Publications by Anders Krogh

• Click here for a list with abstracts.
• Available papers are in pdf or compressed postscript (gzip).
• There may be slight differences between the available papers and the published versions.

• J. C. Bryne, E. Valen, M. H. Tang, T. Marstrand, O. Winther, I. da Piedade, A. Krogh, B. Lenhard, and A. Sandelin.
  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
  Nucleic Acids Research, 2007.
  Epub ahead of print.
  

• C. Bystroff and A. Krogh.
  Hidden Markov models for prediction of protein features.
  In M. Zaki and C. Bystroff, editors, Protein Structure Prediction. Springer, Humana Press, 2007.
  

• P. Fariselli, D. Molinini, R. Casadio, and A. Krogh.
  Prediction of structurally-determined coiled-coil domains with hidden Markov models.
  In S. Hochreiter and R. Wagner, editors, Bioinformatics Research and Development, pages 292-302. Springer-Verlag, March 2007.
  (PDF, 192671 bytes)

• L. B. Frankel, N. R. Christoffersen, A. Jacobsen, M. Lindow, A. Krogh, and A. H. Lund.
  Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells.
  J. Biol. Chem., 2007.
  Epub ahead of print.
  

• M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin.
  A code for transcription initiation in mammalian genomes.
  Genome Research, 2007.
  To appear.
  

• L. Jonson, J. Vikesaa, A. Krogh, L. K. Nielsen, T. V. Hansen, R. Borup, A. H. Johnsen, J. Christiansen, and F. C. Nielsen.
  Molecular composition of IMP1 RNP granules.
  Mol. & Cell. Proteomics, 6(5), 2007.
  

• L. Kall, A. Krogh, and E. L. Sonnhammer.
  Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server.
  Nucleic Acids Research, 35(Web Server issue):W429-432, July 2007.
  

• S. Lindgreen, P. P. Gardner, and A. Krogh.
  MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
  Bioinformatics, 2007.
  Epub ahead of print.
  

• M. Lindow, A. Jacobsen, S Nygaard, Y. Mang, and A Krogh.
  Intragenomic matching reveals a huge potential for miRNA mediated regulation in plants.
  PLoS Computational Biology, 2007.
  To appear.
  

• K. J. Won, T. Hamelryck, A. Prugel-Bennett, and A. Krogh.
  An evolving method for learning HMM structure: prediction of protein secondary structure.
  BMC Bioinformatics, 8(1):357, 2007.
  Epub ahead of print.
  

• M. Amico, M. Finelli, I. Rossi, A. Zauli, A. Elofsson, H. Viklund, G. von Heijne, D. Jones, A. Krogh, P. Fariselli, P. L. Martelli, and R. Casadio.
  PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.
  Nucleic Acids Research, 34:W169-W172, 2006.
  (PDF, 585631 bytes)

• T. Hamelryck, J. T. Kent, and A. Krogh.
  Sampling realistic protein conformations using local structural bias.
  PLoS Comput. Biol., 2(9):e131, 2006.
  (PDF, 2447369 bytes)

• K. T. Jensen, L. Petersen, S. Falk, P. Iversen, P. Andersen, M. Theisen, and A. Krogh.
  Novel overlapping coding sequences in Chlamydia trachomatis.
  FEMS Microbiol. Lett., 265(1):106-117, 2006.
  (PDF, 195664 bytes)

• S. Lindgreen, P. P. Gardner, and A. Krogh.
  Measuring covariation in RNA alignments: physical realism improves information measures.
  Bioinformatics, 22(24):2988-2995, 2006.
  (PDF, 134720 bytes)

• K Munch and A. Krogh.
  Automatic generation of gene finders for eukaryotic species.
  BMC Bioinformatics, 7(1):263, 2006.
  (PDF, 409817 bytes)

• K. Munch, P. P. Gardner, P. Arctander, and A. Krogh.
  A hidden Markov model approach for determining expression from genomic tiling micro arrays.
  BMC Bioinformatics, 7(1):239, 2006.
  (PDF, 568372 bytes)

• K.-J. Won, A. Prugel-Bennett, and A. Krogh.
  Evolving the structure of hidden Markov models.
  IEEE Transactions on Evolutionary Computation, 10(1):39-49, 2006.
  (PDF, 597786 bytes)

• L. Käll, A. Krogh, and E. L. Sonnhammer.
  An HMM posterior decoder for sequence feature prediction that includes homology information.
  Bioinformatics, 21(Suppl. 1):i251-i257, 2005.
  (PDF, 83426 bytes)

• M. Lindow and A. Krogh.
  Computational evidence for hundreds of non-conserved plant microRNAs.
  BMC Genomics, 6:119, 2005.
  (PDF, 317514 bytes)

• P. Nielsen and A. Krogh.
  Large-scale prokaryotic gene prediction and comparison to genome annotation.
  Bioinformatics, 21(24):4322-4329, 2005.
  (PDF, 295624 bytes)

• L. Käll, A. Krogh, and E. L. L. Sonnhammer.
  A combined transmembrane topology and signal peptide prediction method.
  Journal of Molecular Biology, 338(5):1027-1036, 2004.
  (PDF, 615083 bytes)

• O. Winther and A. Krogh.
  Teaching computers to fold proteins.
  Phys. Rev. E, 70:030903(R), 2004.
  (PDF, 294280 bytes)

• K.-J. Won, A. Prugel-Bennett, and A. Krogh.
  Training HMM structure with genetic algorithm for biological sequence analysis.
  Bioinformatics, 20(18):3613-3619, 2004.
  (PDF, 122027 bytes)

• A. S. Juncker, H. Willenbrock, G. von Heijne, S. Brunak, H. Nielsen, and A. Krogh.
  Prediction of lipoprotein signal peptides in Gram-negative bacteria.
  Protein Sci., 12(8):1652-1662, 2003.
  (PDF, 338425 bytes)

• T. S. Larsen and A. Krogh.
  EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance.
  BMC Bioinformatics, 4(1):21, 2003.
  (PDF, 832391 bytes)

• K. Melén, A. Krogh, and G. von Heijne.
  Reliability measures for membrane protein topology prediction algorithms.
  Journal of Molecular Biology, 327(3):735-744, 2003.
  (PDF, 298308 bytes)

• L. Petersen, T. S. Larsen, D. W. Ussery, S. L. W. On, and A. Krogh.
  RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.
  Journal of Molecular Biology, 326(5):1361-1372, 2003.
  (PDF, 630427 bytes)

• L. J. Jensen, R. Gupta, N. Blom, D. Devos, J. Tamames, C. Kesmir, H. Nielsen, H. H. Staerfeldt, K. Rapacki, C. Workman, C. A. Andersen, S. Knudsen, A. Krogh, A. Valencia, and S. Brunak.
  Prediction of human protein function from post-translational modifications and localization features.
  Journal of Molecular Biology, 319(5):1257-1265, 2002.
  (PDF, 441510 bytes)

• P. L. Martelli, P. Fariselli, A. Krogh, and R. Casadio.
  A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.
  Bioinformatics, 18:S46-S53, 2002.
  Proceedings of ISMB 2002.
  (PDF, 147765 bytes)

• D. Ussery, D. M. Soumpasis, S. Brunak, H. H. Staerfeldt, P. Worning, and A. Krogh.
  Bias of purine stretches in sequenced chromosomes.
  Computers and Chemistry, 26(5):531-541, 2002.
  (PDF, 593359 bytes)

• S. Brunak and A. Krogh.
  ISMB 2001 (editorial).
  Bioinformatics, 17(Suppl. 1):S1-S4, 2001.
  Proceedings of ISMB 2001.
  (PDF, 51658 bytes)

• H. Jarmer, T. S. Larsen, A. Krogh, H. H. Saxild, S. Brunak, and S. Knudsen.
  Sigma A recognition sites in the Bacillus subtilis genome.
  Microbiology, 147:2417-2424, 2001.
  (PDF, 579429 bytes)

• A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer.
  Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes.
  Journal of Molecular Biology, 305(3):567-580, January 2001.
  (PDF, 959503 bytes)

• J. Parkhill, G. Dougan, K. D. James, N. R. Thomson, D. Pickard, J. Wain, C. Churcher, K. L. Mungall, S. D. Bentley, M. T. G. Holden, M. Sebaihia, S. Baker, D. Basham, K. Brooks, T. Chillingworth, P. Connerton, A. Cronin, P. Davis, R. M. Davies, L. Dowd, N. White, J. Farrar, T. Feltwell, N. Hamlin, A. Haque, T. T. Hien, S. Holroyd, K. Jagels, A. Krogh, T. S. Larsen, S. Leather, S. Moule, P. Ò'Gaora, C. Parry, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell.
  Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
  Nature, 413(6858):848-852, 2001.
  (PDF, 1044232 bytes)

• M. Skovgaard, L. J. Jensen, S. Brunak, D. Ussery, and A. Krogh.
  On the total number of genes and their length distribution in complete microbial genomes.
  Trends in Genetics, 17(8):425-428, August 2001.
  (PDF, 44091 bytes)

• D. Ussery, T. S. Larsen, K. T. Wilkes, C. Friis, P. Worning, A. Krogh, and S. Brunak.
  Genome organisation and chromatin structure in Escherichia coli.
  Biochimie, 83(2):201-212, 2001.
  (PDF, 489822 bytes)

• J. V. Hansen and A. Krogh.
  A general method for combining predictors tested on protein secondary structure prediction.
  In H. Malmgren, M. Borga, and L. Niklasson, editors, Proceedings of Artificial Neural Networks in Medicine and Biology, pages 259-264, London, May 2000. Springer-Verlag.
  (Gzipped PostScript, 6 pages, 31321 bytes) (PDF, 63819 bytes)

• A. Krogh.
  Using database matches with HMMgene for automated gene detection in Drosophila.
  Genome Research, 10(4):523-528, 2000.
  (PDF, 345831 bytes)

• A. Krogh and S. K. Riis.
  Hidden neural networks.
  Neural Computation, 11(2):541-563, 1999.
  (PDF, 308921 bytes)

• C. Workman and A. Krogh.
  No evidence that mRNA have lower folding free energies than random sequences with the same dinucleotide distribution.
  Nucleic Acids Research, 27(24):4816-4822, 1999.
  (PDF, 322485 bytes)

• S. T. Cole, R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M. A. Quail, M.-A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell.
  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
  Nature, 393:537-544, 1998.
  (PDF, 2784947 bytes)

• R. M. Durbin, S. R. Eddy, A. Krogh, and G. Mitchison.
  Biological Sequence Analysis.
  Cambridge University Press, Cambridge, UK, 1998.
  

• A. Krogh.
  Gene finding: putting the parts together.
  In Martin J. Bishop, editor, Guide to Human Genome Computing, chapter 11, pages 261-274. Academic Press, San Diego, CA, 2nd edition, 1998.
  (Gzipped PostScript, 12 pages, 42693 bytes) (PDF, 945426 bytes)

• A. Krogh.
  An introduction to hidden Markov models for biological sequences.
  In S. L. Salzberg, D. B. Searls, and S. Kasif, editors, Computational Methods in Molecular Biology, chapter 4, pages 45-63. Elsevier, Amsterdam, 1998.
  (Gzipped PostScript, 24 pages, 67831 bytes) (PDF, 1483458 bytes)

• H. Nielsen and A. Krogh.
  Prediction of signal peptides and signal anchors by a hidden Markov model.
  In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 122-130, Menlo Park, CA, 1998. AAAI Press.
  (Gzipped PostScript, 9 pages, 58984 bytes) (PDF, 1081707 bytes)

• E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.
  A hidden Markov model for predicting transmembrane helices in protein sequences.
  In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.
  (Gzipped PostScript, 8 pages, 42470 bytes) (PDF, 844205 bytes)

• J. A. Hertz, A. Krogh, B. Lautrup, and T. Lehmann.
  Non-linear backpropagation: Doing back-propagation without derivatives of the activation function.
  IEEE Transactions on Neural Networks, 8(6):1321-1327, 1997.
  (PDF, 170227 bytes)

• A. Krogh.
  Two methods for improving performance of a HMM and their application for gene finding.
  In T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, and A. Valencia, editors, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, pages 179-186, Menlo Park, CA, 1997. AAAI Press.
  (Gzipped PostScript, 8 pages, 41953 bytes) (PDF, 145092 bytes)

• A. Krogh and P. Sollich.
  Statistical mechanics of ensemble learning.
  Physical Review E, 55(1):811-825, 1997.
  (PDF, 297146 bytes)

• S. K. Riis and A. Krogh.
  Hidden neural networks: A framework for HMM/NN hybrids.
  In Proceedings of IEEE International Conference on Acoustics, Speech, and Signal Processing, pages 3233-3236, New York, USA, 1997. IEEE.
  (PDF, 446055 bytes)

• P. Baldi, S. Brunak, Y. Chauvin, and A. Krogh.
  Hidden Markov models for human genes: Periodic patterns in exon sequences.
  In S. Suhai, editor, Theoretical and Computational Methods in Genome Research, N.Y., 1996. Plenum Press.
  

• P. Baldi, S. Brunak, Y. Chauvin, and A. Krogh.
  Naturally occurring nucleosome positioning signals in human exons.
  Journal of Molecular Biology, 263:503-510, 1996.
  

• R. Hughey and A. Krogh.
  Hidden Markov models for sequence analysis: extension and analysis of the basic method.
  CABIOS, 12:95-107, 1996.
  (Gzipped PostScript, 23 pages, 272331 bytes) (PDF, 710025 bytes)

• A. Krogh and S. K. Riis.
  Prediction of beta sheets in proteins.
  In D. S. Touretzky, M. C. Mozer, and M. E. Hasselmo, editors, Advances in Neural Information Processing Systems, volume 8, pages 917-923, Cambridge, MA, USA, 1996. MIT Press.
  (Gzipped PostScript, 7 pages, 124377 bytes) (PDF, 1364585 bytes)

• S. K. Riis and A. Krogh.
  Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments.
  Journal of Computational Biology, 3:163-183, 1996.
  (Gzipped PostScript, 27 pages, 112928 bytes) (PDF, 308269 bytes)

• S. K. Riis and A. Krogh.
  Joint estimation of parameters in hidden neural networks.
  In Proceedings of IEEE Nordic Signal Processing Symposium, pages 431-434. IEEE, 1996.
  (Gzipped PostScript, 4 pages, 64324 bytes) (PDF, 169200 bytes)

• K. Sjölander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler.
  Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology.
  CABIOS, 12(4):327-345, 1996.
  (Gzipped PostScript, 33 pages, 105486 bytes) (PDF, 364242 bytes)

• P. Sollich and A. Krogh.
  Learning with ensembles: How over-fitting can be useful.
  In M. E. Hasselmo D. S. Touretzky, M. C. Mozer, editor, Advances in Neural Information Processing Systems, volume 8, pages 190-196, Cambridge, MA, USA, 1996. MIT Press.
  (Gzipped PostScript, 7 pages, 57751 bytes) (PDF, 155044 bytes)

• P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, and A. Krogh.
  Periodic sequence patterns in human exons.
  In C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer, and S. Wodak, editors, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pages 30-38, Menlo Park, CA, July 1995. AAAI Press.
  (Gzipped PostScript, 9 pages, 75028 bytes) (PDF, 465226 bytes)

• A. Krogh and G. Mitchison.
  Maximum entropy weighting of aligned sequences of proteins or DNA.
  In C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer, and S. Wodak, editors, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pages 215-221, Menlo Park, CA, July 1995. AAAI Press.
  (Gzipped PostScript, 7 pages, 46748 bytes) (PDF, 168255 bytes)

• A. Krogh and J. Vedelsby.
  Neural network ensembles, cross validation and active learning.
  In D. S. Touretzky G. Tesauro and T. K. Leen, editors, Advances in Neural Information Processing Systems, pages 231-238, Cambridge MA, 1995. MIT Press.
  (Gzipped PostScript, 8 pages, 66341 bytes) (PDF, 237918 bytes)

• P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, and A. Krogh.
  Hidden Markov models for human genes.
  In J.D. Cowan, G. Tesauro, and J. Alspector, editors, Advances in Neural Information Processing Systems, volume 6, pages 761-768, San Francisco, CA, 1994. Morgan Kauffmann Publishers.
  

• N. Cesa-Bianchi, A. Krogh, and M. K. Warmuth.
  Bounds on approximate steepest descent for likelihood maximization in exponential families.
  IEEE Transactions on Information Theory, 40(4):1215-1220, July 1994.
  (PDF, 344865 bytes)

• A. Krogh.
  Hidden Markov models for labeled sequences.
  In Proceedings of the 12th IAPR International Conference on Pattern Recognition, pages 140-144, Los Alamitos, California, October 1994. IEEE Computer Society Press.
  (PDF, 431509 bytes)

• A. Krogh, M. Brown, I. S. Mian, K. Sjölander, and D. Haussler.
  Hidden Markov models in computational biology: Applications to protein modeling.
  Journal of Molecular Biology, 235:1501-1531, Feb. 1994.
  (PDF, 1961051 bytes)

• A. Krogh, I. S. Mian, and D. Haussler.
  A hidden Markov model that finds genes in E. coli DNA.
  Nucleic Acids Research, 22:4768-4778, 1994.
  (Gzipped PostScript, 22 pages, 104898 bytes) (PDF, 1425261 bytes)

• M. Brown, R. Hughey, A. Krogh, I. S. Mian, K. Sjölander, and D. Haussler.
  Using Dirichlet mixture priors to derive hidden Markov models for protein families.
  In L. Hunter, D. Searls, and J. Shavlik, editors, Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, pages 47-55, Menlo Park, CA, July 1993. AAAI/MIT Press.
  

• J. Gorodkin, L. K. Hansen, A. Krogh, C. Svarer, and O. Winther.
  A quantitative study of pruning by optimal brain damage.
  International Journal of Neural Systems, 4(2):159-169, 1993.
  

• D. Haussler, A. Krogh, I. S. Mian, and K. Sjölander.
  Protein modeling using hidden Markov models: Analysis of globins.
  In T. N. Mudge, V. Milutinovic, and L. Hunter, editors, Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, volume 1, pages 792-802, Los Alamitos, California, 1993. IEEE Computer Society Press.
  (PDF, 935916 bytes)

• A. Krogh.
  Learning with noise in a linear perceptron.
  Journal of Physics A, 25:1119-1133, 1992.
  

• A. Krogh and J. A. Hertz.
  Generalization in a linear perceptron in the presence of noise.
  Journal of Physics A, 25:1135-1147, 1992.
  

• A. Krogh and J. A. Hertz.
  A simple weight decay can improve generalization.
  In J. E. Moody, S. J. Hanson, and R. P. Lippmann, editors, Advances in Neural Information Processing Systems, volume 4, pages 950-957, San Mateo, CA, 1992. Morgan Kauffmann Publishers.
  (Gzipped PostScript, 8 pages, 36458 bytes) (PDF, 137373 bytes)

• J. A. Hertz and A. Krogh.
  Statistical dynamics of learning.
  In T. Kohonen et al., editor, Artificial Neural Networks, volume 1, pages 125-131. Elsevier, 1991.
  Proceedings ICANN-91, Helsinki.
  

• J. A. Hertz, A. Krogh, and R. Palmer.
  Introduction to the Theory of Neural Computation.
  Addison-Wesley, Redwood City, 1991.
  

• A. Krogh.
  Learning and Generalization in Neural Networks.
  PhD thesis, The Niels Bohr Institute, University of Copenhagen, Denmark, 1991.
  

• A. Krogh and J. A. Hertz.
  Dynamics of generalization in linear perceptrons.
  In R.P. Lippmann, J.E. Moody, and D.E. Touretzky, editors, Advances in Neural Information Processing Systems, volume 3, pages 897-903, San Mateo, CA, 1991. Morgan Kauffmann Publishers.
  

• A. Krogh and J. A. Hertz.
  Hebbian learning of principal components.
  In R. Eckmiller, G. Hartmann, and G. Hauske, editors, Parallel Processing in Neural Systems and Computers, pages 183-186. Elsevier, 1990.
  

• A. Krogh, G. I. Thorbergsson, and J. A. Hertz.
  A cost function for internal representations.
  In D. S. Touretzky, editor, Advances in Neural Information Processing Systems, volume 2, pages 733-740, San Mateo, 1990. Morgan Kaufmann.
  

• J. A. Hertz, A. Krogh, and G. I. Thorbergsson.
  Phase transitions in simple learning.
  Journal of Physics A, 22:2133-2150, 1989.
  

• J. A. Hertz, G. I. Thorbergsson, and A. Krogh.
  Dynamics of learning in simple perceptrons.
  Physica Scripta, T25:149-151, 1989.
  

• A. Krogh and J. A. Hertz.
  Hierarchical associative networks.
  In L. Personnaz and G.Dreyfus, editors, Neural Networks from Models to Applications, pages 336-342, Paris, 1989. I.D.S.E.T.
  Proceedings of nEuro'88, Paris, June 88.
  

• A. Krogh and J. A. Hertz.
  Mean field analysis of hierarchical associative networks with magnetization.
  Journal of Physics A, 21:2211-2224, 1988.
  

• C. Cortes, A. Krogh, and J. A. Hertz.
  Hierarchical associative networks.
  Journal of Physics A, 20:4449-4455, 1987.
  

• A. Krogh.
  Neurale netværk: En hierarkisk model.
  Master's thesis, The Niels Bohr Institute, University of Copenhagen, Denmark, 1987.
  In Danish.