| Year |
Citation |
Score |
| 2020 |
Tovo A, Menzel P, Krogh A, Lagomarsino MC, Suweis S. Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju. Nucleic Acids Research. 48. PMID 32633756 DOI: 10.1093/Nar/Gkaa568 |
0.331 |
|
| 2020 |
Terkelsen T, Krogh A, Papaleo E. CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data. Plos Computational Biology. 16: e1007665. PMID 32176694 DOI: 10.1371/Journal.Pcbi.1007665 |
0.323 |
|
| 2018 |
Sibbesen JA, Maretty L, Krogh A. Accurate genotyping across variant classes and lengths using variant graphs Nature Genetics. 50: 1054-1059. PMID 29915429 DOI: 10.1038/S41588-018-0145-5 |
0.307 |
|
| 2017 |
Elcheninov AG, Menzel P, Gudbergsdottir SR, Slesarev AI, Kadnikov VV, Krogh A, Bonch-Osmolovskaya EA, Peng X, Kublanov IV. Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches. Frontiers in Microbiology. 8: 2140. PMID 29163426 DOI: 10.3389/Fmicb.2017.02140 |
0.316 |
|
| 2017 |
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, ... ... Krogh A, et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature. PMID 28746312 DOI: 10.1038/Nature23264 |
0.362 |
|
| 2017 |
Plass M, Rasmussen SH, Krogh A. Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors. Plos Computational Biology. 13: e1005460. PMID 28410363 DOI: 10.1371/Journal.Pcbi.1005460 |
0.325 |
|
| 2016 |
Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications. 7: 11257. PMID 27071849 DOI: 10.1038/Ncomms11257 |
0.344 |
|
| 2015 |
Liu S, Huang S, Rao J, Ye W, Krogh A, Wang J. Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. Gigascience. 4: 64. PMID 26705468 DOI: 10.1186/S13742-015-0103-4 |
0.387 |
|
| 2015 |
Gudbergsdóttir SR, Menzel P, Krogh A, Young M, Peng X. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environmental Microbiology. PMID 26439881 DOI: 10.1111/1462-2920.13079 |
0.348 |
|
| 2015 |
Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, ... ... Krogh A, et al. Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications. 6: 8051. PMID 26264976 DOI: 10.1038/Ncomms9051 |
0.305 |
|
| 2015 |
Wen J, Leucci E, Vendramin R, Kauppinen S, Lund AH, Krogh A, Parker BJ. Transcriptome dynamics of the microRNA inhibition response. Nucleic Acids Research. PMID 26089393 DOI: 10.1093/Nar/Gkv603 |
0.308 |
|
| 2015 |
Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, ... ... Krogh A, et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology. 33: 617-22. PMID 26006006 DOI: 10.1038/Nbt.3200 |
0.374 |
|
| 2015 |
Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, ... ... Krogh A, et al. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications. 6: 5969. PMID 25597990 DOI: 10.1038/Ncomms6969 |
0.329 |
|
| 2014 |
Cao H, Hastie AR, Cao D, Lam ET, Sun Y, Huang H, Liu X, Lin L, Andrews W, Chan S, Huang S, Tong X, Requa M, Anantharaman T, Krogh A, et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience. 3: 34. PMID 25671094 DOI: 10.1186/2047-217X-3-34 |
0.379 |
|
| 2014 |
Maretty L, Sibbesen JA, Krogh A. Bayesian transcriptome assembly. Genome Biology. 15: 501. PMID 25367074 DOI: 10.1186/S13059-014-0501-4 |
0.331 |
|
| 2014 |
Lindgreen S, Krogh A, Pedersen JS. SNPest: a probabilistic graphical model for estimating genotypes. Bmc Research Notes. 7: 698. PMID 25294605 DOI: 10.1186/1756-0500-7-698 |
0.33 |
|
| 2014 |
Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, ... ... Krogh A, et al. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Reports. 8: 1354-64. PMID 25176646 DOI: 10.1016/J.Celrep.2014.07.030 |
0.338 |
|
| 2014 |
Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, ... ... Krogh A, et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications. 5: 3966. PMID 24892994 DOI: 10.1038/Ncomms4966 |
0.342 |
|
| 2014 |
Kerpedjiev P, Frellsen J, Lindgreen S, Krogh A. Adaptable probabilistic mapping of short reads using position specific scoring matrices. Bmc Bioinformatics. 15: 100. PMID 24717095 DOI: 10.1186/1471-2105-15-100 |
0.337 |
|
| 2014 |
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, ... ... Krogh A, et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences of the United States of America. 111: 5135-40. PMID 24591624 DOI: 10.1073/Pnas.1400975111 |
0.383 |
|
| 2014 |
Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, ... ... Krogh A, et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Research. 24: 454-66. PMID 24299735 DOI: 10.1101/Gr.163592.113 |
0.337 |
|
| 2013 |
Cao H, Wang Y, Zhang W, Chai X, Zhang X, Chen S, Yang F, Zhang C, Guo Y, Liu Y, Tang Z, Chen C, Xue Y, Zhen H, Xu Y, ... ... Krogh A, et al. A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Human Mutation. 34: 1715-20. PMID 24014314 DOI: 10.1002/Humu.22439 |
0.313 |
|
| 2013 |
Menzel P, Frellsen J, Plass M, Rasmussen SH, Krogh A. On the accuracy of short read mapping. Methods in Molecular Biology (Clifton, N.J.). 1038: 39-59. PMID 23872968 DOI: 10.1007/978-1-62703-514-9_3 |
0.315 |
|
| 2013 |
Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF, Seguin-Orlando A, Wales N, Orlando L, Ho SY, Dietrich FS, Mieczkowski PA, Heitman J, Willerslev E, Krogh A, Ristaino JB, et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications. 4: 2172. PMID 23863894 DOI: 10.1038/Ncomms3172 |
0.311 |
|
| 2013 |
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, ... ... Krogh A, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499: 74-8. PMID 23803765 DOI: 10.1038/Nature12323 |
0.35 |
|
| 2013 |
Rasmussen SH, Jacobsen A, Krogh A. cWords - systematic microRNA regulatory motif discovery from mRNA expression data. Silence. 4: 2. PMID 23688306 DOI: 10.1186/1758-907X-4-2 |
0.318 |
|
| 2013 |
Rehfeld A, Plass M, Krogh A, Friis-Hansen L. Alterations in polyadenylation and its implications for endocrine disease. Frontiers in Endocrinology. 4: 53. PMID 23658553 DOI: 10.3389/Fendo.2013.00053 |
0.324 |
|
| 2013 |
Bagger FO, Jendholm J, Mora-Jensen HI, Krogh A, Kohlmann A, Thiede C, Borregaard N, Bullinger L, Winther O, Theilgaard-Mönch K, Porse B. Improving The Analysis Of Gene Expression Profiles By Comparing AML Blasts With Their Nearest Normal Counterparts Blood. 122: 2568-2568. DOI: 10.1182/Blood.V122.21.2568.2568 |
0.309 |
|
| 2012 |
Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L. Improving ancient DNA read mapping against modern reference genomes. Bmc Genomics. 13: 178. PMID 22574660 DOI: 10.1186/1471-2164-13-178 |
0.37 |
|
| 2011 |
Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJ, Wang J, et al. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Research. 21: 1339-48. PMID 21719571 DOI: 10.1101/Gr.121392.111 |
0.368 |
|
| 2011 |
Wen J, Parker BJ, Jacobsen A, Krogh A. MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. Rna (New York, N.Y.). 17: 820-34. PMID 21389147 DOI: 10.1261/Rna.2387911 |
0.311 |
|
| 2010 |
Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC. Long- and short-term selective forces on malaria parasite genomes. Plos Genetics. 6: e1001099. PMID 20838588 DOI: 10.1371/Journal.Pgen.1001099 |
0.352 |
|
| 2010 |
Jacobsen A, Wen J, Marks DS, Krogh A. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Research. 20: 1010-9. PMID 20508147 DOI: 10.1101/Gr.103259.109 |
0.315 |
|
| 2010 |
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, ... ... Krogh A, et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 463: 757-62. PMID 20148029 DOI: 10.1038/Nature08835 |
0.355 |
|
| 2009 |
Valen E, Sandelin A, Winther O, Krogh A. Discovery of regulatory elements is improved by a discriminatory approach. Plos Computational Biology. 5: e1000562. PMID 19911049 DOI: 10.1371/Journal.Pcbi.1000562 |
0.395 |
|
| 2009 |
Bartoli L, Fariselli P, Krogh A, Casadio R. CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics (Oxford, England). 25: 2757-63. PMID 19744995 DOI: 10.1093/Bioinformatics/Btp539 |
0.369 |
|
| 2009 |
Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, ... ... Krogh A, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41: 553-62. PMID 19377474 DOI: 10.1038/Ng.375 |
0.314 |
|
| 2009 |
Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research. 19: 255-65. PMID 19074369 DOI: 10.1101/Gr.084541.108 |
0.377 |
|
| 2008 |
Boomsma W, Mardia KV, Taylor CC, Ferkinghoff-Borg J, Krogh A, Hamelryck T. A generative, probabilistic model of local protein structure. Proceedings of the National Academy of Sciences of the United States of America. 105: 8932-7. PMID 18579771 DOI: 10.1073/Pnas.0801715105 |
0.313 |
|
| 2008 |
Won KJ, Sandelin A, Marstrand TT, Krogh A. Modeling promoter grammars with evolving hidden Markov models. Bioinformatics (Oxford, England). 24: 1669-75. PMID 18535083 DOI: 10.1093/Bioinformatics/Btn254 |
0.348 |
|
| 2008 |
Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A. Asap: a framework for over-representation statistics for transcription factor binding sites. Plos One. 3: e1623. PMID 18286180 DOI: 10.1371/Journal.Pone.0001623 |
0.326 |
|
| 2008 |
Bystroff C, Krogh A. Hidden Markov Models for prediction of protein features. Methods in Molecular Biology (Clifton, N.J.). 413: 173-98. PMID 18075166 DOI: 10.1007/978-1-59745-574-9_7 |
0.337 |
|
| 2008 |
Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome Research. 18: 1-12. PMID 18032727 DOI: 10.1101/Gr.6831208 |
0.34 |
|
| 2007 |
Lindgreen S, Gardner PP, Krogh A. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics (Oxford, England). 23: 3304-11. PMID 18006551 DOI: 10.1093/Bioinformatics/Btm525 |
0.342 |
|
| 2007 |
Won KJ, Hamelryck T, Prügel-Bennett A, Krogh A. An evolutionary method for learning HMM structure: prediction of protein secondary structure. Bmc Bioinformatics. 8: 357. PMID 17888163 DOI: 10.1186/1471-2105-8-357 |
0.371 |
|
| 2007 |
Lindgreen S, Gardner PP, Krogh A. Multiple alignment and structure prediction of non-coding RNA sequences Bmc Bioinformatics. 8: 8. DOI: 10.1186/1471-2105-8-S8-P8 |
0.332 |
|
| 2006 |
Jensen KT, Petersen L, Falk S, Iversen P, Andersen P, Theisen M, Krogh A. Novel overlapping coding sequences in Chlamydia trachomatis. Fems Microbiology Letters. 265: 106-17. PMID 17038047 DOI: 10.1111/J.1574-6968.2006.00480.X |
0.334 |
|
| 2006 |
Hamelryck T, Kent JT, Krogh A. Sampling realistic protein conformations using local structural bias. Plos Computational Biology. 2: e131. PMID 17002495 DOI: 10.1371/Journal.Pcbi.0020131 |
0.309 |
|
| 2006 |
Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Luigi Martelli P, Casadio R. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Research. 34: W169-72. PMID 16844984 DOI: 10.1093/Nar/Gkl208 |
0.362 |
|
| 2006 |
Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. Bmc Bioinformatics. 7: 263. PMID 16712739 DOI: 10.1186/1471-2105-7-263 |
0.338 |
|
| 2006 |
Munch K, Gardner PP, Arctander P, Krogh A. A hidden Markov model approach for determining expression from genomic tiling micro arrays. Bmc Bioinformatics. 7: 239. PMID 16672042 DOI: 10.1186/1471-2105-7-239 |
0.329 |
|
| 2005 |
Nielsen P, Krogh A. Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics (Oxford, England). 21: 4322-9. PMID 16249266 DOI: 10.1093/Bioinformatics/Bti701 |
0.387 |
|
| 2005 |
Käll L, Krogh A, Sonnhammer EL. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (Oxford, England). 21: i251-7. PMID 15961464 DOI: 10.1093/Bioinformatics/Bti1014 |
0.344 |
|
| 2003 |
Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Science : a Publication of the Protein Society. 12: 1652-62. PMID 12876315 DOI: 10.1110/Ps.0303703 |
0.326 |
|
| 2003 |
Melén K, Krogh A, von Heijne G. Reliability measures for membrane protein topology prediction algorithms. Journal of Molecular Biology. 327: 735-44. PMID 12634065 DOI: 10.1016/S0022-2836(03)00182-7 |
0.348 |
|
| 2002 |
Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319: 1257-65. PMID 12079362 DOI: 10.1016/S0022-2836(02)00379-0 |
0.323 |
|
| 2001 |
Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, ... ... Krogh A, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 413: 848-52. PMID 11677608 DOI: 10.1038/35101607 |
0.332 |
|
| 2001 |
Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S. Genome organisation and chromatin structure in Escherichia coli. Biochimie. 83: 201-12. PMID 11278070 DOI: 10.1016/S0300-9084(00)01225-6 |
0.326 |
|
| 2001 |
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology. 305: 567-80. PMID 11152613 DOI: 10.1006/Jmbi.2000.4315 |
0.335 |
|
| 1999 |
Workman C, Krogh A. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Research. 27: 4816-22. PMID 10572183 DOI: 10.1093/Nar/27.24.4816 |
0.308 |
|
| 1998 |
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, ... ... Krogh A, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393: 537-44. PMID 9634230 DOI: 10.1038/31159 |
0.345 |
|
| 1998 |
Krogh A. Chapter 4 - An introduction to hidden Markov models for biological sequences New Comprehensive Biochemistry. 32: 45-63. DOI: 10.1016/S0167-7306(08)60461-5 |
0.351 |
|
| 1996 |
Riis SK, Krogh A. Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. Journal of Computational Biology. 3: 163-183. PMID 8697234 DOI: 10.1089/Cmb.1996.3.163 |
0.309 |
|
| 1994 |
Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. Journal of Molecular Biology. 235: 1501-31. PMID 8107089 DOI: 10.1006/Jmbi.1994.1104 |
0.334 |
|
| 1994 |
Krogh A, Mian IS, Haussler D. A Hidden Markov Model That Finds Genes In E. Coli Dna Nucleic Acids Research. 22: 4768-4778. PMID 7984429 DOI: 10.1093/Nar/22.22.4768 |
0.354 |
|
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