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SBC Publications


2017
1Nilsson, 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
2Dimou, N.L., Tsirigos, K.D., Elofsson, A. and Bagos, P.G. (Epub 2017) GWAR: Robust Analysis and Meta-Analysis of Genome-Wide Association Studies. Bioinformatics (Epub ahead of print)  Link to
article
PubMed
3Kaduk, M. and Sonnhammer, E. (Epub 2017) Improved orthology inference with Hieranoid 2. Bioinformatics (Epub ahead of print)  Link to
article
PubMed
4Sennblad, 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. (Epub 2017) Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels. Hum Mol Genet (Epub ahead of print)  Link to
article
PubMed
5Uziela, K., Menendez Hurtado, D., Shu, N., Wallner, B. and Elofsson, A. (Epub 2017) ProQ3D: improved model quality assessments using deep learning. Bioinformatics (Epub ahead of print)  Link to
article
PubMed
6Ranganathan, 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
7Farias-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
8Piovesan, 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
9Kaduk, 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
10Ogris, 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
11Kimanius, 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
article
PubMed
12Nys, 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
13Uziela, 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
14Mishima, 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
15Stone, 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
16Ojemalm, 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
17Tsirigos, 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
18Schibich, 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
19Rodriguez, 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
20Martyna, 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
21Conti, 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
22Saripella, 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
23Haider, 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
24Ogris, 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
25Heusser, 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
26Soderstrom, 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
27Altenhoff, 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
28Nilsson, 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
29Marino, 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
30Beerenwinkel, N., Greenman, C.D. and Lagergren, J. (2016) Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput Biol 12 (2) : e1004717. Link to
article
PubMed
31Hayat, 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
32Yazdi, 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
33Gomez-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
34Uziela, K. and Wallner, B. (2016) ProQ2: estimation of model accuracy implemented in Rosetta. Bioinformatics 32 (9) : 1411-1413. Link to
article
PubMed
35Peters, 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
36Ranganathan, 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
37Wennberg, 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
38Kimanius, 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
39Pronk, 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
40Mahmudi, 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
41Shiota, 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
42Nilsson, 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
43Ullah, 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
44Rodriguez, 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
45Daniel, 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
46Yoluk, 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
47De 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
48Tsirigos, 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
49Ullah, 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
50Mirzadeh, 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
51Hayat, 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
52Goel, 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
53Cymer, 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
54Stone, 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
55Rodriguez, 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
56Uhlen, 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
57Ismail, 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
58Sonnhammer, 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
59Tjarnberg, 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
60Lundborg, 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
61Lindahl, E. (2015) Molecular dynamics simulations. Methods Mol Biol 1215: 3-26. Link to
article
PubMed
62Vargas-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
63Cymer, 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
64Norholm, 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
65Nilsson, 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
66Botelho, 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
67Skwark, 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
68Ranganathan, 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
69Kutsenko, 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
70Ulmschneider, 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
71Michel, 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
72Borroto-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
73Sahlin, 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
74Johnson, 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
75Sonnhammer, 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
76Rodriguez, 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
77Rodriguez, 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
78Ge, 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
79Light, 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
80Studham, 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
81Virkki, 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
82Guala, 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
83Bjorkholm, 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
84Virkki, 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
PubMed
85Virkki, M.T., Agrawal, N., Edsbacker, E., Cristobal, S., Elofsson, A. and Kauko, A. (2014) Folding of Aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core. Protein Sci 23 (7) : 981-992. Link to
article
PubMed
86Peters, C. and Elofsson, A. (2014) Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins 82 (9) : 2190-2198. Link to
article
PubMed
87Cymer, F., Ismail, N. and von Heijne, G. (2014) Weak pulling forces exerted on Nin-orientated transmembrane segments during co-translational insertion into the inner membrane of Escherichia coli. FEBS Lett 588 (10) : 1930-1934. Link to
article
PubMed
88Moruz, L. and Kall, L. (2014) GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography. Proteomics 14 (12) : 1464-1466. Link to
article
PubMed
89Lloris-Garcera, P., Seppala, S., Slusky, J.S., Rapp, M. and von Heijne, G. (2014) Why have small multidrug resistance proteins not evolved into fused, internally duplicated structures? J Mol Biol 426 (11) : 2246-2254. Link to
article
PubMed
90Soderstrom, B., Skoog, K., Blom, H., Weiss, D.S., von Heijne, G. and Daley, D.O. (2014) Disassembly of the divisome in Escherichia coli: evidence that FtsZ dissociates before compartmentalization. Mol Microbiol 92 (1) : 1-9. Link to
article
PubMed
91Karamyshev, A.L., Patrick, A.E., Karamysheva, Z.N., Griesemer, D.S., Hudson, H., Tjon-Kon-Sang, S., Nilsson, I., Otto, H., Liu, Q., Rospert, S., von Heijne, G., Johnson, A.E. and Thomas, P.J. (2014) Inefficient SRP Interaction with a Nascent Chain Triggers a mRNA Quality Control Pathway. Cell 156 (1-2) : 146-157. Link to
article
PubMed
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192Botelho, 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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196Bertaccini, 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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197Lima, 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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198Ray, A., Lindahl, E. and Wallner, B. (2010) Model quality assessment for membrane proteins. Bioinformatics 26 (24) : 3067-3074. Link to
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199Hennerdal, 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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201Runesson, 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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202Larsson, 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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203Lind, 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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204Moruz, 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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205Bjorklund, 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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206Henricson, A., Forslund, K. and Sonnhammer, E.L. (2010) Orthology confers intron position conservation. BMC Genomics 11 (1) : 412. Link to
