Anders Krogh
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Danish bioinformatician
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Anders Kroghcomputer-science Degrees
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Computer Science Biology
Anders Krogh's Degrees
- PhD Bioinformatics Technical University of Denmark
- Masters Computer Science Technical University of Denmark
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Why Is Anders Krogh Influential?
(Suggest an Edit or Addition)According to Wikipedia, Anders Krogh is a bioinformatician at the University of Copenhagen, where he leads the university's bioinformatics center. He is known for his pioneering work on the use of hidden Markov models in bioinformatics , and is co-author of a widely used textbook in bioinformatics. In addition, he also co-authored one of the early textbooks on neural networks. His current research interests include promoter analysis, non-coding RNA, gene prediction and protein structure prediction.
Anders Krogh's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. (2001) (11236)
- Introduction to the theory of neural computation (1994) (8287)
- Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence (1998) (7740)
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998) (4580)
- A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences (1998) (2552)
- A combined transmembrane topology and signal peptide prediction method. (2004) (2142)
- Neural Network Ensembles, Cross Validation, and Active Learning (1994) (2092)
- Hidden Markov models in computational biology. Applications to protein modeling. (1993) (2055)
- A Simple Weight Decay Can Improve Generalization (1991) (1563)
- Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server (2007) (1361)
- Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 (2001) (1206)
- Programmed Cell Death 4 (PDCD4) Is an Important Functional Target of the MicroRNA miR-21 in Breast Cancer Cells* (2008) (1094)
- Prediction of lipoprotein signal peptides in Gram‐negative bacteria (2003) (1090)
- Fast and sensitive taxonomic classification for metagenomics with Kaiju (2016) (1003)
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update (2007) (761)
- Ancient human genome sequence of an extinct Palaeo-Eskimo (2010) (754)
- Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse (2013) (706)
- An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia (2011) (675)
- Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model (1998) (569)
- Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization (2014) (567)
- Hidden Markov models for sequence analysis: extension and analysis of the basic method (1996) (533)
- Correction: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax (2015) (531)
- The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line (2009) (441)
- Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology (1996) (395)
- A hidden Markov model that finds genes in E. coli DNA. (1994) (383)
- Learning with ensembles: How overfitting can be useful (1995) (376)
- Prediction of human protein function from post-translational modifications and localization features. (2002) (333)
- microRNA‐101 is a potent inhibitor of autophagy (2011) (330)
- An HMM posterior decoder for sequence feature prediction that includes homology information (2005) (324)
- Two Methods for Improving Performance of a HMM and their Application for Gene Finding (1997) (298)
- A code for transcription initiation in mammalian genomes. (2007) (254)
- What are artificial neural networks? (2008) (250)
- miR-449 inhibits cell proliferation and is down-regulated in gastric cancer (2011) (239)
- The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. (2011) (236)
- No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. (1999) (236)
- Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii (2013) (226)
- Reliability measures for membrane protein topology prediction algorithms. (2003) (223)
- Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families (1993) (220)
- A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins (2002) (212)
- Molecular Composition of IMP1 Ribonucleoprotein Granules*S (2007) (212)
- On the total number of genes and their length distribution in complete microbial genomes. (2001) (194)
- Chapter 4 - An introduction to hidden Markov models for biological sequences (1998) (185)
- EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance (2003) (181)
- Biological sequence analysis: Background on probability (1998) (172)
- Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History (2018) (170)
- MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells (2010) (170)
- A generative, probabilistic model of local protein structure (2008) (158)
- Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome (2014) (156)
- Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology (2014) (151)
- Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. (2014) (150)
- Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. (2009) (149)
- Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios (2015) (148)
- Large-scale prokaryotic gene prediction and comparison to genome annotation (2005) (147)
- MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells (2012) (140)
- Sampling Realistic Protein Conformations Using Local Structural Bias (2006) (136)
- Protein modeling using hidden Markov models: analysis of globins (1993) (133)
- Signatures of RNA binding proteins globally coupled to effective microRNA target sites. (2010) (132)
- Improving ancient DNA read mapping against modern reference genomes (2012) (132)
- SAM: SEQUENCE ALIGNMENT AND MODELING SOFTWARE SYSTEM (1995) (128)
- Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns (2012) (126)
- Statistical mechanics of ensemble learning (1997) (125)
- Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients. (2014) (125)
- DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks (2022) (124)
- Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax (2014) (121)
- Sequencing and de novo assembly of 150 genomes from Denmark as a population reference (2017) (118)
- Reconstructing genome evolution in historic samples of the Irish potato famine pathogen (2013) (108)
- Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. (1996) (108)
- Generalization in a linear perceptron in the presence of noise (1992) (105)
- Biological sequence analysis: Preface (1998) (100)
- Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs (2015) (96)
- Improving Predicition of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments (1996) (95)
- Using database matches with for HMMGene for automated gene detection in Drosophila. (2000) (95)
- Genome organisation and chromatin structure in Escherichia coli. (2001) (94)
- Erratum: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence (1998) (91)
- microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer (2012) (91)
- Computational evidence for hundreds of non-conserved plant microRNAs (2005) (91)
- Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny (2018) (89)
- Hidden Markov models for labeled sequences (1994) (87)
- RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. (2003) (82)
- MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing (2007) (81)
- MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. (2011) (81)
- Sigma A recognition sites in the Bacillus subtilis genome. (2001) (80)
- Naturally occurring nucleosome positioning signals in human exons and introns. (1996) (79)
- Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants (2007) (73)
- Two methods for improving performance of an HMM application for gene finding (1997) (67)
- Hidden Neural Networks (1999) (65)
- De novo assembly of a haplotype-resolved human genome (2015) (65)
- Maximum Entropy Weighting of Aligned Sequences of Proteins or DNA (1995) (64)
- Training HMM structure with genetic algorithm for biological sequence analysis (2004) (63)
- , Introduction to the Theory of Neural Computation 1 (2007) (62)
- Bayesian transcriptome assembly (2014) (60)
- Measuring covariation in RNA alignments: physical realism improves information measures (2006) (55)
- Phase transitions in simple learning (1989) (54)
- An evolutionary method for learning HMM structure: prediction of protein secondary structure (2007) (53)
- Adaptable probabilistic mapping of short reads using position specific scoring matrices (2014) (52)
- Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing (2009) (49)
- A Short‐Read Multiplex Sequencing Method for Reliable, Cost‐Effective and High‐Throughput Genotyping in Large‐Scale Studies (2013) (48)
- Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites (2008) (47)
- CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. (2005) (44)
- Accurate genotyping across variant classes and lengths using variant graphs (2018) (44)
- PONGO: a web server for multiple predictions of all-alpha transmembrane proteins (2006) (43)
- Loss of miR-10a Activates Lpo and Collaborates with Activated Wnt Signaling in Inducing Intestinal Neoplasia in Female Mice (2013) (43)
- Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors (2017) (42)
- A Cost Function for Internal Representations (1989) (42)
- SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. (2015) (41)
- CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information (2009) (41)
- Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin (2015) (39)
- Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. (2016) (39)
- Hidden neural networks: a framework for HMM/NN hybrids (1997) (37)
- Bias of Purine Stretches in Sequenced Chromosomes (2002) (37)
- Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation (2015) (35)
- Hidden Markov Models for prediction of protein features. (2008) (33)
- A Quantitative Study Of Pruning By Optimal Brain Damage (1993) (33)
- Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads (2019) (31)
- Automatic generation of gene finders for eukaryotic species (2006) (31)
- A hidden Markov model approach for determining expression from genomic tiling micro arrays (2006) (31)
- Discovery of Regulatory Elements is Improved by a Discriminatory Approach (2009) (30)
- Evolving the structure of hidden Markov models (2006) (30)
- Learning with noise in a linear perceptron (1992) (29)
