[{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0168-9479"]},"year":"2001","intvolume":" 17","pmid":1,"extern":"1","quality_controlled":"1","doi":"10.1016/S0168-9525(01)02376-9","citation":{"ama":"Wolf Y, Kondrashov F, Koonin E. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 2001;17(9):499-501. doi:10.1016/S0168-9525(01)02376-9","short":"Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.","chicago":"Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics. Elsevier, 2001. https://doi.org/10.1016/S0168-9525(01)02376-9.","apa":"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","mla":"Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier, 2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.","ista":"Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.","ieee":"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. Elsevier, pp. 499–501, 2001."},"external_id":{"pmid":["11721681"]},"page":"499 - 501","day":"01","status":"public","volume":17,"title":"Footprints of primordial introns on the eukaryotic genome: still no clear traces ","publication":"Trends in Genetics","article_processing_charge":"No","_id":"841","type":"journal_article","issue":"9","oa_version":"None","date_created":"2018-12-11T11:48:47Z","author":[{"full_name":"Wolf, Yuri","first_name":"Yuri","last_name":"Wolf"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koonin, Eugene","last_name":"Koonin","first_name":"Eugene"}],"article_type":"original","date_published":"2001-09-01T00:00:00Z","month":"09","date_updated":"2023-06-02T09:38:37Z","publist_id":"6805","publisher":"Elsevier","publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis."}],"page":"83 - 102","external_id":{"pmid":["11180592"]},"pmid":1,"intvolume":" 17","year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1059-7794"]},"acknowledgement":"Russian Fund of Fundamental Research. Grant Number: 99-04-49535. NIH. Grant Number: GM 20293. NASA. Grant Number: NCC2-1057","doi":"10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E","citation":{"ama":"Rogozin I, Kondrashov F, Glazko G. Use of mutation spectra analysis software. Human Mutation. 2001;17(2):83-102. doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E","apa":"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<83::AID-HUMU1>3.0.CO;2-E","chicago":"Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra Analysis Software.” Human Mutation. Wiley-Blackwell, 2001. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.","short":"I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.","ista":"Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis software. Human Mutation. 17(2), 83–102.","ieee":"I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102, 2001.","mla":"Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E."},"quality_controlled":"1","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","publisher":"Wiley-Blackwell","publist_id":"6796","date_updated":"2023-06-02T09:22:17Z","month":"01","date_published":"2001-01-01T00:00:00Z","article_type":"original","scopus_import":"1","title":"Use of mutation spectra analysis software","volume":17,"status":"public","day":"01","author":[{"full_name":"Rogozin, Igor","last_name":"Rogozin","first_name":"Igor"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Galina","last_name":"Glazko","full_name":"Glazko, Galina"}],"date_created":"2018-12-11T11:48:50Z","oa_version":"None","issue":"2","_id":"851","type":"journal_article","article_processing_charge":"No","publication":"Human Mutation"},{"keyword":["General Mathematics"],"abstract":[{"text":"We continue the previous article's discussion of bounds, for prevalent diffeomorphisms of smooth compact manifolds, on the growth of the number of periodic points and the decay of their hyperbolicity as a function of their period $n$. In that article we reduced the main results to a problem, for certain families of diffeomorphisms, of bounding the measure of parameter values for which the diffeomorphism has (for a given period $n$) an almost periodic point that is almost nonhyperbolic. We also formulated our results for $1$-dimensional endomorphisms on a compact interval. In this article we describe some of the main techniques involved and outline the rest of the proof. To simplify notation, we concentrate primarily on the $1$-dimensional case.","lang":"eng"}],"date_published":"2001-04-24T00:00:00Z","month":"04","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"American Mathematical Society","date_updated":"2021-01-12T08:19:51Z","page":"28-36","year":"2001","day":"24","publication_identifier":{"issn":["1079-6762"]},"language":[{"iso":"eng"}],"volume":7,"title":"A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II","status":"public","intvolume":" 7","citation":{"short":"V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American Mathematical Society 7 (2001) 28–36.","chicago":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms II.” Electronic Research Announcements of the American Mathematical Society. American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00091-9.","apa":"Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00091-9","mla":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms II.” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 5, American Mathematical Society, 2001, pp. 28–36, doi:10.1090/s1079-6762-01-00091-9.","ista":"Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. 7(5), 28–36.","ieee":"V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II,” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 5. American Mathematical Society, pp. 28–36, 2001.","ama":"Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. 2001;7(5):28-36. doi:10.1090/s1079-6762-01-00091-9"},"doi":"10.1090/s1079-6762-01-00091-9","oa_version":"None","quality_controlled":"1","date_created":"2020-09-18T10:49:43Z","_id":"8521","issue":"5","type":"journal_article","article_processing_charge":"No","extern":"1","publication":"Electronic Research Announcements of the American Mathematical Society","author":[{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Hunt, Brian R.","last_name":"Hunt","first_name":"Brian R."}]},{"status":"public","intvolume":" 7","title":"A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I","volume":7,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1079-6762"]},"year":"2001","day":"18","author":[{"last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"},{"full_name":"Hunt, Brian R.","first_name":"Brian R.","last_name":"Hunt"}],"article_processing_charge":"No","_id":"8522","issue":"4","type":"journal_article","publication":"Electronic Research Announcements of the American Mathematical Society","extern":"1","citation":{"ama":"Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. 2001;7(4):17-27. doi:10.1090/s1079-6762-01-00090-7","chicago":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Electronic Research Announcements of the American Mathematical Society. American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00090-7.","short":"V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American Mathematical Society 7 (2001) 17–27.","apa":"Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00090-7","mla":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 4, American Mathematical Society, 2001, pp. 17–27, doi:10.1090/s1079-6762-01-00090-7.","ista":"Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. 7(4), 17–27.","ieee":"V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I,” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 4. American Mathematical Society, pp. 17–27, 2001."},"doi":"10.1090/s1079-6762-01-00090-7","date_created":"2020-09-18T10:49:56Z","quality_controlled":"1","oa_version":"None","publisher":"American Mathematical Society","date_updated":"2021-01-12T08:19:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2001-04-18T00:00:00Z","month":"04","article_type":"original","keyword":["General Mathematics"],"abstract":[{"text":"For diffeomorphisms of smooth compact manifolds, we consider the problem of how fast the number of periodic points with period $n$grows as a function of $n$. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for $C^2$ or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call ``prevalence'', the growth is not much faster than exponential. Specifically, we show that for each $\\delta > 0$, there is a prevalent set of ( $C^{1+\\rho}$ or smoother) diffeomorphisms for which the number of period $n$ points is bounded above by $\\operatorname{exp}(C n^{1+\\delta})$ for some $C$ independent of $n$. We also obtain a related bound on the decay of the hyperbolicity of the periodic points as a function of $n$. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity shows this to be a subtle and complex phenomenon, reminiscent of KAM theory.","lang":"eng"}],"page":"17-27"},{"page":"953-970","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:52Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"A number α∈R is diophantine if it is not well approximable by rationals, i.e. for some C,ε>0 and any relatively prime p,q∈Z we have |αq−p|>Cq−1−ε. It is well-known and is easy to prove that almost every α in R is diophantine. In this paper we address a noncommutative version of the diophantine properties. Consider a pair A,B∈SO(3) and for each n∈Z+ take all possible words in A, A -1, B, and B - 1 of length n, i.e. for a multiindex I=(i1,i1,…,im,jm) define |I|=∑mk=1(|ik|+|jk|)=n and \\( W_n(A,B ) = \\{W_{\\cal I}(A,B) = A^{i_1} B^{j_1} \\dots A^{i_m} B^{j_m}\\}_{|{\\cal I|}=n \\).¶Gamburd—Jakobson—Sarnak [GJS] raised the problem: prove that for Haar almost every pair A,B∈SO(3) the closest distance of words of length n to the identity, i.e. sA,B(n)=min|I|=n∥WI(A,B)−E∥, is bounded from below by an exponential function in n. This is the analog of the diophantine property for elements of SO(3). In this paper we prove that s A,B (n) is bounded from below by an exponential function in n 2. We also exhibit obstructions to a “simple” proof of the exponential estimate in n."}],"article_type":"original","month":"12","date_published":"2001-12-01T00:00:00Z","author":[{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin"},{"last_name":"Rodnianski","first_name":"I.","full_name":"Rodnianski, I."}],"quality_controlled":"1","date_created":"2020-09-18T10:50:11Z","oa_version":"None","citation":{"ama":"Kaloshin V, Rodnianski I. Diophantine properties of elements of SO(3). Geometric And Functional Analysis. 2001;11(5):953-970. doi:10.1007/s00039-001-8222-8","ista":"Kaloshin V, Rodnianski I. 2001. Diophantine properties of elements of SO(3). Geometric And Functional Analysis. 11(5), 953–970.","ieee":"V. Kaloshin and I. Rodnianski, “Diophantine properties of elements of SO(3),” Geometric And Functional Analysis, vol. 11, no. 5. Springer Nature, pp. 953–970, 2001.","mla":"Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements of SO(3).” Geometric And Functional Analysis, vol. 11, no. 5, Springer Nature, 2001, pp. 953–70, doi:10.1007/s00039-001-8222-8.","apa":"Kaloshin, V., & Rodnianski, I. (2001). Diophantine properties of elements of SO(3). Geometric And Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-001-8222-8","chicago":"Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements of SO(3).” Geometric And Functional Analysis. Springer Nature, 2001. https://doi.org/10.1007/s00039-001-8222-8.","short":"V. Kaloshin, I. Rodnianski, Geometric And Functional Analysis 11 (2001) 953–970."},"doi":"10.1007/s00039-001-8222-8","publication":"Geometric And Functional Analysis","extern":"1","_id":"8524","article_processing_charge":"No","type":"journal_article","issue":"5","volume":11,"title":"Diophantine properties of elements of SO(3)","intvolume":" 11","status":"public","year":"2001","day":"01","publication_identifier":{"issn":["1016-443X","1420-8970"]},"language":[{"iso":"eng"}]},{"pmid":1,"intvolume":" 17","publication_identifier":{"issn":["1367-4803"]},"language":[{"iso":"eng"}],"year":"2001","acknowledgement":"This work has been partially supported by EU 'TRADAT' project and by CNR Genetic Engineering (Italy), the RFBR grant for support of scientific schools (00-15-97968) and SD RAS grant for young scientists (AVK). The authors wish to thank J.Lyons-Weiler for helpful comments and A. Sorokin for help with the ATG_EVALUATOR program.","extern":"1","citation":{"ieee":"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. Oxford University Press, pp. 890–900, 2001.","ista":"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. 17(10), 890–900.","mla":"Rogozin, Igor, et al. “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, Oxford University Press, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890.","apa":"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","short":"I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics 17 (2001) 890–900.","chicago":"Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics. Oxford University Press, 2001. https://doi.org/10.1093/bioinformatics/17.10.890.","ama":"Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 2001;17(10):890-900. doi:10.1093/bioinformatics/17.10.890"},"doi":"10.1093/bioinformatics/17.10.890","quality_controlled":"1","abstract":[{"lang":"eng","text":"Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing."}],"external_id":{"pmid":["11673233"]},"page":"890 - 900","status":"public","volume":17,"title":"Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon","day":"01","author":[{"last_name":"Rogozin","first_name":"Igor","full_name":"Rogozin, Igor"},{"first_name":"Alex","last_name":"Kochetov","full_name":"Kochetov, Alex"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Koonin, Eugene","last_name":"Koonin","first_name":"Eugene"},{"first_name":"Luciano","last_name":"Milanesi","full_name":"Milanesi, Luciano"}],"type":"journal_article","_id":"855","article_processing_charge":"No","issue":"10","publication":"Bioinformatics","oa_version":"None","date_created":"2018-12-11T11:48:52Z","publisher":"Oxford University Press","publist_id":"6795","date_updated":"2023-06-02T09:08:25Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","month":"10","date_published":"2001-10-01T00:00:00Z","article_type":"original","scopus_import":"1"},{"page":"2661 - 2669","external_id":{"pmid":["11726553"]},"abstract":[{"lang":"eng","text":"Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes."}],"doi":"10.1093/hmg/10.23.2661","citation":{"ama":"Kondrashov F, Koonin E. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 2001;10(23):2661-2669. doi:10.1093/hmg/10.23.2661","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics. Oxford University Press, 2001. https://doi.org/10.1093/hmg/10.23.2661.","short":"F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.","apa":"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","mla":"Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661.","ista":"Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 10(23), 2661–2669.","ieee":"F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University Press, pp. 2661–2669, 2001."},"quality_controlled":"1","extern":"1","pmid":1,"intvolume":" 10","year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0964-6906"]},"scopus_import":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","publisher":"Oxford University Press","date_updated":"2023-06-02T08:39:47Z","publist_id":"6777","date_published":"2001-11-01T00:00:00Z","month":"11","article_type":"original","author":[{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Koonin, Eugene","last_name":"Koonin","first_name":"Eugene"}],"oa_version":"Published Version","date_created":"2018-12-11T11:48:55Z","article_processing_charge":"No","_id":"867","type":"journal_article","issue":"23","publication":"Human Molecular Genetics","volume":10,"title":"Origin of alternative splicing by tandem exon duplication","status":"public","day":"01"},{"publication_identifier":{"issn":["0027-8424"]},"language":[{"iso":"eng"}],"year":"2001","intvolume":" 98","pmid":1,"extern":"1","quality_controlled":"1","doi":"10.1073/pnas.211214298","citation":{"mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences, 2001, pp. 12089–92, doi:10.1073/pnas.211214298.","ista":"Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage of sex. PNAS. 98(21), 12089–12092.","ieee":"F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092, 2001.","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS. National Academy of Sciences, 2001. https://doi.org/10.1073/pnas.211214298.","short":"F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.","apa":"Kondrashov, F., & Kondrashov, A. (2001). Multidimensional epistasis and the disadvantage of sex. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.211214298","ama":"Kondrashov F, Kondrashov A. Multidimensional epistasis and the disadvantage of sex. PNAS. 2001;98(21):12089-12092. doi:10.1073/pnas.211214298"},"abstract":[{"text":"Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability.","lang":"eng"}],"oa":1,"external_id":{"pmid":["11593020"]},"page":"12089 - 12092","day":"09","status":"public","title":"Multidimensional epistasis and the disadvantage of sex","volume":98,"publication":"PNAS","_id":"874","article_processing_charge":"No","type":"journal_article","issue":"21","date_created":"2018-12-11T11:48:58Z","oa_version":"Published Version","author":[{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey"}],"article_type":"original","month":"10","date_published":"2001-10-09T00:00:00Z","date_updated":"2023-06-02T08:18:22Z","publist_id":"6774","publisher":"National Academy of Sciences","publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59772/","open_access":"1"}],"scopus_import":"1"},{"article_type":"original","date_published":"2001-01-01T00:00:00Z","month":"01","publist_id":"6758","date_updated":"2023-05-31T12:15:37Z","publisher":"BioMed Central","publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/"}],"scopus_import":"1","day":"01","status":"public","article_number":"research0053.1","title":"Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ","volume":2,"publication":"Genome Biology","type":"journal_article","_id":"888","issue":"12","article_processing_charge":"No","date_created":"2018-12-11T11:49:02Z","oa_version":"Published Version","author":[{"full_name":"Jordan, Ingo","last_name":"Jordan","first_name":"Ingo"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"first_name":"Igor","last_name":"Rogozin","full_name":"Rogozin, Igor"},{"last_name":"Tatusov","first_name":"Roman","full_name":"Tatusov, Roman"},{"first_name":"Yuri","last_name":"Wolf","full_name":"Wolf, Yuri"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene"}],"abstract":[{"lang":"eng","text":"BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins."}],"oa":1,"external_id":{"pmid":["11790256"]},"publication_identifier":{"issn":["1465-6906"]},"language":[{"iso":"eng"}],"year":"2001","intvolume":" 2","pmid":1,"extern":"1","quality_controlled":"1","doi":"10.1186/gb-2001-2-12-research0053","citation":{"ama":"Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053","mla":"Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001, doi:10.1186/gb-2001-2-12-research0053.","ista":"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. 2(12), research0053.1.","ieee":"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. BioMed Central, 2001.","short":"I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome Biology 2 (2001).","chicago":"Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf, and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053.","apa":"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"},"acknowledgement":"We thank Alexey Kondrashov for many helpful discussions and constructive criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and Itai Yanai for critical reading of the manuscript and constructive comments and L. Aravind for advice on protein function prediction. The release of the unpublished P. furiosus genome sequence by the Utah Genome Center at the University of Utah is acknowledged and appreciated."},{"date_published":"2001-08-15T00:00:00Z","month":"08","article_type":"original","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","publisher":"Elsevier","publist_id":"5742","date_updated":"2023-05-31T09:57:48Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0106140"}],"scopus_import":"1","day":"15","volume":333,"title":"Examples of mirror partners arising from integrable systems","status":"public","date_created":"2018-12-11T11:52:06Z","oa_version":"Preprint","_id":"1452","article_processing_charge":"No","type":"journal_article","issue":"4","publication":"Comptes Rendus de l'Academie des Sciences - Series I: Mathematics","author":[{"full_name":"Hausel, Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel"},{"last_name":"Thaddeus","first_name":"Michael","full_name":"Thaddeus, Michael"}],"oa":1,"abstract":[{"text":"In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system.","lang":"eng"}],"page":"313 - 318","external_id":{"arxiv":["math/0106140"]},"year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0764-4442"]},"arxiv":1,"intvolume":" 333","citation":{"ama":"Hausel T, Thaddeus M. Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics. 2001;333(4):313-318. doi:10.1016/S0764-4442(01)02057-2","ista":"Hausel T, Thaddeus M. 2001. Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics. 333(4), 313–318.","ieee":"T. Hausel and M. Thaddeus, “Examples of mirror partners arising from integrable systems,” Comptes Rendus de l’Academie des Sciences - Series I: Mathematics, vol. 333, no. 4. Elsevier, pp. 313–318, 2001.","mla":"Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics, vol. 333, no. 4, Elsevier, 2001, pp. 313–18, doi:10.1016/S0764-4442(01)02057-2.","apa":"Hausel, T., & Thaddeus, M. (2001). Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics. Elsevier. https://doi.org/10.1016/S0764-4442(01)02057-2","chicago":"Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics. Elsevier, 2001. https://doi.org/10.1016/S0764-4442(01)02057-2.","short":"T. Hausel, M. Thaddeus, Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics 333 (2001) 313–318."},"doi":"10.1016/S0764-4442(01)02057-2","quality_controlled":"1","extern":"1","acknowledgement":"The authors are grateful for Nigel Hitchin for suggesting the similarity between [4] and [12] in 1996 and for Pierre Deligne for numerous useful comments"},{"oa_version":"Preprint","date_created":"2018-12-11T11:52:07Z","_id":"1453","issue":"1-2","article_processing_charge":"No","type":"journal_article","publication":"Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics","author":[{"last_name":"Etesi","first_name":"Gábor","full_name":"Etesi, Gábor"},{"full_name":"Hausel, Tamas","last_name":"Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"day":"09","title":"Geometric construction of new Yang-Mills instantons over Taub-NUT space","volume":514,"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/hep-th/0105118"}],"scopus_import":"1","date_published":"2001-08-09T00:00:00Z","month":"08","article_type":"original","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","publisher":"Elsevier","date_updated":"2023-05-31T11:51:37Z","publist_id":"5743","citation":{"ama":"Etesi G, Hausel T. Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. 2001;514(1-2):189-199. doi:10.1016/S0370-2693(01)00821-8","mla":"Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, vol. 514, no. 1–2, Elsevier, 2001, pp. 189–99, doi:10.1016/S0370-2693(01)00821-8.","ieee":"G. Etesi and T. Hausel, “Geometric construction of new Yang-Mills instantons over Taub-NUT space,” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, vol. 514, no. 1–2. Elsevier, pp. 189–199, 2001.","ista":"Etesi G, Hausel T. 2001. Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. 514(1–2), 189–199.","short":"G. Etesi, T. Hausel, Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics 514 (2001) 189–199.","chicago":"Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. Elsevier, 2001. https://doi.org/10.1016/S0370-2693(01)00821-8.","apa":"Etesi, G., & Hausel, T. (2001). Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. Elsevier. https://doi.org/10.1016/S0370-2693(01)00821-8"},"doi":"10.1016/S0370-2693(01)00821-8","quality_controlled":"1","extern":"1","acknowledgement":"We would like to acknowledge the financial support provided by the Miller Institute of Basic Research in Science, the Japan Society for the Promotion of Science, grant No. P99736 and the partial support by OTKA grant No. T032478.","year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0370-2693"]},"arxiv":1,"intvolume":" 514","page":"189 - 199","external_id":{"arxiv":["hep-th/0105118"]},"oa":1,"abstract":[{"lang":"eng","text":"In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon."}]},{"publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","date_updated":"2023-05-31T12:08:45Z","publist_id":"5744","publisher":"Elsevier","article_type":"original","month":"01","date_published":"2001-01-01T00:00:00Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/hep-th/0003239"}],"title":"Geometric interpretation of Schwarzschild instantons","volume":37,"status":"public","day":"01","author":[{"first_name":"Gábor","last_name":"Etesi","full_name":"Etesi, Gábor"},{"full_name":"Hausel, Tamas","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"}],"oa_version":"Preprint","date_created":"2018-12-11T11:52:07Z","publication":"Journal of Geometry and Physics","article_processing_charge":"No","_id":"1454","issue":"1-2","type":"journal_article","abstract":[{"text":"We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.","lang":"eng"}],"oa":1,"page":"126 - 136","external_id":{"arxiv":["hep-th/0003239"]},"arxiv":1,"intvolume":" 37","year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0393-0440"]},"acknowledgement":"The work in this paper was done when Tamás Hausel visited the Yukawa Institute of Kyoto University in February 2000. We are grateful for Prof. G.W. Gibbons for insightful discussions and Prof. H. Kodama and the Yukawa Institute for the invitation and hospitality.","quality_controlled":"1","citation":{"mla":"Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild Instantons.” Journal of Geometry and Physics, vol. 37, no. 1–2, Elsevier, 2001, pp. 126–36, doi:10.1016/S0393-0440(00)00040-1.","ista":"Etesi G, Hausel T. 2001. Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. 37(1–2), 126–136.","ieee":"G. Etesi and T. Hausel, “Geometric interpretation of Schwarzschild instantons,” Journal of Geometry and Physics, vol. 37, no. 1–2. Elsevier, pp. 126–136, 2001.","short":"G. Etesi, T. Hausel, Journal of Geometry and Physics 37 (2001) 126–136.","chicago":"Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild Instantons.” Journal of Geometry and Physics. Elsevier, 2001. https://doi.org/10.1016/S0393-0440(00)00040-1.","apa":"Etesi, G., & Hausel, T. (2001). Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. Elsevier. https://doi.org/10.1016/S0393-0440(00)00040-1","ama":"Etesi G, Hausel T. Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. 2001;37(1-2):126-136. doi:10.1016/S0393-0440(00)00040-1"},"doi":"10.1016/S0393-0440(00)00040-1","extern":"1"},{"scopus_import":"1","date_published":"2001-06-15T00:00:00Z","month":"06","article_type":"original","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","publisher":"American Association for the Advancement of Science","date_updated":"2021-12-14T08:40:32Z","date_created":"2021-06-02T13:35:16Z","oa_version":"None","_id":"9444","article_processing_charge":"No","issue":"5524","type":"journal_article","publication":"Science","author":[{"full_name":"Lindroth, A. M.","last_name":"Lindroth","first_name":"A. M."},{"full_name":"Cao, Xiaofeng","first_name":"Xiaofeng","last_name":"Cao"},{"first_name":"James P.","last_name":"Jackson","full_name":"Jackson, James P."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"McCallum, Claire M.","first_name":"Claire M.","last_name":"McCallum"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."}],"department":[{"_id":"DaZi"}],"day":"15","title":"Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation","volume":292,"status":"public","page":"2077-2080","external_id":{"pmid":["11349138"]},"keyword":["Multidisciplinary"],"abstract":[{"text":"Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.","lang":"eng"}],"doi":"10.1126/science.1059745","citation":{"mla":"Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science, vol. 292, no. 5524, American Association for the Advancement of Science, 2001, pp. 2077–80, doi:10.1126/science.1059745.","ista":"Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 292(5524), 2077–2080.","ieee":"A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation,” Science, vol. 292, no. 5524. American Association for the Advancement of Science, pp. 2077–2080, 2001.","short":"A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff, S.E. Jacobsen, Science 292 (2001) 2077–2080.","chicago":"Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science. American Association for the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.","apa":"Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff, S., & Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1059745","ama":"Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745"},"quality_controlled":"1","extern":"1","year":"2001","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"pmid":1,"intvolume":" 292"},{"date_published":"2001-01-01T00:00:00Z","month":"01","abstract":[{"text":"This chapter contains sections titled:\r\n\r\nIntroduction\r\n\r\n- History\r\n\r\n- Developing an Intuition of Likelihood\r\n\r\n- Method of Maximum Likelihood\r\n\r\n- Bayesian Inference\r\n\r\n- Markov Chain Monte Carlo\r\n\r\n- Assessing Uncertainty of Phylogenies\r\n\r\n- Hypothesis Testing and Model Choice\r\n\r\n- Comparative Analysis\r\n\r\n- Conclusions\r\n\r\n- References","lang":"eng"}],"publisher":"Wiley-Blackwell","publist_id":"2966","date_updated":"2023-05-15T14:43:39Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","editor":[{"full_name":"Balding, David","last_name":"Balding","first_name":"David"},{"last_name":"Bishop","first_name":"Martin","full_name":"Bishop, Martin"},{"first_name":"Chriss","last_name":"Cannings","full_name":"Cannings, Chriss"}],"page":"415 - 439","publication_identifier":{"isbn":["9781119429142 "]},"language":[{"iso":"eng"}],"day":"01","year":"2001","status":"public","title":"Application of the likelihood function in phylogenetic analysis","article_processing_charge":"No","_id":"3434","type":"book_chapter","publication":"Handbook of Statistical Genetics","extern":"1","doi":"10.1002/9780470061619.ch15","citation":{"ama":"Huelsenbeck J, Bollback JP. Application of the likelihood function in phylogenetic analysis. In: Balding D, Bishop M, Cannings C, eds. Handbook of Statistical Genetics. Wiley-Blackwell; 2001:415-439. doi:10.1002/9780470061619.ch15","mla":"Huelsenbeck, John, and Jonathan P. Bollback. “Application of the Likelihood Function in Phylogenetic Analysis.” Handbook of Statistical Genetics, edited by David Balding et al., Wiley-Blackwell, 2001, pp. 415–39, doi:10.1002/9780470061619.ch15.","ieee":"J. Huelsenbeck and J. P. Bollback, “Application of the likelihood function in phylogenetic analysis,” in Handbook of Statistical Genetics, D. Balding, M. Bishop, and C. Cannings, Eds. Wiley-Blackwell, 2001, pp. 415–439.","ista":"Huelsenbeck J, Bollback JP. 2001.Application of the likelihood function in phylogenetic analysis. In: Handbook of Statistical Genetics. , 415–439.","chicago":"Huelsenbeck, John, and Jonathan P Bollback. “Application of the Likelihood Function in Phylogenetic Analysis.” In Handbook of Statistical Genetics, edited by David Balding, Martin Bishop, and Chriss Cannings, 415–39. Wiley-Blackwell, 2001. https://doi.org/10.1002/9780470061619.ch15.","short":"J. Huelsenbeck, J.P. Bollback, in:, D. Balding, M. Bishop, C. Cannings (Eds.), Handbook of Statistical Genetics, Wiley-Blackwell, 2001, pp. 415–439.","apa":"Huelsenbeck, J., & Bollback, J. P. (2001). Application of the likelihood function in phylogenetic analysis. In D. Balding, M. Bishop, & C. Cannings (Eds.), Handbook of Statistical Genetics (pp. 415–439). Wiley-Blackwell. https://doi.org/10.1002/9780470061619.ch15"},"date_created":"2018-12-11T12:03:19Z","quality_controlled":"1","oa_version":"None","author":[{"first_name":"John","last_name":"Huelsenbeck","full_name":"Huelsenbeck, John"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}]},{"page":"2310 - 2314","external_id":{"pmid":["11743192 "]},"abstract":[{"text":"As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.","lang":"eng"}],"quality_controlled":"1","doi":"10.1126/science.1065889","citation":{"mla":"Huelsenbeck, John, et al. “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.” Science, vol. 294, no. 5550, American Association for the Advancement of Science, 2001, pp. 2310–14, doi:10.1126/science.1065889.","ista":"Huelsenbeck J, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294(5550), 2310–2314.","ieee":"J. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback, “Bayesian inference of phylogeny and its impact on evolutionary biology,” Science, vol. 294, no. 5550. American Association for the Advancement of Science, pp. 2310–2314, 2001.","short":"J. Huelsenbeck, F. Ronquist, R. Nielsen, J.P. Bollback, Science 294 (2001) 2310–2314.","chicago":"Huelsenbeck, John, Fredrik Ronquist, Rasmus Nielsen, and Jonathan P Bollback. “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.” Science. American Association for the Advancement of Science, 2001. https://doi.org/10.1126/science.1065889.","apa":"Huelsenbeck, J., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1065889","ama":"Huelsenbeck J, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001;294(5550):2310-2314. doi:10.1126/science.1065889"},"extern":"1","intvolume":" 294","pmid":1,"year":"2001","publication_identifier":{"issn":["0036-8075"]},"language":[{"iso":"eng"}],"publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publist_id":"2962","date_updated":"2023-05-15T14:10:13Z","publisher":"American Association for the Advancement of Science","month":"12","date_published":"2001-12-14T00:00:00Z","author":[{"full_name":"Huelsenbeck, John","last_name":"Huelsenbeck","first_name":"John"},{"full_name":"Ronquist, Fredrik","last_name":"Ronquist","first_name":"Fredrik"},{"first_name":"Rasmus","last_name":"Nielsen","full_name":"Nielsen, Rasmus"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"oa_version":"None","date_created":"2018-12-11T12:03:20Z","publication":"Science","article_processing_charge":"No","issue":"5550","type":"journal_article","_id":"3438","title":"Bayesian inference of phylogeny and its impact on evolutionary biology","volume":294,"status":"public","day":"14"},{"author":[{"full_name":"Conn, Jan","last_name":"Conn","first_name":"Jan"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"},{"full_name":"Onyabe, David","last_name":"Onyabe","first_name":"David"},{"first_name":"Tessa","last_name":"Robinson","full_name":"Robinson, Tessa"},{"first_name":"Richard","last_name":"Wilkerson","full_name":"Wilkerson, