77 Publications

Mark all

[77]
2020 | Journal Article | IST-REx-ID: 7889
T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38, pp. 944–946, 2020.
View | Files available | DOI | PubMed | Europe PMC
 
[76]
2020 | Journal Article | IST-REx-ID: 7931 | OA
L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10, 2020.
View | Files available | DOI
 
[75]
2020 | Report | IST-REx-ID: 8151
M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
View | Files available
 
[74]
2020 | Journal Article | IST-REx-ID: 8645 | OA
L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6, pp. 1960–1962, 2020.
View | Files available | DOI | PubMed | Europe PMC
 
[73]
2019 | Journal Article | IST-REx-ID: 7181 | OA
E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12, pp. 1466–1470, 2019.
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[72]
2019 | Journal Article | IST-REx-ID: 6419 | OA
V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4, 2019.
View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 5780 | OA
A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, pp. 12728–12732, 2018.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995 | OA
D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21, pp. 3653–3658, 2018.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279 | OA
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19, 2018.
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 849
A. Saint Léger et al., “Saturation of recognition elements blocks evolution of new tRNA identities,” Science advances, vol. 2, no. 4, pp. e1501860–e1501860, 2016.
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 850
K. Sarkisyan et al., “Local fitness landscape of the green fluorescent protein,” Nature, vol. 533, pp. 397–401, 2016.
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 853
E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions,” Biogeosciences, vol. 13, no. 7, pp. 2207–2219, 2016.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 896
K. Howe et al., “Structure and evolutionary history of a large family of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4, 2016.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 848
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2, pp. 542–554, 2015.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 866
C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30, pp. 9328–9333, 2015.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 886
D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1, pp. 24–33, 2015.
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 906
O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5, 2015.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11, pp. 3016–3025, 2014.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8, pp. 1949–1955, 2014.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 856
K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5, 2014.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 863
L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503, pp. 109–114, 2014.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 865
A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4, pp. 571–578, 2014.
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 892
D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26, no. 1, pp. 104–112, 2014.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 894
R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1, 2013.
View | DOI
 
[53]
2013 | Journal Article | IST-REx-ID: 899
M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451, pp. E2–E3, 2013.
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 905 | OA
V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29, pp. 25–30, 2013.
View | Download (ext.)
 
[51]
2012 | Journal Article | IST-REx-ID: 846
O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12, pp. 1213–1222, 2012.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7, 2012.
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 887
F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, pp. 5048–5057, 2012.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 900
M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421, pp. 535–538, 2012.
View | DOI
 
[47]
2011 | Book Chapter | IST-REx-ID: 881
F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.
View | DOI
 
[46]
2011 | Journal Article | IST-REx-ID: 890
E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,” PLoS One, vol. 6, no. 4, 2011.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” Nature, vol. 465, no. 7300, pp. 922–926, 2010.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 862
M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature, vol. 464, no. 7286, pp. 279–282, 2010.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 872
F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, pp. 1169–1176, 2010.
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 884
A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” Biology Direct, vol. 5, 2010.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 891
H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” Nature Reviews Genetics, vol. 11, no. 2, pp. 97–108, 2010.
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 901
M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” Biology Direct, vol. 5, 2010.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing archaea,” FEBS Letters, vol. 583, no. 21, pp. 3455–3460, 2009.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 844
S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” PLoS Genetics, vol. 4, no. 11, 2008.
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 895
Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary Biology, vol. 8, no. 1, 2008.
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 907
R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” Trends in Genetics, vol. 24, no. 10, pp. 475–478, 2008.
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 860
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” American Journal of Human Genetics, vol. 81, no. 1, pp. 32–43, 2007.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 861
K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC Bioinformatics, vol. 8, 2007.
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 879
F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity of tuf duplicates in γ-proteobacteria,” Trends in Genetics, vol. 23, no. 5, pp. 215–218, 2007.
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 904
G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov, “Extensive parallelism in protein evolution,” Biology Direct, vol. 2, 2007.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 854
E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3, pp. 0403–0410, 2006.
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 868
F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova, “Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation,” Biology Direct, vol. 1, 2006.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 869
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4, pp. 616–626, 2006.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,” Journal of Theoretical Biology, vol. 239, no. 2, pp. 141–151, 2006.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 903
V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis,” BMC Cancer, vol. 6, 2006.
View | DOI
 
[26]
2005 | Journal Article | IST-REx-ID: 843
L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21, pp. 3191–3201, 2005.
View | DOI
 
[25]
2005 | Journal Article | IST-REx-ID: 877
F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3, pp. 389–395, 2005.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
2005 | Journal Article | IST-REx-ID: 878
F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1, pp. 9–10, 2005.
View | DOI
 
[23]
2005 | Journal Article | IST-REx-ID: 880
F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3, pp. 396–403, 2005.
View | Download None (ext.) | PubMed | Europe PMC
 
[22]
2005 | Journal Article | IST-REx-ID: 882
F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16, pp. 2415–2419, 2005.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 893
I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026, pp. 633–638, 2005.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4, pp. 884–892, 2004.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 870
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5, pp. 1731–1737, 2004.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 875
F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7, pp. 287–291, 2004.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 889
A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11, pp. 1207–1212, 2004.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 898
G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” Nature, vol. 429, no. 6991, pp. 558–562, 2004.
View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5, pp. 802–811, 2004.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 847
S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection, mutation rate and genetic drift on human genetic variation,” Human Molecular Genetics, vol. 12, no. 24, pp. 3325–3330, 2003.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 876
F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences,” Trends in Genetics, vol. 19, no. 3, pp. 115–119, 2003.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 859
A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no. 2, pp. 202–210, 2002.
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 871
F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution of gene duplications ,” Genome Biology, vol. 3, no. 2, 2002.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities in protein evolution,” PNAS, vol. 99, no. 23, pp. 14878–14883, 2002.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection for short introns in highly expressed genes,” Nature Genetics, vol. 31, no. 4, pp. 415–418, 2002.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 841
Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9, pp. 499–501, 2001.
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 851
I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2, pp. 83–102, 2001.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 855
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10, pp. 890–900, 2001.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 867
F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23, pp. 2661–2669, 2001.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 874
F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21, pp. 12089–12092, 2001.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 888
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12, 2001.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8, pp. 333–334, 2000.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in the course of sympatric speciation,” Nature, vol. 400, no. 6742, pp. 351–354, 1999.
View | DOI
 

Search

Filter Publications

77 Publications

Mark all

[77]
2020 | Journal Article | IST-REx-ID: 7889
T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38, pp. 944–946, 2020.
View | Files available | DOI | PubMed | Europe PMC
 
[76]
2020 | Journal Article | IST-REx-ID: 7931 | OA
L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10, 2020.
View | Files available | DOI
 
[75]
2020 | Report | IST-REx-ID: 8151
M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
View | Files available
 
[74]
2020 | Journal Article | IST-REx-ID: 8645 | OA
L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6, pp. 1960–1962, 2020.
View | Files available | DOI | PubMed | Europe PMC
 
[73]
2019 | Journal Article | IST-REx-ID: 7181 | OA
E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12, pp. 1466–1470, 2019.
View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[72]
2019 | Journal Article | IST-REx-ID: 6419 | OA
V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4, 2019.
View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 5780 | OA
A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, pp. 12728–12732, 2018.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995 | OA
D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21, pp. 3653–3658, 2018.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279 | OA
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19, 2018.
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 849
A. Saint Léger et al., “Saturation of recognition elements blocks evolution of new tRNA identities,” Science advances, vol. 2, no. 4, pp. e1501860–e1501860, 2016.
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 850
K. Sarkisyan et al., “Local fitness landscape of the green fluorescent protein,” Nature, vol. 533, pp. 397–401, 2016.
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 853
E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions,” Biogeosciences, vol. 13, no. 7, pp. 2207–2219, 2016.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 896
K. Howe et al., “Structure and evolutionary history of a large family of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4, 2016.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 848
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2, pp. 542–554, 2015.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 866
C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30, pp. 9328–9333, 2015.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 886
D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1, pp. 24–33, 2015.
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 906
O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5, 2015.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11, pp. 3016–3025, 2014.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8, pp. 1949–1955, 2014.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 856
K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5, 2014.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 863
L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503, pp. 109–114, 2014.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 865
A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4, pp. 571–578, 2014.
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 892
D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26, no. 1, pp. 104–112, 2014.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 894
R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1, 2013.
View | DOI
 
[53]
2013 | Journal Article | IST-REx-ID: 899
M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451, pp. E2–E3, 2013.
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 905 | OA
V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29, pp. 25–30, 2013.
View | Download (ext.)
 
[51]
2012 | Journal Article | IST-REx-ID: 846
O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12, pp. 1213–1222, 2012.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7, 2012.
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 887
F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, pp. 5048–5057, 2012.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 900
M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421, pp. 535–538, 2012.
View | DOI
 
[47]
2011 | Book Chapter | IST-REx-ID: 881
F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.
View | DOI
 
[46]
2011 | Journal Article | IST-REx-ID: 890
E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,” PLoS One, vol. 6, no. 4, 2011.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” Nature, vol. 465, no. 7300, pp. 922–926, 2010.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 862
M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature, vol. 464, no. 7286, pp. 279–282, 2010.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 872
F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, pp. 1169–1176, 2010.
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 884
A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” Biology Direct, vol. 5, 2010.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 891
H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” Nature Reviews Genetics, vol. 11, no. 2, pp. 97–108, 2010.
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 901
M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” Biology Direct, vol. 5, 2010.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing archaea,” FEBS Letters, vol. 583, no. 21, pp. 3455–3460, 2009.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 844
S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” PLoS Genetics, vol. 4, no. 11, 2008.
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 895
Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary Biology, vol. 8, no. 1, 2008.
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 907
R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” Trends in Genetics, vol. 24, no. 10, pp. 475–478, 2008.
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 860
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” American Journal of Human Genetics, vol. 81, no. 1, pp. 32–43, 2007.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 861
K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC Bioinformatics, vol. 8, 2007.
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 879
F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity of tuf duplicates in γ-proteobacteria,” Trends in Genetics, vol. 23, no. 5, pp. 215–218, 2007.
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 904
G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov, “Extensive parallelism in protein evolution,” Biology Direct, vol. 2, 2007.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 854
E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3, pp. 0403–0410, 2006.
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 868
F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova, “Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation,” Biology Direct, vol. 1, 2006.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 869
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4, pp. 616–626, 2006.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,” Journal of Theoretical Biology, vol. 239, no. 2, pp. 141–151, 2006.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 903
V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis,” BMC Cancer, vol. 6, 2006.
View | DOI
 
[26]
2005 | Journal Article | IST-REx-ID: 843
L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21, pp. 3191–3201, 2005.
View | DOI
 
[25]
2005 | Journal Article | IST-REx-ID: 877
F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3, pp. 389–395, 2005.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
2005 | Journal Article | IST-REx-ID: 878
F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1, pp. 9–10, 2005.
View | DOI
 
[23]
2005 | Journal Article | IST-REx-ID: 880
F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3, pp. 396–403, 2005.
View | Download None (ext.) | PubMed | Europe PMC
 
[22]
2005 | Journal Article | IST-REx-ID: 882
F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16, pp. 2415–2419, 2005.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 893
I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026, pp. 633–638, 2005.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4, pp. 884–892, 2004.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 870
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5, pp. 1731–1737, 2004.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 875
F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7, pp. 287–291, 2004.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 889
A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11, pp. 1207–1212, 2004.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 898
G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” Nature, vol. 429, no. 6991, pp. 558–562, 2004.
View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5, pp. 802–811, 2004.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 847
S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection, mutation rate and genetic drift on human genetic variation,” Human Molecular Genetics, vol. 12, no. 24, pp. 3325–3330, 2003.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 876
F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences,” Trends in Genetics, vol. 19, no. 3, pp. 115–119, 2003.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 859
A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no. 2, pp. 202–210, 2002.
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 871
F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution of gene duplications ,” Genome Biology, vol. 3, no. 2, 2002.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities in protein evolution,” PNAS, vol. 99, no. 23, pp. 14878–14883, 2002.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection for short introns in highly expressed genes,” Nature Genetics, vol. 31, no. 4, pp. 415–418, 2002.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 841
Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9, pp. 499–501, 2001.
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 851
I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2, pp. 83–102, 2001.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 855
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10, pp. 890–900, 2001.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 867
F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23, pp. 2661–2669, 2001.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 874
F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21, pp. 12089–12092, 2001.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 888
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12, 2001.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8, pp. 333–334, 2000.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in the course of sympatric speciation,” Nature, vol. 400, no. 6742, pp. 351–354, 1999.
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