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207Kasson, 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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208Illergard, 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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209Frygelius, 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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210Seppala, 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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211Stranneheim, 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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212Niemela, 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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213Alexeyenko, 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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214Fagerberg, 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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215Stromqvist, 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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216Sehat, 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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217Kauko, 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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218Enstero, 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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219Jornvall, 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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221Ostlund, 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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222Ekman, 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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223Daniels, 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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224Hedin, 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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225Finn, 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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233Fugelstad, 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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237Michino, 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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243Messina, 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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244Ollila, 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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256Lage, 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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263Rajangam, 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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275Drew, 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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298Lundin, 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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299Hollich, V. and Sonnhammer, E.L. (2007) PfamAlyzer: domain-centric homology search. Bioinformatics 23 (24) : 3382-3383. Link to
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300Kall, 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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301Wallner, 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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302Granseth, 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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303Newstead, 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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304Ekman, 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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305Andersson, 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
306Lundin, 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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307Bertaccini, 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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308Wallner, 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
309Stenberg, 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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PubMed
310Elofsson, 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
311Lassmann, 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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312von Heijne, G. (2007) Membrane proteins up for grabs. Nat Biotechnol 25 (6) : 646-647. Link to
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313von 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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314Hughes, 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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315Julenius, K. (2007) NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology 17 (8) : 868-876. Link to
article
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316Zhang, 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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317Kall, 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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318Vogt, 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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PubMed
319Emanuelsson, 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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320von 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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321Kutzner, 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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322Wang, 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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323Elias, I. and Lagergren, J. (2007) Fast computation of distance estimators. BMC Bioinformatics 8: 89. Link to
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324Rapp, 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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325Andersson, 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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326Roth, 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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327Lindahl, E. (2007) Molecular dynamics Simulations Molecular Modeling of Proteins : 1-24.   

2006
328von Heijne, G. (2006) Membrane-protein topology. Nat Rev Mol Cell Biol 7 (12) : 909-918. Link to
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329Johansson, 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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330Meindl-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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331Alexeyenko, 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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PubMed
332Bjorklund, 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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333Julenius, 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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334Alexeyenko, 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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335Granseth, 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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336Ohlson, 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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337Viklund, 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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338Kim, 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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339Osterberg, 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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340Lassmann, 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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341Lindahl, 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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342Azuara, 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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343Amico, 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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344Mackinnon, R. and von Heijne, G. (2006) Membranes. Curr Opin Struct Biol 16 (4) : 431. Link to
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345Ekman, 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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346Hjelm, 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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347Svensson, 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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348Abhiman, 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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349Lundin, 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
350Kemmer, 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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351Marani, 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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352Wallner, 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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353Wistrand, 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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354Rapp, 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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355Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34 (Database issue) : D247-51. Link to
article
PubMed
356Asa 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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357Bryant, D. and Lagergren, J. (2006) Compatibility of unrooted phylogenetic trees is FPT. Theo Comp Sci 351: 296-302.   
