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List of works by Anders Krogh

A Cost Function for Internal Representations ⬇️

scientific article published in January 1990

A QUANTITATIVE STUDY OF PRUNING BY OPTIMAL BRAIN DAMAGE

scientific article (publication date: June 1993)

A Short-Read Multiplex Sequencing Method for Reliable, Cost-Effective and High-Throughput Genotyping in Large-Scale Studies

A Simple Weight Decay Can Improve Generalization ⬇️

scientific article published in January 1992

A code for transcription initiation in mammalian genomes

scientific article

A combined transmembrane topology and signal peptide prediction method

scientific article (publication date: 14 May 2004)

A generative, probabilistic model of local protein structure

scientific article

A hidden Markov model approach for determining expression from genomic tiling micro arrays

scientific article

A hidden Markov model that finds genes in E. coli DNA

scientific article

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins

scientific article

A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies

scientific article published on 7 October 2013

Accurate genotyping across variant classes and lengths using variant graphs

scientific article published on 18 June 2018

Adaptable probabilistic mapping of short reads using position specific scoring matrices

scientific article

Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes.

scientific article

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

scientific article

Algorithms for Mapping High-Throughput DNA Sequences

Alterations in Polyadenylation and Its Implications for Endocrine Disease ⬇️

scientific article published on May 8, 2013

Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors

scientific article published on 15 April 2014

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An HMM posterior decoder for sequence feature prediction that includes homology information

scientific article published in June 2005

An evolutionary method for learning HMM structure: prediction of protein secondary structure

scientific article

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Asap: a framework for over-representation statistics for transcription factor binding sites

scientific article published in 2008

Automatic generation of gene finders for eukaryotic species

scientific article published in 2006

BayesMD: flexible biological modeling for motif discovery

scientific article published in December 2008

Bayesian transcriptome assembly

scientific article

Bias of purine stretches in sequenced chromosomes

scientific article published in July 2002

Bounds on approximate steepest descent for likelihood maximization in exponential families

article by N. Cesa-Bianchi et al published July 1994 in IEEE Transactions on Information Theory

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.

scientific article

Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin

scientific article published on 19 March 2015

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

scientific article published on 25 February 2015

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients.

scientific article

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

scientific article

Computational evidence for hundreds of non-conserved plant microRNAs

scientific article

Context dependency of nucleotide probabilities and variants in human DNA

scientific article published on 31 January 2022

De novo assembly of a haplotype-resolved human genome.

scientific article

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

scientific article published in Nature

Discovery of regulatory elements is improved by a discriminatory approach

scientific article

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale

scientific article

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

scientific article published on 9 June 2015

Dynamics of Generalization in Linear Perceptrons ⬇️

Dynamics of Learning in Simple Perceptrons

article

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

scholarly article published 10 September 2018

EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance

scientific article

Erratum: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

scientific article published in Nature Communications

Evolving the structure of hidden Markov models

Fast and sensitive taxonomic classification for metagenomics with Kaiju

scientific article published on 13 April 2016

Gene Finding: Putting the Parts Together

article

Generalization in a linear perceptron in the presence of noise

Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii

scientific article

Genome organisation and chromatin structure in Escherichia coli

scientific article published on February 2001

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.

scientific article published on 3 June 2014

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

scientific article

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

scientific article (publication date: March 2014)

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Hidden Markov Models for Human Genes ⬇️

scientific article published in January 1994

Hidden Markov Models for prediction of protein features.

scientific article

Hidden Markov models in computational biology. Applications to protein modeling

scientific article (publication date: 4 February 1994)

Hidden neural networks

scientific article published in February 1999

Hierarchical associative networks

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors

scientific article

ISMB 2001

scientific article (publication date: June 2001)

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

scientific article

Improving ancient DNA read mapping against modern reference genomes

scientific article (publication date: 10 May 2012)

Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments

scientific article published in January 1996

Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants

scientific article

Introduction to the Theory of Neural Computation

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

scientific article

Large-scale prokaryotic gene prediction and comparison to genome annotation

scientific article

Learning with ensembles: How overfitting can be useful ⬇️

scientific article published in January 1996

Learning with noise in a linear perceptron

Long- and short-term selective forces on malaria parasite genomes

scientific article

Loss of miR-10a activates lpo and collaborates with activated Wnt signaling in inducing intestinal neoplasia in female mice

scientific article

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

scientific article

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

scientific article

Mean-field analysis of hierarchical associative networks with 'magnetisation'

Measuring covariation in RNA alignments: physical realism improves information measures

scientific article

MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action

scientific article

MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells ⬇️

scientific article published on June 12, 2012

MicroRNA-145 targets YES and STAT1 in colon cancer cells

scientific article

Modeling promoter grammars with evolving hidden Markov models.

scientific article published on 05 June 2008

Molecular composition of IMP1 ribonucleoprotein granules

scientific article

Multiple alignment and structure prediction of non-coding RNA sequences

Naturally occurring nucleosome positioning signals in human exons and introns

scientific article published in November 1996

Neural Network Ensembles, Cross Validation, and Active Learning ⬇️

scientific article published in January 1995

No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

scientific article published on December 1999

Nonlinear backpropagation: doing backpropagation without derivatives of the activation function

scientific article published in January 1997

Novel overlapping coding sequences in Chlamydia trachomatis

scientific article published on 13 October 2006

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios ⬇️

scientific article

Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs

scientific article published on 6 October 2015

On the accuracy of short read mapping

scientific article

On the total number of genes and their length distribution in complete microbial genomes

scientific article published in August 2001

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

scientific article published on July 2006

Periodic sequence patterns in human exons

scientific article published on January 1, 1995

Phase transitions in simple learning

article by J A Hertz et al published 21 June 1989 in Journal of Physics A

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

scientific article (publication date: 19 January 2001)

Prediction of Beta Sheets in Proteins ⬇️

scientific article published in January 1996

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

scientific article (publication date: June 2002)

Prediction of lipoprotein signal peptides in Gram-negative bacteria

scientific article published on August 2003

Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells

scientific article

RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine

scientific article

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

scientific article

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

scientific article

Reliability measures for membrane protein topology prediction algorithms

scientific article

RpoD Promoters in Campylobacter jejuni Exhibit a Strong Periodic Signal Instead of a −35 Box

scientific article published on 01 March 2003

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

scientific article

SNPest: a probabilistic graphical model for estimating genotypes

scientific article

Sampling realistic protein conformations using local structural bias ⬇️

scientific article

Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads ⬇️

scientific article published on 12 December 2019

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

scientific article published in Nature

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

scientific article (publication date: August 2010)

Statistical mechanics of ensemble learning

Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches

scientific article published on 2 November 2017

Teaching computers to fold proteins

scientific article

The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming.

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Training HMM structure with genetic algorithm for biological sequence analysis

article

Transcriptome dynamics of the microRNA inhibition response

scientific article published on 18 June 2015

Transcriptome dynamics of the microRNA inhibition response

scientific article published on 09 February 2016

Using database matches with for HMMGene for automated gene detection in Drosophila

scientific article

What are artificial neural networks?

scientific article published on February 2008

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

scientific article

cWords - systematic microRNA regulatory motif discovery from mRNA expression data

scientific article

miR-449 inhibits cell proliferation and is down-regulated in gastric cancer

scientific article

miRMaid: a unified programming interface for microRNA data resources

scientific article

microRNA-101 is a potent inhibitor of autophagy

scientific article published on 13 September 2011

microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer

scientific article

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