SBC Publications


2013



1	Skwark, M.J. and Elofsson, A. (Epub 2013) PconsD: Ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (Epub ahead of print)	Link to article	PubMed

2	Johansson, A.L., Hogbom, M., Carlsson, J., Gennis, R.B. and Brzezinski, P. (Epub 2013) Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase. Proc Natl Acad Sci U S A (Epub ahead of print)	Link to article	PubMed

3	Ojemalm, K., Botelho, S.C., Studle, C. and von Heijne, G. (Epub 2013) Quantitative Analysis of SecYEG-Mediated Insertion of Transmembrane alpha-Helices into the Bacterial Inner Membrane. J Mol Biol (Epub ahead of print)	Link to article	PubMed

4	Skwark, M.J., Abdel-Rehim, A. and Elofsson, A. (Epub 2013) PconsC: Combination of direct information methods and alignments improves contact prediction. Bioinformatics (Epub ahead of print)	Link to article	PubMed

5	Tjarnberg, A., Nordling, T.E., Studham, M. and Sonnhammer, E.L. (2013) Optimal sparsity criteria for network inference. J Comput Biol 20 (5) : 398-408.	Link to article	PubMed

6	Frings, O., Augsten, M., Tobin, N.P., Carlson, J., Paulsson, J., Pena, C., Olsson, E., Veerla, S., Bergh, J., Ostman, A. and Sonnhammer, E.L. (Epub 2013) Prognostic Significance in Breast Cancer of a Gene Signature Capturing Stromal PDGF Signaling. Am J Pathol (Epub ahead of print)	Link to article	PubMed

7	Light, S. and Elofsson, A. (Epub 2013) The impact of splicing on protein domain architecture. Curr Opin Struct Biol (Epub ahead of print)	Link to article	PubMed

8	Bendz, M., Skwark, M., Nilsson, D., Granholm, V., Cristobal, S., Kall, L. and Elofsson, A. (2013) Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics 13 (9) : 1467-1480.	Link to article	PubMed

9	Schreiber, F. and Sonnhammer, E.L. (2013) Hieranoid: hierarchical orthology inference. J Mol Biol 425 (11) : 2072-2081.	Link to article	PubMed

10	Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M.R., Smith, J.C., Kasson, P.M., van der Spoel, D., Hess, B. and Lindahl, E. (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29 (7) : 845-854.	Link to article	PubMed

11	Frings, O., Alexeyenko, A. and Sonnhammer, E.L. (Epub 2013) MGclus: network clustering employing shared neighbors. Mol Biosyst (Epub ahead of print)	Link to article	PubMed

12	Persson, F., Linden, M., Unoson, C. and Elf, J. (2013) Extracting intracellular diffusive states and transition rates from single-molecule tracking data. Nat Methods 10 (3) : 265-269.	Link to article	PubMed

13	McCormack, T., Frings, O., Alexeyenko, A. and Sonnhammer, E.L. (2013) Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks. PLoS One 8 (1) : e54945.	Link to article	PubMed

14	Light, S., Sagit, R., Ekman, D. and Elofsson, A. (2013) Long indels are disordered: A study of disorder and indels in homologous eukaryotic proteins. Biochim Biophys Acta 1834 (5) : 890-897.	Link to article	PubMed

15	Kasson, P.M., Hess, B. and Lindahl, E. (Epub 2013) Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions. Chem Phys Lipids (Epub ahead of print) 169: 106-112.	Link to article	PubMed

16	Johansson, A.L., Carlsson, J., Hogbom, M., Hosler, J.P., Gennis, R.B. and Brzezinski, P. (2013) Proton Uptake and pK(a) Changes in the Uncoupled Asn139Cys Variant of Cytochrome c Oxidase. Biochemistry 52 (5) : 827-836.	Link to article	PubMed

17	Botelho, S.C., Tatsuta, T., von Heijne, G. and Kim, H. (2013) Dislocation by the m-AAA Protease Increases the Threshold Hydrophobicity for Retention of Transmembrane Helices in the Inner Membrane of Yeast Mitochondria. J Biol Chem 288 (7) : 4792-4798.	Link to article	PubMed

18	Jurkowski, W., Yazdi, S. and Elofsson, A. (2013) Ligand binding properties of human galanin receptors. Mol Membr Biol 30 (2) : 206-216.	Link to article	PubMed