358Andersson, 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.   
359Lindberg, J., Alexeyenko, A., Perez-Bercoff, A. and Sonnhammer, E. (2006) Overview and comparison of ortholog databases Drug Discovery Today: Technologies 3: 137-143.   

2005
360Lassmann, T. and Sonnhammer, E.L. (2005) Automatic assessment of alignment quality. Nucleic Acids Res 33 (22) : 7120-7128. Link to
article
PubMed
361Lassmann, T. and Sonnhammer, E.L. (2005) Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298. Link to
article
PubMed
362Villarejo, A., Buren, S., Larsson, S., Dejardin, A., Monne, M., Rudhe, C., Karlsson, J., Jansson, S., Lerouge, P., Rolland, N., von Heijne, G., Grebe, M., Bako, L. and Samuelsson, G. (2005) Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. Nat Cell Biol 7 (12) : 1224-1231. Link to
article
PubMed
363Light, S., Kraulis, P. and Elofsson, A. (2005) Preferential attachment in the evolution of metabolic networks. BMC Genomics 6: 159. Link to
article
PubMed
364White, S.H. and von Heijne, G. (2005) Do protein-lipid interactions determine the recognition of transmembrane helices at the ER translocon? Biochem Soc Trans 33 (Pt 5) : 1012-1015. Link to
article
PubMed
365Ohlson, T. and Elofsson, A. (2005) ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics 6: 253. Link to
article
PubMed
366Freites, J.A., Tobias, D.J., von Heijne, G. and White, S.H. (2005) Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A 102 (42) : 15059-15064. Link to
article
PubMed
367Karamyshev, 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
368Van 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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PubMed
369von Heijne, G. (2005) Helices on the move. Nat Struct Mol Biol 12 (10) : 834-835. Link to
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PubMed
370Pasche, 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
article
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371Wallner, 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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PubMed
372Bjorklund, 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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PubMed
373Medigue, 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
374Luirink, 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
375Granseth, E., Daley, D.O., Rapp, M., Melen, K. and von Heijne, G. (2005) Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J Mol Biol 352 (3) : 489-494. Link to
article
PubMed
376Lindahl, 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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377Stenberg, 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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PubMed
378von Heijne, G. (2005) Microbiology. Translocation of anthrax toxin: lord of the rings. Science 309 (5735) : 709-710. Link to
article
PubMed
379Hollich, 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
380Laudon, 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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PubMed
381White, 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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382Nilsson, 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
383McCarthy, S., Mottagui-Tabar, S., Mizuno, Y., Sennblad, B., Hoffstedt, J., Arner, P., Wahlestedt, C. and Andersson, B. (2005) Complex HTR2C linkage disequilibrium and promoter associations with body mass index and serum leptin. Hum Genet 117 (6) : 545-557. Link to
article
PubMed
384Abhiman, 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
385Bernsel, 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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PubMed
386Kall, 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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PubMed
387Henricson, 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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388Daley, 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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PubMed
389Berglund, 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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PubMed
390Sonnhammer, 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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391Wallner, 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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392Wistrand, 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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PubMed
393Ekman, 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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PubMed
394Kim, 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
395Tie, 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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396Hessa, 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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397Ding, 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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398Hessa, 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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399Granseth, 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
400Sonnhammer, E.L. (2005) Genome informatics: taming the avalanche of genomic data. Genome Biol 6 (1) : 301. Link to
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PubMed
401Monne, 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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402O'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
403Abhiman, 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
404Chalk, 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
405Julenius, 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
406Kerje, 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
407Henricson, 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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PubMed