- Alterations in Polyadenylation and Its Implications for Endocrine Disease (2013) (28)
- cWords - systematic microRNA regulatory motif discovery from mRNA expression data (2013) (28)
- 11 – Gene Finding: Putting the Parts Together (1998) (27)
- Hierarchical associative networks (1987) (25)
- Kaiju: Fast and sensitive taxonomic classification for metagenomics (2015) (25)
- Nonlinear backpropagation: doing backpropagation without derivatives of the activation function (1997) (25)
- Long- and Short-Term Selective Forces on Malaria Parasite Genomes (2010) (22)
- Hidden Markov Models in Computational Biology Applications to Protein Modeling UCSC CRL (1993) (22)
- miRMaid: a unified programming interface for microRNA data resources (2010) (21)
- Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale (2015) (18)
- Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios (2018) (17)
- Teaching computers to fold proteins. (2003) (15)
- Evolving hidden Markov models for protein secondary structure prediction (2005) (15)
- Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads (2019) (15)
- Novel overlapping coding sequences in Chlamydia trachomatis. (2006) (14)
- Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches (2017) (14)
- On the accuracy of short read mapping. (2013) (14)
- Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models (2007) (14)
- Adaptation of Saccharomyces cerevisiae expressing a heterologous protein. (2008) (13)
- Modeling promoter grammars with evolving hidden Markov models (2008) (13)
- Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors (2014) (13)
- Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju (2020) (13)
- Mean-field analysis of hierarchical associative networks with 'magnetisation' (1988) (13)
- Prediction of Beta Sheets in Proteins (1995) (13)
- A General Method for Combining Predictors Tested on Protein Secondary Structure Prediction (2000) (12)
- Periodic Sequence Patterns in Human Exons (1995) (12)
- Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration (2020) (12)
- Biological sequence analysis: Markov chains and hidden Markov models (1998) (11)
- Bounds on approximate steepest descent for likelihood maximization in exponential families (1994) (11)
- High‐throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype‐specific serologically relevant biomarkers (2020) (10)
- BayesMD: Flexible Biological Modeling for Motif Discovery (2008) (10)
- Rpo D Promoters in Campylobacter jejuni Exhibit a Strong Periodic Signal Instead of a 2 35 Box (2003) (9)
- CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data (2020) (8)
- Multiple alignment and structure prediction of non-coding RNA sequences (2007) (8)
- Hidden Markov Models for Human Genes (1993) (8)
- RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine (2016) (7)
- SNPest: a probabilistic graphical model for estimating genotypes (2014) (7)
- Dynamics of Generalization in Linear Perceptrons (1990) (7)
- The Block Hidden Markov Model for Biological Sequence Analysis (2004) (6)
- Biological sequence analysis: Building phylogenetic trees (1998) (5)
- Fast and sensitive taxonomic classification for metagenomics with (2016) (5)
- 6.03 – Algorithms for Mapping High-Throughput DNA Sequences* (2014) (5)
- Biological sequence analysis: Pairwise alignment (1998) (5)
- Context dependency of nucleotide probabilities and variants in human DNA (2021) (5)
- Multi-Layer Networks (2018) (4)
- Dynamics of Learning in Simple Perceptrons (1989) (4)
- Finiteness Results for Sigmoidal "Neural" Networks (1993) (4)
- A Cost Function for Internal Representations 733 A Cost Function for Internal Representations (1989) (4)
- microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer (2012) (4)
- Algorithms for Mapping High-Throughput DNA Sequences**Jes Frellsen and Peter Menzel contributed equally. (2014) (3)
- Modeling of Rho Dependent Transcription Termination Sites in the Bacterium Helicobacter pylori (2003) (3)
- A Manifold Learning Perspective on Representation Learning: Learning Decoder and Representations without an Encoder (2021) (3)
- Biological sequence analysis: Probabilistic approaches to phylogeny (1998) (3)
- Biological sequence analysis: Profile HMMs for sequence families (1998) (3)
- Biological sequence analysis: RNA structure analysis (1998) (3)
- Transcriptome dynamics of the microRNA inhibition response (2016) (3)
- Biological sequence analysis: Pairwise alignment using HMMs (1998) (3)
- Hidden Markov Models in Computational Biology: Applications to Protein Modeling UCSC-CRL-93-32 (1993) (3)
- Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs (2015) (2)
- Low pass genomes of 141,431 Chinese reveal patterns of viral infection, novel phenotypic associations, and the genetic history of China (2019) (2)
- Prediction of DNA from context using neural networks (2021) (2)
- Non-Linear Back-propagation: Doing Back-Propagation withoutDerivatives of the Activation Function (1997) (2)
- Biological sequence analysis: Multiple sequence alignment methods (1998) (1)
- Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns (2012) (1)
- A Short‐Read Multiplex Sequencing Method for Reliable, Cost‐Effective and High‐Throughput Genotyping in Large‐Scale Studies (2014) (1)
- SNPest: a probabilistic graphical model for estimating genotypes (2014) (1)
- Transcriptome dynamics of the microRNA inhibition response (2015) (1)
- Biological sequence analysis: Introduction (1998) (1)
- Adaptable probabilistic mapping of short reads using position specific scoring matrices (2014) (1)
- ProgrammedCellDeath4(PDCD4)IsanImportantFunctional TargetoftheMicroRNAmiR-21inBreastCancerCells *□ (2008) (1)
- An Exercises Supplement to the Introduction To The Theory Of Neural Computation (2004) (1)
- microRNA target sites Signatures of RNA binding proteins globally coupled to effective Material (2010) (1)
- Joint Estimation of Parameters in Hidden Neural Networks (1996) (1)
- Stability of heterologous protein production by Saccharomyces cerevisiae in continuous cultures (2009) (1)
- Improving The Analysis Of Gene Expression Profiles By Comparing AML Blasts With Their Nearest Normal Counterparts (2013) (0)
- Experiments concerning the Biology of Pyrausta nubilalis Hb. (0)
- The deep generative decoder: Using MAP estimates of representations (2021) (0)
- N-of-one differential gene expression without control samples using a deep generative model (2023) (0)
- Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation (2015) (0)
- Context dependency of nucleotide probabilities and variants in human DNA (2022) (0)
- Probabilities and probabilistic models (2002) (0)
- Formal Statistical Mechanics of Neural Networks (2018) (0)
- Biological sequence analysis: Transformational grammars (1998) (0)
- Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration (2020) (0)
- Sequence MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing (2007) (0)
- Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios (2018) (0)
- 57 miRNA regulation during oncogene-induced senescence (2008) (0)
- Multi-Modal Analysis and Federated Learning Approach for Classification and Personalized Prognostic Assessment in Myeloid Neoplasms (2022) (0)
- Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin (2015) (0)
- Correction to: Context dependency of nucleotide probabilities and variants in human DNA (2022) (0)
- Handout for the Phylogenetics Lecture (2017) (0)
- The Xor Problem (1991) (0)
- The Hopfield Model (2018) (0)
- Biological sequence analysis: Bibliography (1998) (0)
- Extensions of the Hopfield Model (2018) (0)
- The origin of Aboriginal Australians as inferred from the genomic sequence of a hundred-year-old lock of hair (2011) (0)
- Correction to: Context dependency of nucleotide probabilities and variants in human DNA (2022) (0)
- The chemical composition of the phytoplankton of the Friederiksborg-Schlosssee and its importance for the maxima of Cladocera. (0)
- BIOL 495S/ CS 490B/ MATH 490B/ STAT 490B (2002) (0)
- an ancient human genome Genome-wide nucleosome map and cytosine methylation levels of Material Supplemental (2014) (0)
- Improving ancient DNA read mapping against modern reference genomes (2012) (0)
- CAncer bioMarker Prediction Pipeline (CAMPP) - A standardised and user-friendly framework for the analysis of quantitative biological data (2019) (0)
- Unsupervised Hebbian Learning (2018) (0)
- Context dependent prediction in DNA sequence using neural networks (2022) (0)
- Summary of Current Work on Active Learning (2006) (0)
- The Deep Generative Decoder: MAP estimation of representations improves modeling of single-cell RNA data (2021) (0)
- Unsupervised Competitive Learning (2018) (0)
- Artificial neural networks have been applied to problems ranging from speech recognition to prediction of protein secondary structure, classification of cancers and gene prediction. How do they work and what might they be good for? (2008) (0)
- Hongzhi Cao MHC region and its related disease study Method for decipher the polymorphism and fine-mapping disease causal mutations of MHC region (2015) (0)
- Source 2 Feature 1 (0)
- Subdomain Epoch % Improvement Subdomain Epoch % Improvement Substructure Generation in the 2-d Nite Element Mesh Shown in Fig. 2 Using Competitive Learning. Subdomain Epoch % Improvement Subdomain Epoch % Improvement (1993) (0)
- Book review (1998) (0)
- Universitet microRNA-143 down-regulates Hexokinase 2 in colon cancer cells (2012) (0)
- Synthetic Data Generation By Artificial Intelligence to Accelerate Translational Research and Precision Medicine in Hematological Malignancies (2022) (0)
- Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of proteins and miRNAs (2016) (0)
- Bayesian transcriptome assembly (2014) (0)
- METHOD Open Access (2014) (0)
- The transm ission of beet mosaic and beet yellows viruses by aphides ; a com parative study of a non-persistent and a persisten t virus having host plants and vectors (2017) (0)
- Accurate genotyping across variant classes and lengths using variant graphs (2018) (0)
- MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells (2012) (0)
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What Schools Are Affiliated With Anders Krogh?
Anders Krogh is affiliated with the following schools:
