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SBC Publications


2017
1Su, T., Cheng, J., Sohmen, D., Hedman, R., Berninghausen, O., von Heijne, G., Wilson, D.N. and Beckmann, R. (2017) The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. Elife 6 Link to
article
PubMed
2Michel, M., Skwark, M.J., Menendez Hurtado, D., Ekeberg, M. and Elofsson, A. (Epub 2017) Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinformatics (Epub ahead of print)  Link to
article
PubMed
3Renault, H., De Marothy, M., Jonasson, G., Lara, P., Nelson, D.R., Nilsson, I., Andre, F., von Heijne, G. and Werck-Reichhart, D. (Epub 2017) Gene duplication leads to altered membrane topology of a cytochrome P450 enzyme in seed plants. Mol Biol Evol (Epub ahead of print)  Link to
article
PubMed
4Tjarnberg, A., Morgan, D.C., Studham, M., Nordling, T.E.M. and Sonnhammer, E.L.L. (Epub 2017) GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties. Mol Biosyst (Epub ahead of print)  Link to
article
PubMed
5Guala, D. and Sonnhammer, E.L.L. (2017) A large-scale benchmark of gene prioritization methods. Sci Rep 7: 46598. Link to
article
PubMed
6Ulmschneider, M.B., Ulmschneider, J.P., Freites, J.A., von Heijne, G., Tobias, D.J. and White, S.H. (Epub 2017) Transmembrane helices containing a charged arginine are thermodynamically stable. Eur Biophys J (Epub ahead of print)  Link to
article
PubMed
7Salvatore, M., Warholm, P., Shu, N., Basile, W. and Elofsson, A. (Epub 2017) SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinformatics (Epub ahead of print)  Link to
article
PubMed
8Basile, W., Sachenkova, O., Light, S. and Elofsson, A. (2017) High GC content causes orphan proteins to be intrinsically disordered. PLoS Comput Biol 13 (3) : e1005375. Link to
article
PubMed
9Nilsson, O.B., Nickson, A.A., Hollins, J.J., Wickles, S., Steward, A., Beckmann, R., von Heijne, G. and Clarke, J. (2017) Cotranslational folding of spectrin domains via partially structured states. Nat Struct Mol Biol 24 (3) : 221-225. Link to
article
PubMed
10Dimou, N.L., Tsirigos, K.D., Elofsson, A. and Bagos, P.G. (2017) GWAR: robust analysis and meta-analysis of genome-wide association studies. Bioinformatics 33 (10) : 1521-1527. Link to
article
PubMed
11Kaduk, M. and Sonnhammer, E. (2017) Improved orthology inference with Hieranoid 2. Bioinformatics 33 (8) : 1154-1159. Link to
article
PubMed
12Sennblad, B., Basu, S., Mazur, J., Suchon, P., Martinez-Perez, A., van Hylckama Vlieg, A., Truong, V., Li, Y., Gadin, J.R., Tang, W., Grossman, V., de Haan, H.G., Handin, N., Silveira, A., Souto, J.C., Franco-Cereceda, A., Morange, P.E., Gagnon, F., Soria, J.M., Eriksson, P., Hamsten, A., Maegdefessel, L., Rosendaal, F.R., Wild, P., Folsom, A.R., Tregouet, D.A. and Sabater-Lleal, M. (2017) Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels. Hum Mol Genet 26 (3) : 637-649. Link to
article
PubMed
13Uziela, K., Menendez Hurtado, D., Shu, N., Wallner, B. and Elofsson, A. (2017) ProQ3D: improved model quality assessments using deep learning. Bioinformatics 33 (10) : 1578-1580. Link to
article
PubMed
14Ranganathan, A., Heine, P., Rudling, A., Pluckthun, A., Kummer, L. and Carlsson, J. (2017) Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries. ACS Chem Biol 12 (3) : 735-745. Link to
article
PubMed
15Farias-Rico, J.A., Goetz, S.K., Marino, J. and von Heijne, G. (2017) Mutational analysis of protein folding inside the ribosome exit tunnel. FEBS Lett 591 (1) : 155-163. Link to
article
PubMed
16Piovesan, D., Tabaro, F., Micetic, I., Necci, M., Quaglia, F., Oldfield, C.J., Aspromonte, M.C., Davey, N.E., Davidovic, R., Dosztanyi, Z., Elofsson, A., Gasparini, A., Hatos, A., Kajava, A.V., Kalmar, L., Leonardi, E., Lazar, T., Macedo-Ribeiro, S., Macossay-Castillo, M., Meszaros, A., Minervini, G., Murvai, N., Pujols, J., Roche, D.B., Salladini, E., Schad, E., Schramm, A., Szabo, B., Tantos, A., Tonello, F., Tsirigos, K.D., Veljkovic, N., Ventura, S., Vranken, W., Warholm, P., Uversky, V.N., Dunker, A.K., Longhi, S., Tompa, P. and Tosatto, S.C. (2017) DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 45 (D1) : D219-D227. Link to
article
PubMed
17Kaduk, M., Riegler, C., Lemp, O. and Sonnhammer, E.L. (2017) HieranoiDB: a database of orthologs inferred by Hieranoid. Nucleic Acids Res 45 (D1) : D687-D690. Link to
article
PubMed
18Ogris, C., Guala, D., Helleday, T. and Sonnhammer, E.L. (2017) A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation. Nucleic Acids Res 45 (2) : e8. Link to
article
PubMed

2016
19Kimanius, D., Forsberg, B.O., Scheres, S.H. and Lindahl, E. (2016) Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife 5 Link to
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PubMed
20Nys, M., Wijckmans, E., Farinha, A., Yoluk, O., Andersson, M., Brams, M., Spurny, R., Peigneur, S., Tytgat, J., Lindahl, E. and Ulens, C. (2016) Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine. Proc Natl Acad Sci U S A 113 (43) : E6696-E6703. Link to
article
PubMed
21Uziela, K., Shu, N., Wallner, B. and Elofsson, A. (2016) ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep 6: 33509. Link to
article
PubMed
22Mishima, E., Sato, Y., Nanatani, K., Hoshi, N., Lee, J.K., Schiller, N., von Heijne, G., Sakaguchi, M. and Uozumi, N. (2016) The topogenic function of S4 promotes membrane insertion of the voltage-sensor domain in the KvAP channel. Biochem J 473 (23) : 4361-4372. Link to
article
PubMed
23Stone, T.A., Schiller, N., Workewych, N., von Heijne, G. and Deber, C.M. (2016) Hydrophobic Clusters Raise the Threshold Hydrophilicity for Insertion of Transmembrane Sequences in Vivo. Biochemistry 55 (40) : 5772-5779. Link to
article
PubMed
24Ojemalm, K., Higuchi, T., Lara, P., Lindahl, E., Suga, H. and von Heijne, G. (2016) Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids. Proc Natl Acad Sci U S A 113 (38) : 10559-10564. Link to
article
PubMed
25Tsirigos, K.D., Elofsson, A. and Bagos, P.G. (2016) PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics 32 (17) : i665-i671. Link to
article
PubMed
26Schibich, D., Gloge, F., Pohner, I., Bjorkholm, P., Wade, R.C., von Heijne, G., Bukau, B. and Kramer, G. (2016) Global profiling of SRP interaction with nascent polypeptides. Nature 536 (7615) : 219-223. Link to
article
PubMed
27Rodriguez, D., Chakraborty, S., Warnick, E., Crane, S., Gao, Z.G., O'Connor, R., Jacobson, K.A. and Carlsson, J. (2016) Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. ACS Chem Biol 11 (10) : 2763-2772. Link to
article
PubMed
28Martyna, A., Gomez-Llobregat, J., Linden, M. and Rossman, J.S. (2016) Curvature Sensing by a Viral Scission Protein. Biochemistry 55 (25) : 3493-3496. Link to
article
PubMed
29Conti, L., Renhorn, J., Gabrielsson, A., Turesson, F., Liin, S.I., Lindahl, E. and Elinder, F. (2016) Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation. Sci Rep 6: 27562. Link to
article
PubMed
30Saripella, G.V., Sonnhammer, E.L. and Forslund, K. (2016) Benchmarking the next generation of homology inference tools. Bioinformatics 32 (17) : 2636-2641. Link to
article
PubMed
31Haider, C., Kavic, M. and Sonnhammer, E.L. (2016) TreeDom: a graphical web tool for analysing domain architecture evolution. Bioinformatics 32 (15) : 2384-2385. Link to
article
PubMed
