larsson, S., Dejardin, A., Monne, M., Rudhe, C., Karlsson, J., Jansson, S., Lerouge, P., Rolland, N., von Heijne, G., Grebe, M., Bako, L. and Samuelsson, G. (2005) Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol 7 (12) : 1224-1231.	Link to article	PubMed

206	Light, S., Kraulis, P. and Elofsson, A. (2005) Preferential attachment in the evolution of metabolic networks. BMC Genomics 6: 159.	Link to article	PubMed

207	White, S.H. and von Heijne, G. (2005) Do protein-lipid interactions determine the recognition of transmembrane helices at the ER translocon? Biochem Soc Trans 33 (Pt 5) : 1012-1015.	Link to article	PubMed

208	Ohlson, T. and Elofsson, A. (2005) ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics 6: 253.	Link to article	PubMed

209	Freites, J.A., Tobias, D.J., von Heijne, G. and White, S.H. (2005) Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A 102 (42) : 15059-15064.	Link to article	PubMed

210	Karamyshev, A.L., Kelleher, D.J., Gilmore, R., Johnson, A.E., von Heijne, G. and Nilsson, I. (2005) Mapping the interaction of the STT3 subunit of the oligosaccharyl transferase complex with nascent polypeptide chains. J Biol Chem 280 (49) : 40489-40493.	Link to article	PubMed

211	Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E. and Berendsen, H.J. (2005) GROMACS: fast, flexible, and free. J Comput Chem 26 (16) : 1701-1718.	Link to article	PubMed

212	von Heijne, G. (2005) Helices on the move. Nat Struct Mol Biol 12 (10) : 834-835.	Link to article	PubMed

213	Pasche, B., Knobloch, T.J., Bian, Y., Liu, J., Phukan, S., Rosman, D., Kaklamani, V., Baddi, L., Siddiqui, F.S., Frankel, W., Prior, T.W., Schuller, D.E., Agrawal, A., Lang, J., Dolan, M.E., Vokes, E.E., Lane, W.S., Huang, C.C., Caldes, T., Di Cristofano, A., Hampel, H., Nilsson, I., von Heijne, G., Fodde, R., Murty, V.V., de la Chapelle, A. and Weghorst, C.M. (2005) Somatic acquisition and signaling of TGFBR16A in cancer. JAMA* 294 (13) : 1634-1646.	Link to article	PubMed

214	Wallner, B. and Elofsson, A. (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21 (23) : 4248-4254.	Link to article	PubMed

215	Bjorklund, A.K., Ekman, D., Light, S., Frey-Skott, J. and Elofsson, A. (2005) Domain rearrangements in protein evolution. J Mol Biol 353 (4) : 911-923.	Link to article	PubMed

216	Medigue, C., Krin, E., Pascal, G., Barbe, V., Bernsel, A., Bertin, P.N., Cheung, F., Cruveiller, S., D'Amico, S., Duilio, A., Fang, G., Feller, G., Ho, C., Mangenot, S., Marino, G., Nilsson, J., Parrilli, E., Rocha, E.P., Rouy, Z., Sekowska, A., Tutino, M.L., Vallenet, D., von Heijne, G. and Danchin, A. (2005) Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res 15 (10) : 1325-1335.	Link to article	PubMed

217	Luirink, J., von Heijne, G., Houben, E. and de Gier, J.W. (2005) Biogenesis of inner membrane proteins in Escherichia coli. Annu Rev Microbiol 59: 329-355.	Link to article	PubMed

218	Granseth, E., Daley, D.O., Rapp, M., Melen, K. and von Heijne, G. (2005) Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J Mol Biol 352 (3) : 489-494.	Link to article	PubMed

219	Lindahl, E. and Delarue, M. (2005) Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res 33 (14) : 4496-4506.	Link to article	PubMed

220	Stenberg, F., Chovanec, P., Maslen, S.L., Robinson, C.V., Ilag, L.L., von Heijne, G. and Daley, D.O. (2005) Protein complexes of the Escherichia coli cell envelope. J Biol Chem 280 (41) : 34409-34419.	Link to article	PubMed

221	von Heijne, G. (2005) Microbiology. Translocation of anthrax toxin: lord of the rings. Science 309 (5735) : 709-710.	Link to article	PubMed