19	Bano-Polo, M., Martinez-Gil, L., Wallner, B., Nieva, J.L., Elofsson, A. and Mingarro, I. (2013) Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. J Mol Biol 425 (4) : 830-840.	Link to article	PubMed

20	Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A. and Horton, P. (2013) Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods Mol Biol 939: 115-140.	Link to article	PubMed

21	Paulsen, P.A., Jurkowski, W., Apostolov, R., Lindahl, E., Nissen, P. and Poulsen, H. (Epub 2013) The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology. Mol Membr Biol (Epub ahead of print) 30 (2) : 195-205.	Link to article	PubMed


2012



22	Carlsson, J., Tosh, D.K., Phan, K., Gao, Z.G. and Jacobson, K.A. (2012) Structure-activity relationships and molecular modeling of 1,2,4-triazoles as adenosine receptor antagonists. ACS Med Chem Lett 3 (9) : 715-720.	Link to article	PubMed

23	Frings, O., Mank, J.E., Alexeyenko, A. and Sonnhammer, E.L. (2012) Network analysis of functional genomics data: application to avian sex-biased gene expression. ScientificWorldJournal 2012: 130491.	Link to article	PubMed

24	Granholm, V., Navarro, J.F., Noble, W.S. and Kall, L. (2012) Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics. J Proteomics 80C: 123-131.	Link to article	PubMed

25	Lindahl, E. (2012) Unraveling the strokes of ion channel molecular machines in computers. Proc Natl Acad Sci U S A 109 (52) : 21186-21187.	Link to article	PubMed

26	Granholm, V., Noble, W.S. and Kall, L. (2012) A cross-validation scheme for machine learning algorithms in shotgun proteomics. BMC Bioinformatics 13 Suppl 16: S3.	Link to article	PubMed

27	Serang, O., Moruz, L., Hoopmann, M.R. and Kall, L. (2012) Recognizing Uncertainty Increases Robustness and Reproducibility of Mass Spectrometry-based Protein Inferences. J Proteome Res 11 (12) : 5586-5591.	Link to article	PubMed

28	Schwaiger, C.S., Borjesson, S.I., Hess, B., Wallner, B., Elinder, F. and Lindahl, E. (2012) The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain. PLoS One 7 (10) : e45880.	Link to article	PubMed

29	Murail, S., Howard, R.J., Broemstrup, T., Bertaccini, E.J., Harris, R.A., Trudell, J.R. and Lindahl, E. (2012) Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. PLoS Comput Biol 8 (10) : e1002710.	Link to article	PubMed

30	Lee, H., Min, J., von Heijne, G. and Kim, H. (2012) Glycosylatable GFP as a compartment-specific membrane topology reporter. Biochem Biophys Res Commun 427 (4) : 780-784.	Link to article	PubMed

31	Ismail, N., Hedman, R., Schiller, N. and von Heijne, G. (2012) A biphasic pulling force acts on transmembrane helices during translocon-mediated membrane integration. Nat Struct Mol Biol 19 (10) : 1018-1022.	Link to article	PubMed

32	Sahlin, K., Street, N., Lundeberg, J. and Arvestad, L. (2012) Improved gap size estimation for scaffolding algorithms. Bioinformatics 28 (17) : 2215-2222.	Link to article	PubMed

33	Toddo, S., Soderstrom, B., Palombo, I., von Heijne, G., Norholm, M.H. and Daley, D.O. (2012) Application of split-green fluorescent protein for topology mapping membrane proteins in Escherichia coli. Protein Sci 21 (10) : 1571-1576.	Link to article	PubMed

34	Johnson, S., Linden, M. and Phillips, R. (2012) Sequence dependence of transcription factor-mediated DNA looping. Nucleic Acids Res 40 (16) : 7728-7738.	Link to article	PubMed

35	Lloris-Garcera, P., Bianchi, F., Slusky, J.S., Seppala, S., Daley, D.O. and von Heijne, G. (2012) Antiparallel Dimers of the Small Multidrug Resistance Protein EmrE Are More Stable Than Parallel Dimers. J Biol Chem 287 (31) : 26052-26059.	Link to article	PubMed

36	Hayat, S. and Elofsson, A. (2012) Ranking models of transmembrane beta-barrel proteins using Z-coordinate predictions. Bioinformatics 28 (12) : i90-i96.	Link to article	PubMed