32Ogris, C., Helleday, T. and Sonnhammer, E.L. (2016) PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res 44 (W1) : W105-W109. Link to
article
PubMed
33Heusser, S.A., Yoluk, O., Klement, G., Riederer, E.A., Lindahl, E. and Howard, R.J. (2016) Functional characterization of neurotransmitter activation and modulation in a nematode model ligand-gated ion channel. J Neurochem 138 (2) : 243-253. Link to
article
PubMed
34Soderstrom, B., Mirzadeh, K., Toddo, S., von Heijne, G., Skoglund, U. and Daley, D.O. (2016) Coordinated disassembly of the divisome complex in Escherichia coli. Mol Microbiol 101 (3) : 425-438. Link to
article
PubMed
35Altenhoff, A.M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D.A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L.P., Schreiber, F., da Silva, A.S., Szklarczyk, D., Train, C.M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjolander, K., Jensen, L.J., Martin, M.J., Muffato, M. and {Quest for Orthologs consortium (2016) Standardized benchmarking in the quest for orthologs. Nat Methods 13 (5) : 425-430. Link to
article
PubMed
36Nilsson, O.B., Muller-Lucks, A., Kramer, G., Bukau, B. and von Heijne, G. (2016) Trigger Factor Reduces the Force Exerted on the Nascent Chain by a Cotranslationally Folding Protein. J Mol Biol 428 (6) : 1356-1364. Link to
article
PubMed
37Marino, J., von Heijne, G. and Beckmann, R. (2016) Small protein domains fold inside the ribosome exit tunnel. FEBS Lett 590 (5) : 655-660. Link to
article
PubMed
38Beerenwinkel, N., Greenman, C.D. and Lagergren, J. (2016) Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput Biol 12 (2) : e1004717. Link to
article
PubMed
39Hayat, S., Peters, C., Shu, N., Tsirigos, K.D. and Elofsson, A. (2016) Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins. Bioinformatics 32 (10) : 1571-1573. Link to
article
PubMed
40Yazdi, S., Stein, M., Elinder, F., Andersson, M. and Lindahl, E. (2016) The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. PLoS Comput Biol 12 (1) : e1004704. Link to
article
PubMed
41Gomez-Llobregat, J., Elias-Wolff, F. and Linden, M. (2016) Anisotropic Membrane Curvature Sensing by Amphipathic Peptides. Biophys J 110 (1) : 197-204. Link to
article
PubMed
42Uziela, K. and Wallner, B. (2016) ProQ2: estimation of model accuracy implemented in Rosetta. Bioinformatics 32 (9) : 1411-1413. Link to
article
PubMed
43Peters, C., Tsirigos, K.D., Shu, N. and Elofsson, A. (2016) Improved topology prediction using the terminal hydrophobic helices rule. Bioinformatics 32 (8) : 1158-1162. Link to
article
PubMed

2015
44Ranganathan, A., Stoddart, L.A., Hill, S.J. and Carlsson, J. (2015) Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models. J Med Chem 58 (24) : 9578-9590. Link to
article
PubMed
45Wennberg, C.L., Murtola, T., Pall, S., Abraham, M.J., Hess, B. and Lindahl, E. (2015) Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation. J Chem Theory Comput 11 (12) : 5737-5746. Link to
article
PubMed
46Kimanius, D., Pettersson, I., Schluckebier, G., Lindahl, E. and Andersson, M. (2015) SAXS-Guided Metadynamics. J Chem Theory Comput 11 (7) : 3491-3498. Link to
article
PubMed
47Pronk, S., Pouya, I., Lundborg, M., Rotskoff, G., Wesen, B., Kasson, P.M. and Lindahl, E. (2015) Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform. J Chem Theory Comput 11 (6) : 2600-2608. Link to
article
PubMed
48Mahmudi, O., Sennblad, B., Arvestad, L., Nowick, K. and Lagergren, J. (2015) Gene-pseudogene evolution: a probabilistic approach. BMC Genomics 16 Suppl 10: S12. Link to
article
PubMed
49Shiota, T., Imai, K., Qiu, J., Hewitt, V.L., Tan, K., Shen, H.H., Sakiyama, N., Fukasawa, Y., Hayat, S., Kamiya, M., Elofsson, A., Tomii, K., Horton, P., Wiedemann, N., Pfanner, N., Lithgow, T. and Endo, T. (2015) Molecular architecture of the active mitochondrial protein gate. Science 349 (6255) : 1544-1548. Link to
article
PubMed
50Nilsson, O.B., Hedman, R., Marino, J., Wickles, S., Bischoff, L., Johansson, M., Muller-Lucks, A., Trovato, F., Puglisi, J.D., O'Brien, E.P., Beckmann, R. and von Heijne, G. (2015) Cotranslational Protein Folding inside the Ribosome Exit Tunnel. Cell Rep 12 (10) : 1533-1540. Link to
article
PubMed
51Ullah, I., Sjostrand, J., Andersson, P., Sennblad, B. and Lagergren, J. (2015) Integrating Sequence Evolution into Probabilistic Orthology Analysis. Syst Biol 64 (6) : 969-982. Link to
article
PubMed
52Rodriguez, D., Ranganathan, A. and Carlsson, J. (2015) Discovery of GPCR Ligands by Molecular Docking Screening: Novel Opportunities Provided by Crystal Structures. Curr Top Med Chem 15 (24) : 2484-2503.  PubMed
53Daniel, C., Lagergren, J. and Ohman, M. (2015) RNA editing of non-coding RNA and its role in gene regulation. Biochimie 117: 22-27. Link to
article
PubMed
54Yoluk, O., Lindahl, E. and Andersson, M. (2015) Conformational Gating Dynamics in the GluCl Anion-Selective Chloride Channel. ACS Chem Neurosci 6 (8) : 1459-1467. Link to
article
PubMed
55De Marothy, M.T. and Elofsson, A. (2015) Marginally hydrophobic transmembrane alpha-helices shaping membrane protein folding. Protein Sci 24 (7) : 1057-1074. Link to
article
PubMed
56Tsirigos, K.D., Peters, C., Shu, N., Kall, L. and Elofsson, A. (2015) The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res 43 (W1) : W401-W407. Link to
article
PubMed
57Ullah, I., Parviainen, P. and Lagergren, J. (2015) Species Tree Inference Using a Mixture Model. Mol Biol Evol 32 (9) : 2469-2482. Link to
article
PubMed
58Mirzadeh, K., Martinez, V., Toddo, S., Guntur, S., Herrgard, M.J., Elofsson, A., Norholm, M.H. and Daley, D.O. (2015) Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. ACS Synth Biol 4 (9) : 959-965. Link to
article
PubMed
59Hayat, S., Sander, C., Marks, D.S. and Elofsson, A. (2015) All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences. Proc Natl Acad Sci U S A 112 (17) : 5413-5418. Link to
article
PubMed
60Goel, S., Palmkvist, M., Moll, K., Joannin, N., Lara, P., R Akhouri, R., Moradi, N., Ojemalm, K., Westman, M., Angeletti, D., Kjellin, H., Lehtio, J., Blixt, O., Idestrom, L., Gahmberg, C.G., Storry, J.R., Hult, A.K., Olsson, M.L., von Heijne, G., Nilsson, I. and Wahlgren, M. (2015) RIFINs are adhesins implicated in severe Plasmodium falciparum malaria. Nat Med 21 (4) : 314-317. Link to
article
PubMed
61Cymer, F., Hedman, R., Ismail, N. and von Heijne, G. (2015) Exploration of the Arrest Peptide Sequence Space Reveals Arrest-enhanced Variants. J Biol Chem 290 (16) : 10208-10215. Link to
article
PubMed
62Stone, T.A., Schiller, N., von Heijne, G. and Deber, C.M. (2015) Hydrophobic blocks facilitate lipid compatibility and translocon recognition of transmembrane protein sequences. Biochemistry 54 (7) : 1465-1473. Link to
article
PubMed
63Rodriguez, D., Gao, Z.G., Moss, S.M., Jacobson, K.A. and Carlsson, J. (2015) Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A2A Adenosine Receptor. J Chem Inf Model 55 (3) : 550-563. Link to
article
PubMed
64Uhlen, M., Fagerberg, L., Hallstrom, B.M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, A., Kampf, C., Sjostedt, E., Asplund, A., Olsson, I., Edlund, K., Lundberg, E., Navani, S., Szigyarto, C.A., Odeberg, J., Djureinovic, D., Takanen, J.O., Hober, S., Alm, T., Edqvist, P.H., Berling, H., Tegel, H., Mulder, J., Rockberg, J., Nilsson, P., Schwenk, J.M., Hamsten, M., von Feilitzen, K., Forsberg, M., Persson, L., Johansson, F., Zwahlen, M., von Heijne, G., Nielsen, J. and Ponten, F. (2015) Proteomics. Tissue-based map of the human proteome. Science 347 (6220) : 1260419. Link to