222	Hollich, V., Milchert, L., Arvestad, L. and Sonnhammer, E.L. (2005) Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol 22 (11) : 2257-2264.	Link to article	PubMed

223	Laudon, H., Hansson, E.M., Melen, K., Bergman, A., Farmery, M.R., Winblad, B., Lendahl, U., von Heijne, G. and Naslund, J. (2005) A nine-transmembrane domain topology for presenilin 1. J Biol Chem 280 (42) : 35352-35360.	Link to article	PubMed

224	White, S.H. and von Heijne, G. (2005) Transmembrane helices before, during, and after insertion. Curr Opin Struct Biol 15 (4) : 378-386.	Link to article	PubMed

225	Nilsson, J., Persson, B. and von Heijne, G. (2005) Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins 60 (4) : 606-616.	Link to article	PubMed

226	McCarthy, S., Mottagui-Tabar, S., Mizuno, Y., Sennblad, B., Hoffstedt, J., Arner, P., Wahlestedt, C. and Andersson, B. (2005) Complex HTR2C linkage disequilibrium and promoter associations with body mass index and serum leptin. Hum Genet 117 (6) : 545-557.	Link to article	PubMed

227	Abhiman, S. and Sonnhammer, E.L. (2005) Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins 60 (4) : 758-768.	Link to article	PubMed

228	Bernsel, A. and Von Heijne, G. (2005) Improved membrane protein topology prediction by domain assignments. Protein Sci 14 (7) : 1723-1728.	Link to article	PubMed

229	Kall, L., Krogh, A. and Sonnhammer, E.L. (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21 Suppl 1: i251-7.	Link to article	PubMed

230	Henricson, A., Kall, L. and Sonnhammer, E.L. (2005) A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. FEBS J 272 (11) : 2727-2733.	Link to article	PubMed

231	Daley, D.O., Rapp, M., Granseth, E., Melen, K., Drew, D. and von Heijne, G. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 (5726) : 1321-1323.	Link to article	PubMed

232	Berglund, A.C., Wallner, B., Elofsson, A. and Liberles, D.A. (2005) Tertiary windowing to detect positive diversifying selection. J Mol Evol 60 (4) : 499-504.	Link to article	PubMed

233	Sonnhammer, E.L. and Hollich, V. (2005) Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics 6: 108.	Link to article	PubMed

234	Wallner, B. and Elofsson, A. (2005) All are not equal: a benchmark of different homology modeling programs. Protein Sci 14 (5) : 1315-1327.	Link to article	PubMed

235	Wistrand, M. and Sonnhammer, E.L. (2005) Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics 6: 99.	Link to article	PubMed

236	Ekman, D., Bjorklund, A.K., Frey-Skott, J. and Elofsson, A. (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol 348 (1) : 231-243.	Link to article	PubMed

237	Kim, H., von Heijne, G. and Nilsson, I. (2005) Membrane topology of the STT3 subunit of the oligosaccharyl transferase complex. J Biol Chem 280 (21) : 20261-20267.	Link to article	PubMed

238	Tie, J.K., Nicchitta, C., von Heijne, G. and Stafford, D.W. (2005) Membrane topology mapping of vitamin K epoxide reductase by in vitro translation/cotranslocation. J Biol Chem 280 (16) : 16410-16416.	Link to article	PubMed

239	Hessa, T., White, S.H. and von Heijne, G. (2005) Membrane insertion of a potassium-channel voltage sensor. Science 307 (5714) : 1427.	Link to article	PubMed

240	Ding, B., Kull, B., Liu, Z., Mottagui-Tabar, S., Thonberg, H., Gu, H.F., Brookes, A.J., Grundemar, L., Karlsson, C., Hamsten, A., Arner, P., Ostenson, C.G., Efendic, S., Monne, M., von Heijne, G., Eriksson, P. and Wahlestedt, C. (2005) Human neuropeptide Y signal peptide gain-of-function polymorphism is associated with increased body mass index: possible mode of function. Regul Pept 127 (1-3) : 45-53.	Link to article	PubMed

241	Hessa, T., Kim, H., Bihlmaier, K., Lundin, C., Boekel, J., Andersson, H., Nilsson, I., White, S.H. and von Heijne, G. (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433 (7024) : 377-381.	Link to article	PubMed

242	Granseth, E., von Heijne, G. and Elofsson, A. (2005) A study of the membrane-water interface region of membrane proteins. J Mol Biol 346 (1) : 377-385.	Link to article	PubMed

243	Sonnhammer, E.L. (2005) Genome informatics: taming the avalanche of genomic data. Genome Biol 6 (1) : 301.	Link to article	PubMed

244	Monne, M., Hessa, T., Thissen, L. and von Heijne, G. (2005) Competition between neighboring topogenic signals during membrane protein insertion into the ER. FEBS J 272 (1) : 28-36.	Link to article	PubMed

245	O'Brien, K.P., Remm, M. and Sonnhammer, E.L. (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33 (Database issue) : D476-80.	Link to article	PubMed

246	Abhiman, S. and Sonnhammer, E.L. (2005) FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res 33 (Database issue) : D197-200.	Link to article	PubMed

247	Chalk, A.M., Warfinge, R.E., Georgii-Hemming, P. and Sonnhammer, E.L. (2005) siRNAdb: a database of siRNA sequences. Nucleic Acids Res 33 (Database issue) : D131-4.	Link to article	PubMed

248	Julenius, K., Molgaard, A., Gupta, R. and Brunak, S. (2005) Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15 (2) : 153-164.		PubMed


2004



249	Kerje, S., Sharma, P., Gunnarsson, U., Kim, H., Bagchi, S., Fredriksson, R., Schutz, K., Jensen, P., von Heijne, G., Okimoto, R. and Andersson, L. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics 168 (3) : 1507-1518.	Link to article	PubMed

250	Henricson, A., Sonnhammer, E.L., Baillie, D.L. and Gomes, A.V. (2004) Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. BMC Genomics 5 (1) : 85.	Link to article	PubMed

251	Sun, X., Zhao, J., Kylberg, K., Soop, T., Palka, K., Sonnhammer, E., Visa, N., Alzhanova-Ericsson, A.T. and Daneholt, B. (2004) Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene. Chromosoma 113 (5) : 244-257.	Link to article	PubMed

252	Camps-Valls, G., Chalk, A.M., Serrano-Lopez, A.J., Martin-Guerrero, J.D. and Sonnhammer, E.L. (2004) Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinformatics 5: 135.		PubMed

253	Ohlson, T., Wallner, B. and Elofsson, A. (2004) Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 57 (1) : 188-197.	Link to article	PubMed

254	O'Brien, K.P., Westerlund, I. and Sonnhammer, E.L. (2004) OrthoDisease: a database of human disease orthologs. Hum Mutat 24 (2) : 112-119.	Link to article	PubMed

255	Bendtsen, J.D., Nielsen, H., von Heijne, G. and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340 (4) : 783-795.		PubMed

256	Viklund, H. and Elofsson, A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 13 (7) : 1908-1917.		PubMed

257	Alkema, W.B., Johansson, O., Lagergren, J. and Wasserman, W.W. (2004) MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res 32 (Web Server issue) : W195-8.	Link to article	PubMed

258	Chalk, A.M., Wahlestedt, C. and Sonnhammer, E.L. (2004) Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun 319 (1) : 264-274.		PubMed

259	Kall, L., Krogh, A. and Sonnhammer, E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338 (5) : 1027-1036.		PubMed

260	Wistrand, M. and Sonnhammer, E.L. (2004) Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol 338 (4) : 847-854.		PubMed

261	Chalk, A.M., Wennerberg, M. and Sonnhammer, E.L. (2004) Sfixem--graphical sequence feature display in Java. Bioinformatics 20 (15) : 2488-2490.		PubMed

262	Wistrand, M. and Sonnhammer, E.L. (2004) transition priors for protein hidden Markov models: an empirical study towards maximum discrimination. J Comput Biol 11 (1) : 181-193.	Link to article	PubMed

263	Ekdahl, S. and Sonnhammer, E.L. (2004) ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics 20 (4) : 576-577.		PubMed

264	Wallner, B., Fang, H., Ohlson, T., Frey-Skott, J. and Elofsson, A. (2004) Using evolutionary information for the query and target improves fold recognition. Proteins 54 (2) : 342-350.	Link to article	PubMed

265	Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., Studholme, D.J., Yeats, C. and Eddy, S.R. (2004) The Pfam protein families database. Nucleic Acids Res 32 (Database issue) : D138-41.	Link to article	PubMed

266	Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad (2004) Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution RECOMB 8: 326 - 335.	Link to article


2003



267	McKay, S.J., Johnsen, R., Khattra, J., Asano, J., Baillie, D.L., Chan, S., Dube, N., Fang, L., Goszczynski, B., Ha, E., Halfnight, E., Hollebakken, R., Huang, P., Hung, K., Jensen, V., Jones, S.J., Kai, H., Li, D., Mah, A., Marra, M., McGhee, J., Newbury, R., Pouzyrev, A., Riddle, D.L., Sonnhammer, E., Tian, H., Tu, D., Tyson, J.R., Vatcher, G., Warner, A., Wong, K., Zhao, Z. and Moerman, D.G. (2003) Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol 68: 159-169.		PubMed

268	Hermansson, M. and von Heijne, G. (2003) Inter-helical hydrogen bond formation during membrane protein integration into the ER membrane. J Mol Biol 334 (4) : 803-809.		PubMed

269	Rychlewski, L., Fischer, D. and Elofsson, A. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins 53 Suppl 6: 542-547.	Link to article	PubMed

270	Wallner, B., Fang, H. and Elofsson, A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 53 Suppl 6: 534-541.	Link to article	PubMed

271	Fischer, D., Rychlewski, L., Dunbrack, Jr., R.L., Ortiz, A.R. and Elofsson, A. (2003) CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 53 Suppl 6: 503-516.	Link to article	PubMed

272	Storm, C.E. and Sonnhammer, E.L. (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13 (10) : 2353-2362.		PubMed

273	Westerlund, I., Von Heijne, G. and Emanuelsson, O. (2003) LumenP--a neural network predictor for protein localization in the thylakoid lumen. Protein Sci 12 (10) : 2360-2366.	Link to article	PubMed

274	Juncker, A.S., Willenbrock, H., Von Heijne, G., Brunak, S., Nielsen, H. and Krogh, A. (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12 (8) : 1652-1662.	Link to article	PubMed

275	Arvestad, L., Berglund, A.C., Lagergren, J. and Sennblad, B. (2003) Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19 Suppl 1: i7-15.		PubMed

276	Emanuelsson, O., Elofsson, A., von Heijne, G. and Cristobal, S. (2003) In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol 330 (2) : 443-456.		PubMed

277	Nilsson, I., Johnson, A.E. and von Heijne, G. (2003) How hydrophobic is alanine? J Biol Chem 278 (32) : 29389-29393.		PubMed

278	Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19 (8) : 1015-1018.		PubMed

279	Wallner, B. and Elofsson, A. (2003) Can correct protein models be identified? Protein Sci 12 (5) : 1073-1086.	Link to article	PubMed

280	Lee, J.M. and Sonnhammer, E.L. (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13 (5) : 875-882.		PubMed

281	Von Heijne, G. (2003) Membrane protein assembly in vivo. Adv Protein Chem 63: 1-18.		PubMed

282	Hessa, T., Monne, M. and von Heijne, G. (2003) Stop-transfer efficiency of marginally hydrophobic segments depends on the length of the carboxy-terminal tail. EMBO Rep 4 (2) : 178-183.		PubMed


2002



283	Chalk, A.M. and Sonnhammer, E.L. (2002) Computational antisense oligo prediction with a neural network model. Bioinformatics 18 (12) : 1567-1575.		PubMed

284	Kall, L. and Sonnhammer, E.L. (2002) Reliability of transmembrane predictions in whole-genome data. FEBS Lett 532 (3) : 415-418.		PubMed

285	Sonnhammer, E.L. and Koonin, E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18 (12) : 619-620.		PubMed

286	Nilsson, J., Persson, B. and Von Heijne, G. (2002) Prediction of partial membrane protein topologies using a consensus approach. Protein Sci 11 (12) : 2974-2980.	Link to article	PubMed

287	Lassmann, T. and Sonnhammer, E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett 529 (1) : 126-130.		PubMed

288	Donnes, P. and Elofsson, A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3: 25.		PubMed

289	Hollich, V., Storm, C.E. and Sonnhammer, E.L. (2002) OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics 18 (9) : 1272-1273.		PubMed