408Sun, X., Zhao, J., Kylberg, K., Soop, T., Palka, K., Sonnhammer, E., Visa, N., Alzhanova-Ericsson, A.T. and Daneholt, B. (2004) Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene. Chromosoma 113 (5) : 244-257. Link to
article
PubMed
409Camps-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
410Ohlson, 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
411O'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
412Bendtsen, 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
413Viklund, 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
414Alkema, 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
415Chalk, 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
416Kall, 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
417Wistrand, M. and Sonnhammer, E.L. (2004) Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol 338 (4) : 847-854.  PubMed
418Chalk, A.M., Wennerberg, M. and Sonnhammer, E.L. (2004) Sfixem--graphical sequence feature display in Java. Bioinformatics 20 (15) : 2488-2490.  PubMed
419Wistrand, 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
420Ekdahl, S. and Sonnhammer, E.L. (2004) ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics 20 (4) : 576-577.  PubMed
421Wallner, 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
422Bateman, 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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PubMed
423Lars 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
424McKay, 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
425Hermansson, 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
426Rychlewski, 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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PubMed
427Wallner, 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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PubMed
428Fischer, 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
429Storm, C.E. and Sonnhammer, E.L. (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13 (10) : 2353-2362.  PubMed
430Westerlund, 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
431Juncker, 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
432Arvestad, 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
433Emanuelsson, 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
434Nilsson, I., Johnson, A.E. and von Heijne, G. (2003) How hydrophobic is alanine? J Biol Chem 278 (32) : 29389-29393.  PubMed
435Ginalski, 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
436Wallner, B. and Elofsson, A. (2003) Can correct protein models be identified? Protein Sci 12 (5) : 1073-1086. Link to
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PubMed
437Lee, J.M. and Sonnhammer, E.L. (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13 (5) : 875-882.  PubMed
438Von Heijne, G. (2003) Membrane protein assembly in vivo. Adv Protein Chem 63: 1-18.  PubMed
439Hessa, 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
440Chalk, A.M. and Sonnhammer, E.L. (2002) Computational antisense oligo prediction with a neural network model. Bioinformatics 18 (12) : 1567-1575.  PubMed
441Kall, L. and Sonnhammer, E.L. (2002) Reliability of transmembrane predictions in whole-genome data. FEBS Lett 532 (3) : 415-418.  PubMed
442Sonnhammer, E.L. and Koonin, E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18 (12) : 619-620.  PubMed
443Nilsson, 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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PubMed
444Lassmann, T. and Sonnhammer, E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett 529 (1) : 126-130.  PubMed
445Donnes, P. and Elofsson, A. (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3: 25.  PubMed
446Hollich, V., Storm, C.E. and Sonnhammer, E.L. (2002) OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics 18 (9) : 1272-1273.  PubMed
447Milchert, L.E., Liberles, D.A. and Elofsson, A. (2002) The salmon genome (and other issues in bioinformatics). Genome Biol 3 (7) : REPORTS4022.  PubMed
448Sennblad, 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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PubMed
449Blomqvist, 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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PubMed
450Nilsson, 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
451Hedman, 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
452Storm, C.E. and Sonnhammer, E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18 (1) : 92-99.  PubMed
453Elofsson, A. (2002) A study on protein sequence alignment quality. Proteins 46 (3) : 330-339.  PubMed
454Bateman, 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
455David 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
456Bujnicki, 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
457Fischer, 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
458Remm, 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
459Hermansson, 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
460Lundstrom, 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
461Sonnhammer, E.L. and Wootton, J.C. (2001) Integrated graphical analysis of protein sequence features predicted from sequence composition. Proteins 45 (3) : 262-273.  PubMed
462Cristobal, 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
463Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L. (2001) Structure prediction meta server. Bioinformatics 17 (8) : 750-751.  PubMed
464Podowski, 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
465Monne, 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
466Storm, C.E. and Sonnhammer, E.L. (2001) NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17 (4) : 343-348.  PubMed
467Bujnicki, 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
468Saaf, 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
469Fang, 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.   
470Eriksson, 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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