article
PubMed
65Ismail, N., Hedman, R., Linden, M. and von Heijne, G. (2015) Charge-driven dynamics of nascent-chain movement through the SecYEG translocon. Nat Struct Mol Biol 22 (2) : 145-149. Link to
article
PubMed
66Sonnhammer, E.L. and Ostlund, G. (2015) InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res 43 (Database issue) : D234-9. Link to
article
PubMed
67Tjarnberg, A., Nordling, T.E., Studham, M., Nelander, S. and Sonnhammer, E.L. (2015) Avoiding pitfalls in L1-regularised inference of gene networks. Mol Biosyst 11 (1) : 287-296. Link to
article
PubMed
68Lundborg, M. and Lindahl, E. (2015) Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations. J Phys Chem B 119 (3) : 810-823. Link to
article
PubMed
69Lindahl, E. (2015) Molecular dynamics simulations. Methods Mol Biol 1215: 3-26. Link to
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PubMed
70Vargas-Uribe, M., Rodnin, M.V., Ojemalm, K., Holgado, A., Kyrychenko, A., Nilsson, I., Posokhov, Y.O., Makhatadze, G., von Heijne, G. and Ladokhin, A.S. (2015) Thermodynamics of Membrane Insertion and Refolding of the Diphtheria Toxin T-Domain. J Membr Biol 248 (3) : 383-394. Link to
article
PubMed
71Cymer, F., von Heijne, G. and White, S.H. (2015) Mechanisms of Integral Membrane Protein Insertion and Folding. J Mol Biol 427 (5) : 999-1022. Link to
article
PubMed
72Norholm, M.H., von Heijne, G. and Draheim, R.R. (2015) Forcing the issue: aromatic tuning facilitates stimulus-independent modulation of a two-component signaling circuit. ACS Synth Biol 4 (4) : 474-481. Link to
article
PubMed
73Nilsson, I., Lara, P., Hessa, T., Johnson, A.E., von Heijne, G. and Karamyshev, A.L. (2015) The Code for Directing Proteins for Translocation across ER Membrane: SRP Cotranslationally Recognizes Specific Features of a Signal Sequence. J Mol Biol 427 (6 Pt A) : 1191-1201. Link to
article
PubMed

2014
74Botelho, S.C., Enquist, K., von Heijne, G. and Draheim, R.R. (2014) Differential repositioning of the second transmembrane helices from E. coli Tar and EnvZ upon moving the flanking aromatic residues. Biochim Biophys Acta 1848 (2) : 615-621. Link to
article
PubMed
75Skwark, M.J., Raimondi, D., Michel, M. and Elofsson, A. (2014) Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol 10 (11) : e1003889. Link to
article
PubMed
76Ranganathan, A., Dror, R.O. and Carlsson, J. (2014) Insights into the Role of Asp79(2.50) in beta2 Adrenergic Receptor Activation from Molecular Dynamics Simulations. Biochemistry 53 (46) : 7283-7296. Link to
article
PubMed
77Kutsenko, A., Svensson, T., Nystedt, B., Lundeberg, J., Bjork, P., Sonnhammer, E., Giacomello, S., Visa, N. and Wieslander, L. (2014) The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 15 (1) : 819. Link to
article
PubMed
78Ulmschneider, M.B., Ulmschneider, J.P., Schiller, N., Wallace, B.A., von Heijne, G. and White, S.H. (2014) Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion. Nat Commun 5: 4863. Link to
article
PubMed
79Michel, M., Hayat, S., Skwark, M.J., Sander, C., Marks, D.S. and Elofsson, A. (2014) PconsFold: improved contact predictions improve protein models. Bioinformatics 30 (17) : i482-i488. Link to
article
PubMed
80Borroto-Escuela, D.O., Narvaez, M., Di Palma, M., Calvo, F., Rodriguez, D., Millon, C., Carlsson, J., Agnati, L.F., Garriga, P., Diaz-Cabiale, Z. and Fuxe, K. (2014) Preferential activation by galanin 1-15 fragment of the GalR1 protomer of a GalR1-GalR2 heteroreceptor complex. Biochem Biophys Res Commun 452 (3) : 347-353. Link to
article
PubMed
81Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J. and Arvestad, L. (2014) BESST - Efficient scaffolding of large fragmented assemblies. BMC Bioinformatics 15 (1) : 281. Link to
article
PubMed
82Johnson, S., van de Meent, J.W., Phillips, R., Wiggins, C.H. and Linden, M. (2014) Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion. Nucleic Acids Res 42 (16) : 10265-10277. Link to
article
PubMed
83Sonnhammer, E.L., Gabaldon, T., Sousa da Silva, A.W., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P.D., Dessimoz, C. and {Quest for Orthologs consortium (2014) Big data and other challenges in the quest for orthologs. Bioinformatics 30 (21) : 2993-2998. Link to
article
PubMed
84Rodriguez, D., Brea, J., Loza, M.I. and Carlsson, J. (2014) Structure-Based Discovery of Selective Serotonin 5-HT1B Receptor Ligands. Structure 22 (8) : 1140-1151. Link to
article
PubMed
85Rodriguez, D., Ranganathan, A. and Carlsson, J. (2014) Strategies for Improved Modeling of GPCR-Drug Complexes: Blind Predictions of Serotonin Receptors Bound to Ergotamine. J Chem Inf Model 54 (7) : 2004-2021. Link to
article
PubMed
86Ge, C., Gomez-Llobregat, J., Skwark, M.J., Ruysschaert, J.M., Wieslander, A. and Linden, M. (2014) Membrane remodeling capacity of a vesicle-inducing glycosyltransferase. FEBS J 281 (16) : 3667-3684. Link to
article
PubMed
87Light, S., Basile, W. and Elofsson, A. (2014) Orphans and new gene origination, a structural and evolutionary perspective. Curr Opin Struct Biol 26C: 73-83. Link to
article
PubMed
88Studham, M.E., Tjarnberg, A., Nordling, T.E., Nelander, S. and Sonnhammer, E.L. (2014) Functional association networks as priors for gene regulatory network inference. Bioinformatics 30 (12) : i130-i138. Link to
article
PubMed
89Virkki, M.T., Peters, C., Nilsson, D., Sorensen, T., Cristobal, S., Wallner, B. and Elofsson, A. (2014) The positive inside rule is stronger when followed by a transmembrane helix. J Mol Biol 426 (16) : 2982-2991. Link to
article
PubMed
90Guala, D., Sjolund, E. and Sonnhammer, E.L. (2014) MaxLink: network-based prioritization of genes tightly linked to a disease seed set. Bioinformatics 30 (18) : 2689-2690. Link to
article
PubMed
91Bjorkholm, P., Ernst, A.M., Hacke, M., Wieland, F., Brugger, B. and von Heijne, G. (2014) Identification of novel sphingolipid-binding motifs in mammalian membrane proteins. Biochim Biophys Acta 1838 (8) : 2066-2070. Link to
article
PubMed
92Virkki, M., Boekel, C., Illergard, K., Peters, C., Shu, N., Tsirigos, K.D., Elofsson, A., von Heijne, G. and Nilsson, I. (2014) Large Tilts in Transmembrane Helices Can Be Induced during Tertiary Structure Formation. J Mol Biol 426 (13) : 2529-2538. Link to
article
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187von Heijne, G. (2011) Introduction to theme "membrane protein folding and insertion". Annu Rev Biochem 80: 157-160. Link to
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188Schmitt, 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
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189Norholm, 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
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190Ojemalm, 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
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191von Heijne, G. (2011) Membrane proteins: from bench to bits. Biochem Soc Trans 39 (3) : 747-750. Link to
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192Forslund, 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