37	Tsirigos, K.D., Hennerdal, A., Kall, L. and Elofsson, A. (2012) A guideline to proteome-wide alpha-helical membrane protein topology predictions. Proteomics 12 (14) : 2282-2294.	Link to article	PubMed

38	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

39	Henrion, U., Renhorn, J., Borjesson, S.I., Nelson, E.M., Schwaiger, C.S., Bjelkmar, P., Wallner, B., Lindahl, E. and Elinder, F. (2012) Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci U S A 109 (22) : 8552-8557.	Link to article	PubMed

40	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. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21 (6) : 769-785.	Link to article	PubMed

41	Wright, J.C., Collins, M.O., Yu, L., Kall, L., Brosch, M. and Choudhary, J.S. (2012) Enhanced Peptide identification by electron transfer dissociation using an improved mascot percolator. Mol Cell Proteomics 11 (8) : 478-491.	Link to article	PubMed

42	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. (2012) Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. ChemMedChem 7 (10) : 1775-1783.	Link to article	PubMed

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

44	Galian, C., Bjorkholm, P., Bulleid, N. and von Heijne, G. (2012) Efficient glycosylphosphatidylinositol (GPI) modification of membrane proteins requires a C-terminal anchoring signal of marginal hydrophobicity. J Biol Chem 287 (20) : 16399-16409.	Link to article	PubMed

45	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) 179 (3) : 289-298.	Link to article	PubMed

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

47	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

48	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

49	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

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

51	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

52	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

53	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

54	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

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


2011



56	Kall, L. and Vitek, O. (2011) Computational mass spectrometry-based proteomics. PLoS Comput Biol 7 (12) : e1002277.	Link to article	PubMed

57	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

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

59	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

60	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

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

62	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

63	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

64	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

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

66	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

67	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

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

69	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

70	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

71	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

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

73	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

74	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

75	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

76	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

77	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



78	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

79	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

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

81	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

82	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

83	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

84	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

85	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

86	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

87	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

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

89	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

90	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

91	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

92	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

93	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

94	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

95	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

96	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

97	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

98	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

99	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

100	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

101	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

102	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

103	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

104	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

105	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

106	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

107	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

108	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



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

110	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

111	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

112	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

113	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

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

115	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

116	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

117	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

118	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

119	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

120	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

121	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

122	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

123	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

124	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

125	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

126	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

127	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

128	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

129	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

130	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

131	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

132	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

133	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

134	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

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

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

137	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



138	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

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

140	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

141	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

142	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

143	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

144	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

145	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

146	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

147	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

148	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

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

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

151	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

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

153	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

154	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

155	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

156	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

157	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

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

159	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

160	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

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

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

163	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

164	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

165	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

166	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

167	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

168	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

169	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

170	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

171	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

172	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

173	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

174	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

175	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

176	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

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


2007



178	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

179	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

180	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

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

182	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

183	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

184	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

185	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

186	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

187	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

188	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

189	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

190	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

191	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

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

193	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

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

195	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

196	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

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

198	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

199	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

200	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

201	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

202	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

203	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

204	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

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

206	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

207	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

208	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

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


2006



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

211	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

212	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

213	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

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

215	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

216	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

217	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

218	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

219	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

220	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

221	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

222	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

223	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

224	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

225	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

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

227	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

228	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

229	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

230	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

231	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

232	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

233	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

234	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

235	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

236	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

237	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

238	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

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

240	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.

241	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



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

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

244	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

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

246	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

247	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

248	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

249	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

250	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

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

252	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

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

254	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

255	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

256	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

257	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

258	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

259	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

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

261	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

262	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

263	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

264	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

265	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

266	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

267	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

268	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

269	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

270	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

271	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

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

273	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

274	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

275	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

276	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

277	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

278	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

279	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

280	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

281	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

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

283	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

284	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

285	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

286	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

287	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



288	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

289	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

290	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

291	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

292	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

293	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

294	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

295	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

296	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

297	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

298	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

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

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

301	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

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

303	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

304	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

305	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



306	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

307	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

308	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

309	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

310	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

311	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

312	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

313	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

314	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

315	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

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

317	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

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

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

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

321	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



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

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

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

325	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

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

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

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

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

330	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

331	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

332	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

333	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

334	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

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

336	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

337	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



338	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

339	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

340	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

341	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

342	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

343	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

344	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

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

346	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

347	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

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

349	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

350	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

351	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.

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