A Cost Function for Internal Representations. - Anders Krogh; C. I. Thorbergsson; John A. Hertz (NIPS, 1989)

Dynamics of Generalization in Linear Perceptrons. - Anders Krogh; John A. Hertz (NIPS, 1990)

Introduction to the theory of neural computation. - John A. Hertz; Anders Krogh; Richard G. Palmer (Addison-Wesley, 1991)

A Simple Weight Decay Can Improve Generalization. - Anders Krogh; John A. Hertz (NIPS, 1991)

Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families. - Michael Brown; Richard Hughey; Anders Krogh; I. Saira Mian; Kimmen Sjölander; David Haussler (ISMB, 1993)

Hidden Markov Models for Human Genes. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (NIPS, 1993)

A Quantitative Study Of Pruning By Optimal Brain Damage. - Jan Gorodkin; Lars Kai Hansen; Anders Krogh; Claus Svarer; Ole Winther (Int. J. Neural Syst., 1993)

Hidden Markov models for labeled sequences. - Anders Krogh (ICPR (2), 1994)

Neural Network Ensembles, Cross Validation, and Active Learning. - Anders Krogh; Jesper Vedelsby (NIPS, 1994)

Bounds on approximate steepest descent for likelihood maximization in exponential families. - Nicolò Cesa-Bianchi; Anders Krogh; Manfred K. Warmuth (IEEE Trans. Inf. Theory, 1994)

Periodic Sequence Patterns in Human Exons. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (ISMB, 1995)

Maximum Entropy Weighting of Aligned Sequences of Proteins or DNA. - Anders Krogh; Graeme J. Mitchison (ISMB, 1995)

Prediction of Beta Sheets in Proteins. - Anders Krogh; Søren Kamaric Riis (NIPS, 1995)

Learning with ensembles: How overfitting can be useful. - Peter Sollich; Anders Krogh (NIPS, 1995)

Hidden Markov models for sequence analysis: extension and analysis of the basic method. - Richard Hughey; Anders Krogh (Comput. Appl. Biosci., 1996)

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. - Kimmen Sjölander; Kevin Karplus; Michael Brown; Richard Hughey; Anders Krogh; I. Saira Mian; David Haussler (Comput. Appl. Biosci., 1996)

Improving Predicition of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments. - Søren Kamaric Riis; Anders Krogh (J. Comput. Biol., 1996)

Hidden neural networks: a framework for HMM/NN hybrids. - Søren Kamaric Riis; Anders Krogh (ICASSP, 1997)

Two Methods for Improving Performance of a HMM and their Application for Gene Finding. - Anders Krogh (ISMB, 1997)

Nonlinear backpropagation: doing backpropagation without derivatives of the activation function. - John A. Hertz; Anders Krogh; Benny Lautrup; Torsten Lehmann (IEEE Trans. Neural Networks, 1997)

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids - Richard Durbin; Sean R. Eddy; Anders Krogh; Graeme J. Mitchison (Cambridge University Press, 1998)

Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model. - Henrik Nielsen; Anders Krogh (ISMB, 1998)

A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. - Erik L. L. Sonnhammer; Gunnar von Heijne; Anders Krogh (ISMB, 1998)

Hidden Neural Networks. - Anders Krogh; Søren Kamaric Riis (Neural Comput., 1999)

A General Method for Combining Predictors Tested on Protein Secondary Structure Prediction. - Jakob V. Hansen; Anders Krogh (ANNIMAB, 2000)

ISMB 2001. - Søren Brunak; Anders Krogh (ISMB (Supplement of Bioinformatics), 2001)

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. - Pier Luigi Martelli; Piero Fariselli; Anders Krogh; Rita Casadio (ISMB, 2002)

Bias of Purine Stretches in Sequenced Chromosomes. - David Ussery; Dikeos Mario Soumpasis; Søren Brunak; Hans Henrik Stærfeldt; Peder Worning; Anders Krogh (Comput. Chem., 2002)

EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance. - Thomas Schou Larsen; Anders Krogh (BMC Bioinform., 2003)

The Block Hidden Markov Model for Biological Sequence Analysis. - Kyoung-Jae Won; Adam Prügel-Bennett; Anders Krogh (KES, 2004)

Training HMM structure with genetic algorithm for biological sequence analysis. - Kyoung-Jae Won; Adam Prügel-Bennett; Anders Krogh (Bioinform., 2004)

Evolving hidden Markov models for protein secondary structure prediction. - Kyoung-Jae Won; Thomas Hamelryck; Adam Prügel-Bennett; Anders Krogh (Congress on Evolutionary Computation, 2005)

An HMM posterior decoder for sequence feature prediction that includes homology information. - Lukas Käll; Anders Krogh; Erik L. L. Sonnhammer (ISMB (Supplement of Bioinformatics), 2005)

Large-scale prokaryotic gene prediction and comparison to genome annotation. - Pernille Nielsen; Anders Krogh (Bioinform., 2005)

Measuring covariation in RNA alignments: physical realism improves information measures. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (Bioinform., 2006)

A hidden Markov model approach for determining expression from genomic tiling micro arrays. - Kasper Munch; Paul P. Gardner; Peter Arctander; Anders Krogh (BMC Bioinform., 2006)

Automatic generation of gene finders for eukaryotic species. - Kasper Munch; Anders Krogh (BMC Bioinform., 2006)

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. - Mauro Amico; Michele Finelli; Ivan Rossi; Andrea Zauli; Arne Elofsson; Håkan Viklund; Gunnar von Heijne; David Jones; Anders Krogh; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2006)

Sampling Realistic Protein Conformations Using Local Structural Bias. - Thomas Hamelryck; John T. Kent; Anders Krogh (PLoS Comput. Biol., 2006)

Evolving the structure of hidden Markov models. - Kyoung-Jae Won; Adam Prügel-Bennett; Anders Krogh (IEEE Trans. Evol. Comput., 2006)

Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models. - Piero Fariselli; Daniele Molinini; Rita Casadio; Anders Krogh (BIRD, 2007)

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (Bioinform., 2007)

Multiple alignment and structure prediction of non-coding RNA sequences. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (BMC Bioinform., 2007)

An evolutionary method for learning HMM structure: prediction of protein secondary structure. - Kyoung-Jae Won; Thomas Hamelryck; Adam Prügel-Bennett; Anders Krogh (BMC Bioinform., 2007)

Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. - Lukas Käll; Anders Krogh; Erik L. L. Sonnhammer (Nucleic Acids Res., 2007)

Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants. - Morten Lindow; Anders Jacobsen Skanderup; Sanne Nygaard; Yuan Mang; Anders Krogh (PLoS Comput. Biol., 2007)

Modeling promoter grammars with evolving hidden Markov models. - Kyoung-Jae Won; Albin Sandelin; Troels Torben Marstrand; Anders Krogh (Bioinform., 2008)

BayesMD: Flexible Biological Modeling for Motif Discovery. - Man-Hung Eric Tang; Anders Krogh; Ole Winther (J. Comput. Biol., 2008)

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. - Jan Christian Bryne; Eivind Valen; Man-Hung Eric Tang; Troels Torben Marstrand; Ole Winther; Isabelle da Piedade; Anders Krogh; Boris Lenhard; Albin Sandelin (Nucleic Acids Res., 2008)

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. - Lisa Bartoli; Piero Fariselli; Anders Krogh; Rita Casadio (Bioinform., 2009)

Discovery of Regulatory Elements is Improved by a Discriminatory Approach. - Eivind Valen; Albin Sandelin; Ole Winther; Anders Krogh (PLoS Comput. Biol., 2009)

miRMaid: a unified programming interface for microRNA data resources. - Anders Jacobsen Skanderup; Anders Krogh; Sakari Kauppinen; Morten Lindow (BMC Bioinform., 2010)

Adaptable probabilistic mapping of short reads using position specific scoring matrices. - Peter Kerpedjiev; Jes Frellsen; Stinus Lindgreen; Anders Krogh (BMC Bioinform., 2014)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors. - Mireya Plass; Simon H. Rasmussen; Anders Krogh (PLoS Comput. Biol., 2017)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)

Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. - Iñigo Prada-Luengo; Anders Krogh; Lasse Maretty; Birgitte Regenberg (BMC Bioinform., 2019)

CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data. - Thilde Terkelsen; Anders Krogh; Elena Papaleo (PLoS Comput. Biol., 2020)

The deep generative decoder: Using MAP estimates of representations. - Viktoria Schuster; Anders Krogh (CoRR, 2021)

A Manifold Learning Perspective on Representation Learning: Learning Decoder and Representations without an Encoder. - Viktoria Schuster; Anders Krogh (Entropy, 2021)

The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data. - Viktoria Schuster; Anders Krogh (Bioinform., 2023)

A primer on synthetic health data. - Jennifer Anne Bartell; Sander Boisen Valentin; Anders Krogh; Henning Langberg; Martin Bøgsted (CoRR, 2024)

Riemannian generative decoder. - Andreas Bjerregaard; Søren Hauberg; Anders Krogh (CoRR, 2025)