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193Shu, N. and Elofsson, A. (2011) KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics 27 (12) : 1702-1703. Link to
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194Hennerdal, A. and Elofsson, A. (2011) Rapid membrane protein topology prediction. Bioinformatics 27 (9) : 1322-1323. Link to
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195Osterberg, 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
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196Granholm, 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
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197Linder, 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
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198Granholm, V. and Kall, L. (2011) Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 11 (6) : 1086-1093. Link to
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199Kasson, 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
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200Botelho, 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
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201Norholm, 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
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202Larsson, 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
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203Illergard, K., Kauko, A. and Elofsson, A. (2011) Why are polar residues within the membrane core evolutionary conserved? Proteins 79 (1) : 79-91. Link to
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2010
204Bertaccini, 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
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205Lima, 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
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206Ray, A., Lindahl, E. and Wallner, B. (2010) Model quality assessment for membrane proteins. Bioinformatics 26 (24) : 3067-3074. Link to
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207Hennerdal, 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
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208Kall, L. (2010) Prediction of transmembrane topology and signal peptide given a protein's amino acid sequence. Methods Mol Biol 673: 53-62. Link to
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209Runesson, 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
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210Larsson, 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
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211Lind, 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
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212Moruz, 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
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213Bjorklund, 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
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214Henricson, A., Forslund, K. and Sonnhammer, E.L. (2010) Orthology confers intron position conservation. BMC Genomics 11 (1) : 412. Link to
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215Kasson, 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
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216Illergard, 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
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217Frygelius, 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
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218Seppala, 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
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219Stranneheim, 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
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220Niemela, 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
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221Alexeyenko, 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
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222Fagerberg, 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
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223Stromqvist, 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
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224Sehat, 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
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225Kauko, 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
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226Enstero, 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
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227Jornvall, 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
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228Sakata, 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
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229Ostlund, G., Lindskog, M. and Sonnhammer, E.L. (2010) Network-based Identification of Novel Cancer Genes. Mol Cell Proteomics 9 (4) : 648-655. Link to
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230Ekman, D. and Elofsson, A. (2010) Identifying and Quantifying Orphan Protein Sequences in Fungi. J Mol Biol 396 (2) : 396-405. Link to
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231Daniels, 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
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232Hedin, 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
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233Finn, 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
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234Ostlund, 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
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2009
235Sennblad, B. and Lagergren, J. (2009) Probabilistic Orthology Analysis. Syst Biol 58 (4) : 411-424. Link to
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236Johansson, 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
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237Klammer, 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
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238Gabaldon, 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
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239Bjorkholm, P. and Sonnhammer, E.L. (2009) Comparative analysis and unification of domain-domain interaction networks. Bioinformatics 25 (22) : 3020-3025. Link to
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240Forslund, K. and Sonnhammer, E.L. (2009) Benchmarking homology detection procedures with low complexity filters. Bioinformatics 25 (19) : 2500-2505. Link to
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241Fugelstad, 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
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242Jaud, 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
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243Larsson, 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
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244Illergard, 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
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245Michino, 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
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246Hessa, 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
247Johansson, 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
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248Bernsel, 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
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249Spivak, 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
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250Akerborg, 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
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251Messina, 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
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252Ollila, 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
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253Alexeyenko, 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
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254Enquist, 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
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255Bjelkmar, 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
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256Juncker, 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
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257Kall, 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
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258Barth, 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
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259Johansson, 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
260Lassmann, 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
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261Arvestad, L., Lagergren, J., Sennblad, B. (2009) The gene evolution model and computing its associated probabilities J ACM 56: 1-44. Link to
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262Sennblad, B., Lagergren, J. (2009) Probabilistic Orthology Analysis Syst Biol 58: 411-424. Link to
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263Hessa, 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
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2008
264Lage, 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
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265Yosef, N. and Kall, L. (2008) From sequence to structure to networks. Genome Biol 9 (11) : 326. Link to
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266Reynolds, 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
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267Viklund, 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
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268Bjorklund, 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
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269Lundin, 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
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270Daub, C.O. and Sonnhammer, E.L. (2008) Employing conservation of co-expression to improve functional inference. BMC Syst Biol 2 (1) : 81. Link to
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271Rajangam, 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
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272Kall, 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
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273Moore, 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
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274Merrihew, 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
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275von Heijne, G. and Rees, D. (2008) Membranes: reading between the lines. Curr Opin Struct Biol 18 (4) : 403-405. Link to
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276Forslund, K. and Sonnhammer, E.L. (2008) Predicting protein function from domain content. Bioinformatics 24 (15) : 1681-1687. Link to
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277Cassel, 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
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278White, S.H. and von Heijne, G. (2008) How translocons select transmembrane helices. Annu Rev Biophys 37: 23-42. Link to
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279Kauko, 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
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280Park, 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
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281Bernsel, 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
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282Viklund, 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
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283Drew, 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
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284Lindahl, E.R. (2008) Molecular dynamics simulations. Methods Mol Biol 443: 3-23. Link to
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285Klammer, 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
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286Larsson, 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
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287Lindahl, E. and Sansom, M.S. (2008) Membrane proteins: molecular dynamics simulations. Curr Opin Struct Biol 18 (4) : 425-431. Link to
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288Chalk, A.M. and Sonnhammer, E.L. (2008) siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics 24 (10) : 1316-1317. Link to
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289Bertaccini, 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
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290Lerch-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
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291Akerborg, O., Sennblad, B. and Lagergren, J. (2008) Birth-death prior on phylogeny and speed dating. BMC Evol Biol 8: 77. Link to
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292Hong, 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
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293Joannin, 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
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294Johansson, 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
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295Papaloukas, 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
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296Bernsel, 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
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297Kall, 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
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298Berglund, 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
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299Kall, 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
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300Finn, 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
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301Forslund, 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
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302Johansson, 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
