Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L.,https://doi.org/10.1126/sciadv.adk1992__Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science.https://doi.org/10.1126/sciadv.adk1992 
LibreCat: https://research-explorer.ista.ac.at/record/15179
DOI: 10.1126/sciadv.adk1992

Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E.,https://doi.org/10.1371/journal.pone.0282689__Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science.https://doi.org/10.1371/journal.pone.0282689 
LibreCat: https://research-explorer.ista.ac.at/record/12758
DOI: 10.1371/journal.pone.0282689
WoS: 000985134400106

Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L.,https://doi.org/10.1038/s41467-023-39317-4__Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature.https://doi.org/10.1038/s41467-023-39317-4 
LibreCat: https://research-explorer.ista.ac.at/record/13164
DOI: 10.1038/s41467-023-39317-4
WoS: 001048208600023

Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O.,https://doi.org/10.1093/gigascience/giad045__Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic.https://doi.org/10.1093/gigascience/giad045 
LibreCat: https://research-explorer.ista.ac.at/record/13976
DOI: 10.1093/gigascience/giad045
WoS: 001081086100001
PMID: 37496156

Rella, S., Kulikova, Y., Minnegalieva, A., &; Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press.https://doi.org/10.1093/eurpub/ckad160.597 
LibreCat: https://research-explorer.ista.ac.at/record/14862
DOI: 10.1093/eurpub/ckad160.597

Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S.,https://doi.org/10.1038/s41592-022-01444-z__Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. Springer Nature.https://doi.org/10.1038/s41592-022-01444-z 
LibreCat: https://research-explorer.ista.ac.at/record/11187
DOI: 10.1038/s41592-022-01444-z
WoS: 000781199600011
PMID: 35396471

Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-022-10827-3 
LibreCat: https://research-explorer.ista.ac.at/record/11344
DOI: 10.1038/s41598-022-10827-3
WoS: 000788639400032
PMID: 35477739

Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J.,https://doi.org/10.7554/elife.75842__Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.75842 
LibreCat: https://research-explorer.ista.ac.at/record/11448
DOI: 10.7554/elife.75842
WoS: 000799197200001

Saona Urmeneta, R. J., Kondrashov, F., &; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature.https://doi.org/10.1007/s11538-022-01029-z 
LibreCat: https://research-explorer.ista.ac.at/record/11447
DOI: 10.1007/s11538-022-01029-z
WoS: 000812509800001

Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S.,https://doi.org/10.1126/science.adg0797__Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.adg0797 
LibreCat: https://research-explorer.ista.ac.at/record/12116
DOI: 10.1126/science.adg0797
WoS: 000963463700023

Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature.https://doi.org/10.1038/s41431-021-00836-7 
LibreCat: https://research-explorer.ista.ac.at/record/9910
DOI: 10.1038/s41431-021-00836-7
WoS: 000625853200001
PMID: 33664501

Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-021-95025-3 
LibreCat: https://research-explorer.ista.ac.at/record/9905
DOI: 10.1038/s41598-021-95025-3
WoS: 000683329100001
PMID: 34330988

Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik, N. N.,  Tomanek, I. (2020). Core Project Proceedings. IST Austria.
LibreCat: https://research-explorer.ista.ac.at/record/8151

Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V.,https://doi.org/10.1038/s41598-020-65406-1__Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-020-65406-1 
LibreCat: https://research-explorer.ista.ac.at/record/7931
DOI: 10.1038/s41598-020-65406-1
WoS: 000560774200007

Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., &; Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic.https://doi.org/10.1093/bioinformatics/btz841 
LibreCat: https://research-explorer.ista.ac.at/record/8645
DOI: 10.1093/bioinformatics/btz841
WoS: 000538696800054
PMID: 31742320

Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B.,https://doi.org/10.1038/s41587-020-0500-9__Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature.https://doi.org/10.1038/s41587-020-0500-9 
LibreCat: https://research-explorer.ista.ac.at/record/7889
DOI: 10.1038/s41587-020-0500-9
WoS: 000529298800003
PMID: 32341562

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079__Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1008079 
LibreCat: https://research-explorer.ista.ac.at/record/6419
DOI: 10.1371/journal.pgen.1008079
WoS: 000466866000029

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s011__Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science.https://doi.org/10.1371/journal.pgen.1008079.s011 
LibreCat: https://research-explorer.ista.ac.at/record/9790
DOI: 10.1371/journal.pgen.1008079.s011

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s011__Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science.https://doi.org/10.1371/journal.pgen.1008079.s011 
LibreCat: https://research-explorer.ista.ac.at/record/9797
DOI: 10.1371/journal.pgen.1008079.s011

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s010__Kondrashov, F. (2019). Multiple alignment of Hi orthologues. Public Library of Science.https://doi.org/10.1371/journal.pgen.1008079.s010 
LibreCat: https://research-explorer.ista.ac.at/record/9789
DOI: 10.1371/journal.pgen.1008079.s010

Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,https://doi.org/10.1038/s41587-019-0333-6__Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature.https://doi.org/10.1038/s41587-019-0333-6 
LibreCat: https://research-explorer.ista.ac.at/record/7181
DOI: 10.1038/s41587-019-0333-6
WoS: 000500748900021
PMID: 31792410

Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,https://doi.org/10.5281/ZENODO.2025846__Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo.https://doi.org/10.5281/ZENODO.2025846 
LibreCat: https://research-explorer.ista.ac.at/record/13059
DOI: 10.5281/ZENODO.2025846

Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M.,https://doi.org/10.1073/pnas.1803615115__Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences.https://doi.org/10.1073/pnas.1803615115 
LibreCat: https://research-explorer.ista.ac.at/record/5780
DOI: 10.1073/pnas.1803615115
WoS: 000452866000068

Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central.https://doi.org/10.1186/s13059-018-1434-0 
LibreCat: https://research-explorer.ista.ac.at/record/279
DOI: 10.1186/s13059-018-1434-0
WoS: 000433986200001

Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature.https://doi.org/10.6084/m9.figshare.6401414.v1 
LibreCat: https://research-explorer.ista.ac.at/record/9812
DOI: 10.6084/m9.figshare.6401414.v1

Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &; Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature.https://doi.org/10.6084/m9.figshare.6401390.v1 
LibreCat: https://research-explorer.ista.ac.at/record/9811
DOI: 10.6084/m9.figshare.6401390.v1

Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M.,https://doi.org/10.1093/bioinformatics/bty340__Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press .https://doi.org/10.1093/bioinformatics/bty340 
LibreCat: https://research-explorer.ista.ac.at/record/5995
DOI: 10.1093/bioinformatics/bty340
WoS: 000450038900008
PMID: 29722803

Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G.,https://doi.org/10.1038/nature17995__Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein. Nature. Nature Publishing Group.https://doi.org/10.1038/nature17995 
LibreCat: https://research-explorer.ista.ac.at/record/850
DOI: 10.1038/nature17995

Howe, K., Schiffer, P., Zielinski, J., Wiehe, T., Laird, G., Marioni, J.,https://doi.org/10.1098/rsob.160009__Leptin, M. (2016). Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. Royal Society, The.https://doi.org/10.1098/rsob.160009 
LibreCat: https://research-explorer.ista.ac.at/record/896
DOI: 10.1098/rsob.160009

Saint Léger, A., Bello, C., Dans, P., Torres, A., Novoa, E., Camacho, N.,https://doi.org/10.1126/sciadv.1501860__Ribas De Pouplana, L. (2016). Saturation of recognition elements blocks evolution of new tRNA identities. Science Advances. American Association for the Advancement of Science.https://doi.org/10.1126/sciadv.1501860 
LibreCat: https://research-explorer.ista.ac.at/record/849
DOI: 10.1126/sciadv.1501860

Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova, L., Tutukina, M.,https://doi.org/10.5194/bg-13-2207-2016__Kondrashov, F. (2016). Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. European Geosciences Union.https://doi.org/10.5194/bg-13-2207-2016 
LibreCat: https://research-explorer.ista.ac.at/record/853
DOI: 10.5194/bg-13-2207-2016

Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., &; Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press.https://doi.org/10.1093/molbev/msu318 
LibreCat: https://research-explorer.ista.ac.at/record/848
DOI: 10.1093/molbev/msu318

Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., &; Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science.https://doi.org/10.1371/journal.pone.0125888 
LibreCat: https://research-explorer.ista.ac.at/record/906
DOI: 10.1371/journal.pone.0125888

Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D.,https://doi.org/10.1073/pnas.1511328112__Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMT. PNAS. National Academy of Sciences.https://doi.org/10.1073/pnas.1511328112 
LibreCat: https://research-explorer.ista.ac.at/record/866
DOI: 10.1073/pnas.1511328112

Kondrashov, D., &; Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier.https://doi.org/10.1016/j.tig.2014.09.009 
LibreCat: https://research-explorer.ista.ac.at/record/886
DOI: 10.1016/j.tig.2014.09.009

Rosello, O., &; Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press.https://doi.org/10.1093/gbe/evu159 
LibreCat: https://research-explorer.ista.ac.at/record/852
DOI: 10.1093/gbe/evu159

Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B.,https://doi.org/10.1038/ncomms5868__Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group.https://doi.org/10.1038/ncomms5868 
LibreCat: https://research-explorer.ista.ac.at/record/856
DOI: 10.1038/ncomms5868

Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I.,https://doi.org/10.1038/nature13400__Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature. Nature Publishing Group.https://doi.org/10.1038/nature13400 
LibreCat: https://research-explorer.ista.ac.at/record/863
DOI: 10.1038/nature13400

Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J.,https://doi.org/10.1016/j.bcp.2013.12.007__Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. Elsevier.https://doi.org/10.1016/j.bcp.2013.12.007 
LibreCat: https://research-explorer.ista.ac.at/record/865
DOI: 10.1016/j.bcp.2013.12.007

Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N.,https://doi.org/10.1093/molbev/msu242__James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. Oxford University Press.https://doi.org/10.1093/molbev/msu242 
LibreCat: https://research-explorer.ista.ac.at/record/845
DOI: 10.1093/molbev/msu242

Ivankov, D., Finkelstein, A., &; Kondrashov, F. (2014). A structural perspective of compensatory evolution. Current Opinion in Structural Biology. Elsevier.https://doi.org/10.1016/j.sbi.2014.05.004 
LibreCat: https://research-explorer.ista.ac.at/record/892
DOI: 10.1016/j.sbi.2014.05.004

Breen, M., Kemena, C., Vlasov, P., Notredame, C., &; Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group.https://doi.org/10.1038/nature12220 
LibreCat: https://research-explorer.ista.ac.at/record/899
DOI: 10.1038/nature12220

Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J.,https://doi.org/10.1186/1756-0500-6-310__Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MR. BMC Research Notes. BioMed Central.https://doi.org/10.1186/1756-0500-6-310 
LibreCat: https://research-explorer.ista.ac.at/record/894
DOI: 10.1186/1756-0500-6-310

Arkhipov, V., Noah, T., Koschkar, S., &; Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.
LibreCat: https://research-explorer.ista.ac.at/record/905

Soylemez, O., &; Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press.https://doi.org/10.1093/gbe/evs096 
LibreCat: https://research-explorer.ista.ac.at/record/846
DOI: 10.1093/gbe/evs096

Povolotskaya, I., Kondrashov, F., Ledda, A., &; Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central.https://doi.org/10.1186/1745-6150-7-30 
LibreCat: https://research-explorer.ista.ac.at/record/858
DOI: 10.1186/1745-6150-7-30

Breen, M., Kemena, C., Vlasov, P., Notredame, C., &; Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group.https://doi.org/10.1038/nature11510 
LibreCat: https://research-explorer.ista.ac.at/record/900
DOI: 10.1038/nature11510

Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The.https://doi.org/10.1098/rspb.2012.1108 
LibreCat: https://research-explorer.ista.ac.at/record/887
DOI: 10.1098/rspb.2012.1108

Koblik, E., Red’Kin, Y., Meer, M., Derelle, R., Golenkina, S., Kondrashov, F., &; Arkhipov, V. (2011). Acrocephalus orinus: A case of Mistaken identity. PLoS One. Public Library of Science.https://doi.org/10.1371/journal.pone.0017716 
LibreCat: https://research-explorer.ista.ac.at/record/890
DOI: 10.1371/journal.pone.0017716

Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell.https://doi.org/10.1002/9780470619902.ch4 
LibreCat: https://research-explorer.ista.ac.at/record/881
DOI: 10.1002/9780470619902.ch4

Innan, H., &; Kondrashov, F. (2010). The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. Nature Publishing Group.https://doi.org/10.1038/nrg2689 
LibreCat: https://research-explorer.ista.ac.at/record/891
DOI: 10.1038/nrg2689

Breen, M., &; Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. Biology Direct. BioMed Central.https://doi.org/10.1186/1745-6150-5-68 
LibreCat: https://research-explorer.ista.ac.at/record/901
DOI: 10.1186/1745-6150-5-68

Povolotskaya, I., &; Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe. Nature. Nature Publishing Group.https://doi.org/10.1038/nature09105 
LibreCat: https://research-explorer.ista.ac.at/record/857
DOI: 10.1038/nature09105

Meer, M., Kondrashov, A., Artzy Randrup, Y., &; Kondrashov, F. (2010). Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. Nature Publishing Group.https://doi.org/10.1038/nature08691 
LibreCat: https://research-explorer.ista.ac.at/record/862
DOI: 10.1038/nature08691

Kondrashov, F., &; Kondrashov, A. (2010). 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. Royal Society, The.https://doi.org/10.1098/rstb.2009.0286 
LibreCat: https://research-explorer.ista.ac.at/record/872
DOI: 10.1098/rstb.2009.0286

Kondrashov, A., Povolotskaya, I., Ivankov, D., &; Kondrashov, F. (2010). Rate of sequence divergence under constant selection. Biology Direct. BioMed Central.https://doi.org/10.1186/1745-6150-5-5 
LibreCat: https://research-explorer.ista.ac.at/record/884
DOI: 10.1186/1745-6150-5-5

Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli, S.,https://doi.org/10.1016/j.febslet.2009.09.044__Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. Elsevier.https://doi.org/10.1016/j.febslet.2009.09.044 
LibreCat: https://research-explorer.ista.ac.at/record/908
DOI: 10.1016/j.febslet.2009.09.044

Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., &; Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1000281 
LibreCat: https://research-explorer.ista.ac.at/record/844
DOI: 10.1371/journal.pgen.1000281

Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., &; Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5 flanking region of the primate AVPA gene. BMC Evolutionary Biology. BioMed Central.https://doi.org/10.1186/1471-2148-8-180 
LibreCat: https://research-explorer.ista.ac.at/record/895
DOI: 10.1186/1471-2148-8-180

Assis, R., Kondrashov, A., Koonin, E., &; Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. Elsevier.https://doi.org/10.1016/j.tig.2008.08.003 
LibreCat: https://research-explorer.ista.ac.at/record/907
DOI: 10.1016/j.tig.2008.08.003

Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &; Rogaev, E. (2007). Conversion and compensatory evolution of the ;3-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. Cell Press.https://doi.org/10.1086/518616 
LibreCat: https://research-explorer.ista.ac.at/record/860
DOI: 10.1086/518616

Kondrashov, F., Gurbich, T., &; Vlasov, P. (2007). Selection for functional uniformity of tuf duplicates in ;3-proteobacteria. Trends in Genetics. Elsevier.https://doi.org/10.1016/j.tig.2007.03.002 
LibreCat: https://research-explorer.ista.ac.at/record/879
DOI: 10.1016/j.tig.2007.03.002

Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I., &; Kondrashov, A. (2007). Extensive parallelism in protein evolution. Biology Direct. BioMed Central.https://doi.org/10.1186/1745-6150-2-20 
LibreCat: https://research-explorer.ista.ac.at/record/904
DOI: 10.1186/1745-6150-2-20

Popadin, K., Mamirova, L., &; Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. BioMed Central.https://doi.org/10.1186/1471-2105-8-441 
LibreCat: https://research-explorer.ista.ac.at/record/861
DOI: 10.1186/1471-2105-8-441

Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov, I., &; Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library of Science.https://doi.org/10.1371/journal.pbio.0040073 
LibreCat: https://research-explorer.ista.ac.at/record/854
DOI: 10.1371/journal.pbio.0040073

Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., &; Kondrashova, M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. BioMed Central.https://doi.org/10.1186/1745-6150-1-31 
LibreCat: https://research-explorer.ista.ac.at/record/868
DOI: 10.1186/1745-6150-1-31

Kondrashov, F., &; Kondrashov, A. (2006). Role of selection in fixation of gene duplications. Journal of Theoretical Biology. Elsevier.https://doi.org/10.1016/j.jtbi.2005.08.033 
LibreCat: https://research-explorer.ista.ac.at/record/873
DOI: 10.1016/j.jtbi.2005.08.033

Kondrashov, F., Ogurtsov, A., &; Kondrashov, A. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier.https://doi.org/10.1016/j.jtbi.2005.10.020 
LibreCat: https://research-explorer.ista.ac.at/record/869
DOI: 10.1016/j.jtbi.2005.10.020

Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., &; Koonin, E. (2006). Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. BioMed Central.https://doi.org/10.1186/1471-2407-6-36 
LibreCat: https://research-explorer.ista.ac.at/record/903
DOI: 10.1186/1471-2407-6-36

Yampolsky, L., Kondrashov, F., &; Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. Oxford University Press.https://doi.org/10.1093/hmg/ddi350 
LibreCat: https://research-explorer.ista.ac.at/record/843
DOI: 10.1093/hmg/ddi350

Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. Pleiades Publishing.
LibreCat: https://research-explorer.ista.ac.at/record/877
PMID: 15977826

Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics. Nature Publishing Group.https://doi.org/10.1038/ng0105-9 
LibreCat: https://research-explorer.ista.ac.at/record/878
DOI: 10.1038/ng0105-9

Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. Oxford University Press.https://doi.org/10.1093/hmg/ddi243 
LibreCat: https://research-explorer.ista.ac.at/record/882
DOI: 10.1093/hmg/ddi243

Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. Pleiades Publishing.
LibreCat: https://research-explorer.ista.ac.at/record/880
PMID: 15977827

Jordan, I., Kondrashov, F., Adzhube0, I., Wolf, Y., Koonin, E., Kondrashov, A., &; Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. Nature. Nature Publishing Group.https://doi.org/10.1038/nature03306 
LibreCat: https://research-explorer.ista.ac.at/record/893
DOI: 10.1038/nature03306

Panchenko, A., Kondrashov, F., &; Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. Wiley-Blackwell.https://doi.org/10.1110/ps.03465504 
LibreCat: https://research-explorer.ista.ac.at/record/864
DOI: 10.1110/ps.03465504

Kondrashov, F., Ogurtsov, A., &; Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research. Oxford University Press.https://doi.org/10.1093/nar/gkh330 
LibreCat: https://research-explorer.ista.ac.at/record/870
DOI: 10.1093/nar/gkh330

Kondrashov, F., &; Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. Elsevier.https://doi.org/10.1016/j.tig.2004.05.001 
LibreCat: https://research-explorer.ista.ac.at/record/875
DOI: 10.1016/j.tig.2004.05.001

Kern, A., &; Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing Group.https://doi.org/10.1038/ng1451 
LibreCat: https://research-explorer.ista.ac.at/record/889
DOI: 10.1038/ng1451

Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., &; Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. Nature Publishing Group.https://doi.org/10.1038/nature02601 
LibreCat: https://research-explorer.ista.ac.at/record/898
DOI: 10.1038/nature02601

Castillo Davis, C., Kondrashov, F., Hartl, D., &; Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring Harbor Laboratory Press.https://doi.org/10.1101/gr.2195604 
LibreCat: https://research-explorer.ista.ac.at/record/902
DOI: 10.1101/gr.2195604

Sunyaev, S., Kondrashov, F., Bork, P., &; Ramensky, V. (2003). Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. Oxford University Press.https://doi.org/10.1093/hmg/ddg359 
LibreCat: https://research-explorer.ista.ac.at/record/847
DOI: 10.1093/hmg/ddg359

Kondrashov, F., &; Koonin, E. (2003). Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. Elsevier.https://doi.org/10.1016/S0168-9525(02)00029-X 
LibreCat: https://research-explorer.ista.ac.at/record/876
DOI: 10.1016/S0168-9525(02)00029-X

Kondrashov, A., Sunyaev, S., &; Kondrashov, F. (2002). Dobzhansky-Muller incompatibilities in protein evolution. PNAS. National Academy of Sciences.https://doi.org/10.1073/pnas.232565499 
LibreCat: https://research-explorer.ista.ac.at/record/885
DOI: 10.1073/pnas.232565499
PMID: 12403824

Castillo Davis, C., Mekhedov, S., Hartl, D., Koonin, E., &; Kondrashov, F. (2002). Selection for short introns in highly expressed genes. Nature Genetics. Nature Publishing Group.https://doi.org/10.1038/ng940 
LibreCat: https://research-explorer.ista.ac.at/record/897
DOI: 10.1038/ng940
PMID: 12134150

Kondrashov, F., Rogozin, I., Wolf, Y., &; Koonin, E. (2002). Selection in the evolution of gene duplications . Genome Biology. BioMed Central.https://doi.org/10.1186/gb-2002-3-2-research0008 
LibreCat: https://research-explorer.ista.ac.at/record/871
DOI: 10.1186/gb-2002-3-2-research0008
PMID: 11864370

Perelygin, A., Kondrashov, F., Rogozin, I., &; Brinton, M. (2002). Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. Springer.https://doi.org/10.1007/s00239-002-2318-0 
LibreCat: https://research-explorer.ista.ac.at/record/859
DOI: 10.1007/s00239-002-2318-0
PMID: 12107596

Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., &; Koonin, E. (2001). Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. BioMed Central.https://doi.org/10.1186/gb-2001-2-12-research0053 
LibreCat: https://research-explorer.ista.ac.at/record/888
DOI: 10.1186/gb-2001-2-12-research0053
PMID: 11790256

Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., &; Milanesi, L. (2001). Presence of ATG triplets in 5 untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. Oxford University Press.https://doi.org/10.1093/bioinformatics/17.10.890 
LibreCat: https://research-explorer.ista.ac.at/record/855
DOI: 10.1093/bioinformatics/17.10.890
PMID: 11673233

Kondrashov, F., &; Kondrashov, A. (2001). Multidimensional epistasis and the disadvantage of sex. PNAS. National Academy of Sciences.https://doi.org/10.1073/pnas.211214298 
LibreCat: https://research-explorer.ista.ac.at/record/874
DOI: 10.1073/pnas.211214298
PMID: 11593020

Kondrashov, F., &; Koonin, E. (2001). Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. Oxford University Press.https://doi.org/10.1093/hmg/10.23.2661 
LibreCat: https://research-explorer.ista.ac.at/record/867
DOI: 10.1093/hmg/10.23.2661
PMID: 11726553

Rogozin, I., Kondrashov, F., &; Glazko, G. (2001). Use of mutation spectra analysis software. Human Mutation. Wiley-Blackwell.https://doi.org/10.1002/1098-1004(200102)17:2&#38;lt;83::AID-HUMU1&#38;gt;3.0.CO;2-E 
LibreCat: https://research-explorer.ista.ac.at/record/851
DOI: 10.1002/1098-1004(200102)17:2&lt;83::AID-HUMU1&gt;3.0.CO;2-E
PMID: 11180592

Wolf, Y., Kondrashov, F., &; Koonin, E. (2001). Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. Elsevier.https://doi.org/10.1016/S0168-9525(01)02376-9 
LibreCat: https://research-explorer.ista.ac.at/record/841
DOI: 10.1016/S0168-9525(01)02376-9
PMID: 11721681

Wolf, Y., Kondrashov, F., &; Koonin, E. (2000). No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. Elsevier.https://doi.org/10.1016/S0168-9525(00)02059-X 
LibreCat: https://research-explorer.ista.ac.at/record/842
DOI: 10.1016/S0168-9525(00)02059-X
PMID: 10904260 

Kondrashov, A., &; Kondrashov, F. (1999). Interactions among quantitative traits in the course of sympatric speciation. Nature. Nature Publishing Group.https://doi.org/10.1038/22514 
LibreCat: https://research-explorer.ista.ac.at/record/883
DOI: 10.1038/22514
PMID: 10432111