290	Milchert, L.E., Liberles, D.A. and Elofsson, A. (2002) The salmon genome (and other issues in bioinformatics). Genome Biol 3 (7) : REPORTS4022.		PubMed

291	Sennblad, B. and Bremer, B. (2002) Classification of apocynaceae s.l. according to a new approach combining Linnaean and phylogenetic taxonomy. Syst Biol 51 (3) : 389-409.	Link to article	PubMed

292	Blomqvist, G., Alvarsson, M., Grill, V., Von Heijne, G., Ingvar, M., Thorell, J.O., Stone-Elander, S., Widen, L. and Ekberg, K. (2002) Effect of acute hyperketonemia on the cerebral uptake of ketone bodies in nondiabetic subjects and IDDM patients. Am J Physiol Endocrinol Metab 283 (1) : E20-8.	Link to article	PubMed

293	Nilsson, I., Johnson, A.E. and von Heijne, G. (2002) Cleavage of a tail-anchored protein by signal peptidase. FEBS Lett 516 (1-3) : 106-108.		PubMed

294	Hedman, M., Deloof, H., Von Heijne, G. and Elofsson, A. (2002) Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci 11 (3) : 652-658.		PubMed

295	Storm, C.E. and Sonnhammer, E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18 (1) : 92-99.		PubMed

296	Elofsson, A. (2002) A study on protein sequence alignment quality. Proteins 46 (3) : 330-339.		PubMed

297	Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M. and Sonnhammer, E.L. (2002) The Pfam protein families database. Nucleic Acids Res 30 (1) : 276-280.	Link to article	PubMed

298	David A. Liberles, Anna Thoren, Gunnar von Heijne and Arne Elofsson (2002) The use of Phylogenetic profils for Gene Predictions Current Genomics 3: 131-138.	Link to article


2001



299	Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins Suppl 5: 184-191.		PubMed

300	Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortiz, A.R. and Dunbrack, Jr., R.L. (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins Suppl 5: 171-183.		PubMed

301	Remm, M., Storm, C.E. and Sonnhammer, E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314 (5) : 1041-1052.		PubMed

302	Hermansson, M., Monne, M. and von Heijne, G. (2001) Formation of helical hairpins during membrane protein integration into the endoplasmic reticulum membrane. Role of the N and C-terminal flanking regions. J Mol Biol 313 (5) : 1171-1179.		PubMed

303	Lundstrom, J., Rychlewski, L., Bujnicki, J. and Elofsson, A. (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 10 (11) : 2354-2362.		PubMed

304	Sonnhammer, E.L. and Wootton, J.C. (2001) Integrated graphical analysis of protein sequence features predicted from sequence composition. Proteins 45 (3) : 262-273.		PubMed

305	Cristobal, S., Zemla, A., Fischer, D., Rychlewski, L. and Elofsson, A. (2001) A study of quality measures for protein threading models. BMC Bioinformatics 2: 5.		PubMed

306	Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) Structure prediction meta server. Bioinformatics 17 (8) : 750-751.		PubMed

307	Podowski, R.M. and Sonnhammer, E.L. (2001) MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs. Bioinformatics 17 (7) : 656-657.		PubMed

308	Monne, M. and von Heijne, G. (2001) Effects of 'hydrophobic mismatch' on the location of transmembrane helices in the ER membrane. FEBS Lett 496 (2-3) : 96-100.		PubMed

309	Storm, C.E. and Sonnhammer, E.L. (2001) NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17 (4) : 343-348.		PubMed

310	Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci 10 (2) : 352-361.		PubMed

311	Saaf, A., Baars, L. and von Heijne, G. (2001) The internal repeats in the Na+/Ca2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. J Biol Chem 276 (22) : 18905-18907.		PubMed

312	Fang, H., Wallner, B. Lundström, J., von Wowern, C. and Elofsson, A. (2001) Improved fold recognition by using the Pcons consensus approach Chapter in “Protein structure prediction:Bioinformatic approach” IUL biotechnology Series, La Jolla, 1: 397-41.

313	Eriksson, O., Xhou, Y. and Elofsson, A. (2001) Side chain-positioning as an integer programming problem. WABI 1: 1-1.	Link to article