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303Wallner, B., and Elofsson, A. (2008) Prediction of global and local model qualities using MQAPs Eds Bujnicki 1: 1-1. Link to
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2007
304Hessa, 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
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305Xie, 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
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306Lundin, 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
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307Hollich, V. and Sonnhammer, E.L. (2007) PfamAlyzer: domain-centric homology search. Bioinformatics 23 (24) : 3382-3383. Link to
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308Kall, 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
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309Wallner, 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
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310Granseth, 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
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311Newstead, 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
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312Ekman, 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
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313Andersson, 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
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PubMed
314Lundin, 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
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315Bertaccini, 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
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316Wallner, B., Larsson, P. and Elofsson, A. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35 (suppl_2) : W369-W374. Link to
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PubMed
317Stenberg, 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
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318Elofsson, A. and von Heijne, G. (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140. Link to
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PubMed
319Lassmann, T. and Sonnhammer, E.L. (2007) Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinformatics 8 Suppl 5: S9. Link to
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320von Heijne, G. (2007) Membrane proteins up for grabs. Nat Biotechnol 25 (6) : 646-647. Link to
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321von Heijne, G. (2007) The membrane protein universe: what's out there and why bother? J Intern Med 261 (6) : 543-557. Link to
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PubMed
322Hughes, 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
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323Julenius, K. (2007) NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology 17 (8) : 868-876. Link to
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324Zhang, 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
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325Kall, 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
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326Vogt, 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
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327Emanuelsson, 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
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328von Heijne, G. (2007) Formation of Transmembrane Helices In Vivo--Is Hydrophobicity All that Matters? J Gen Physiol 129 (5) : 353-356. Link to
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329Kutzner, 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
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330Wang, 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
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331Elias, I. and Lagergren, J. (2007) Fast computation of distance estimators. BMC Bioinformatics 8: 89. Link to
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332Rapp, M., Seppala, S., Granseth, E. and von Heijne, G. (2007) Emulating membrane protein evolution by rational design. Science 315 (5816) : 1282-1284. Link to
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333Andersson, 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
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334Roth, 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
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335Lindahl, E. (2007) Molecular dynamics Simulations Molecular Modeling of Proteins : 1-24.   

2006
336von Heijne, G. (2006) Membrane-protein topology. Nat Rev Mol Cell Biol 7 (12) : 909-918. Link to
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337Johansson, 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
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338Meindl-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
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339Alexeyenko, 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
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340Bjorklund, A.K., Ekman, D. and Elofsson, A. (2006) Expansion of Protein Domain Repeats. PLoS Comput Biol 2 (8) : e114. Link to
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341Julenius, K. and Pedersen, A.G. (2006) Protein evolution is faster outside the cell. Mol Biol Evol 23 (11) : 2039-2048. Link to
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342Alexeyenko, 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
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343Granseth, 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
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344Ohlson, 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
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345Viklund, 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
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346Kim, 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
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347Osterberg, 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
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348Lassmann, 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
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349Lindahl, 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
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350Azuara, 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
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351Amico, 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
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352Mackinnon, R. and von Heijne, G. (2006) Membranes. Curr Opin Struct Biol 16 (4) : 431. Link to
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353Ekman, 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
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354Hjelm, M., Hoglund, M. and Lagergren, J. (2006) New probabilistic network models and algorithms for oncogenesis. J Comput Biol 13 (4) : 853-865. Link to
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355Svensson, O., Arvestad, L. and Lagergren, J. (2006) Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2 (5) : e46. Link to
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356Abhiman, 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
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PubMed
357Lundin, 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
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PubMed
358Kemmer, 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
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359Marani, 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
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360Wallner, 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
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361Wistrand, 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
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362Rapp, 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
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363Finn, 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
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PubMed
364Asa 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
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365Bryant, D. and Lagergren, J. (2006) Compatibility of unrooted phylogenetic trees is FPT. Theo Comp Sci 351: 296-302.   
366Andersson, 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.   
367Lindberg, J., Alexeyenko, A., Perez-Bercoff, A. and Sonnhammer, E. (2006) Overview and comparison of ortholog databases Drug Discovery Today: Technologies 3: 137-143.   

2005
368Lassmann, T. and Sonnhammer, E.L. (2005) Automatic assessment of alignment quality. Nucleic Acids Res 33 (22) : 7120-7128. Link to
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369Lassmann, T. and Sonnhammer, E.L. (2005) Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298. Link to
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PubMed
370Villarejo, 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
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371Light, S., Kraulis, P. and Elofsson, A. (2005) Preferential attachment in the evolution of metabolic networks. BMC Genomics 6: 159. Link to
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372White, 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
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373Ohlson, 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
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PubMed
374Freites, 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
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PubMed
375Karamyshev, 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
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PubMed
376Van 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
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377von Heijne, G. (2005) Helices on the move. Nat Struct Mol Biol 12 (10) : 834-835. Link to
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378Pasche, 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 TGFBR1*6A in cancer. JAMA 294 (13) : 1634-1646. Link to
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379Wallner, B. and Elofsson, A. (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21 (23) : 4248-4254. Link to
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380Bjorklund, 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
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381Medigue, 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
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PubMed
382Luirink, 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
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PubMed
383Granseth, 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
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384Lindahl, 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
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385Stenberg, 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
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386von Heijne, G. (2005) Microbiology. Translocation of anthrax toxin: lord of the rings. Science 309 (5735) : 709-710. Link to
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PubMed
387Hollich, 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
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PubMed
388Laudon, 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
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389White, S.H. and von Heijne, G. (2005) Transmembrane helices before, during, and after insertion. Curr Opin Struct Biol 15 (4) : 378-386. Link to
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390Nilsson, 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
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PubMed
391McCarthy, 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
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392Abhiman, 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
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PubMed
393Bernsel, A. and Von Heijne, G. (2005) Improved membrane protein topology prediction by domain assignments. Protein Sci 14 (7) : 1723-1728. Link to
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394Kall, 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
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395Henricson, 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
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396Daley, 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
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397Berglund, 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
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398Sonnhammer, E.L. and Hollich, V. (2005) Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics 6: 108. Link to
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399Wallner, B. and Elofsson, A. (2005) All are not equal: a benchmark of different homology modeling programs. Protein Sci 14 (5) : 1315-1327. Link to
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400Wistrand, 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
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401Ekman, 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
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402Kim, 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
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PubMed
403Tie, 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
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404Hessa, T., White, S.H. and von Heijne, G. (2005) Membrane insertion of a potassium-channel voltage sensor. Science 307 (5714) : 1427. Link to
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405Ding, 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
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406Hessa, 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
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407Granseth, 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
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PubMed
408Sonnhammer, E.L. (2005) Genome informatics: taming the avalanche of genomic data. Genome Biol 6 (1) : 301. Link to
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409Monne, 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
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PubMed
410O'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
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PubMed
411Abhiman, 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
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PubMed
412Chalk, 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
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PubMed
413Julenius, 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
414Kerje, 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
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PubMed
415Henricson, 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
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416Sun, 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
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PubMed
417Camps-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
418Ohlson, 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
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PubMed
419O'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
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PubMed
420Bendtsen, 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
421Viklund, 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
422Alkema, 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
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PubMed
423Chalk, 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
424Kall, 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
425Wistrand, M. and Sonnhammer, E.L. (2004) Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol 338 (4) : 847-854.  PubMed
426Chalk, A.M., Wennerberg, M. and Sonnhammer, E.L. (2004) Sfixem--graphical sequence feature display in Java. Bioinformatics 20 (15) : 2488-2490.  PubMed
427Wistrand, 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
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PubMed
428Ekdahl, S. and Sonnhammer, E.L. (2004) ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics 20 (4) : 576-577.  PubMed
429Wallner, 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
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PubMed
430Bateman, 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
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431Lars 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
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2003
432McKay, 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
433Hermansson, 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
434Rychlewski, 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
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435Wallner, 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
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436Fischer, 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
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PubMed
437Storm, C.E. and Sonnhammer, E.L. (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13 (10) : 2353-2362.  PubMed
438Westerlund, 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
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PubMed
439Juncker, 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
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PubMed
440Arvestad, 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
441Emanuelsson, 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
442Nilsson, I., Johnson, A.E. and von Heijne, G. (2003) How hydrophobic is alanine? J Biol Chem 278 (32) : 29389-29393.  PubMed
443Ginalski, 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
444Wallner, B. and Elofsson, A. (2003) Can correct protein models be identified? Protein Sci 12 (5) : 1073-1086. Link to
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445Lee, J.M. and Sonnhammer, E.L. (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13 (5) : 875-882.  PubMed
446Von Heijne, G. (2003) Membrane protein assembly in vivo. Adv Protein Chem 63: 1-18.  PubMed
447Hessa, 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
448Chalk, A.M. and Sonnhammer, E.L. (2002) Computational antisense oligo prediction with a neural network model. Bioinformatics 18 (12) : 1567-1575.  PubMed
449Kall, L. and Sonnhammer, E.L. (2002) Reliability of transmembrane predictions in whole-genome data. FEBS Lett 532 (3) : 415-418.  PubMed
450Sonnhammer, E.L. and Koonin, E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18 (12) : 619-620.  PubMed
451Nilsson, 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
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452Lassmann, T. and Sonnhammer, E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett 529 (1) : 126-130.  PubMed
453Donnes, P. and Elofsson, A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3: 25.  PubMed
454Hollich, V., Storm, C.E. and Sonnhammer, E.L. (2002) OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics 18 (9) : 1272-1273.  PubMed
455Milchert, L.E., Liberles, D.A. and Elofsson, A. (2002) The salmon genome (and other issues in bioinformatics). Genome Biol 3 (7) : REPORTS4022.  PubMed
456Sennblad, 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
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457Blomqvist, 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
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458Nilsson, 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
459Hedman, 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
460Storm, C.E. and Sonnhammer, E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18 (1) : 92-99.  PubMed
461Elofsson, A. (2002) A study on protein sequence alignment quality. Proteins 46 (3) : 330-339.  PubMed
462Bateman, 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
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PubMed
463David 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
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2001
464Bujnicki, 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
465Fischer, 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
466Remm, 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
467Hermansson, 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
468Lundstrom, 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
469Sonnhammer, E.L. and Wootton, J.C. (2001) Integrated graphical analysis of protein sequence features predicted from sequence composition. Proteins 45 (3) : 262-273.  PubMed
470Cristobal, 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
471Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) Structure prediction meta server. Bioinformatics 17 (8) : 750-751.  PubMed
472Podowski, 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
473Monne, 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
474Storm, C.E. and Sonnhammer, E.L. (2001) NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17 (4) : 343-348.  PubMed
475Bujnicki, 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
476Saaf, 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
477Fang, 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.   
478Eriksson, O., Xhou, Y. and Elofsson, A. (2001) Side chain-positioning as an integer programming problem. WABI 1: 1-1. Link to
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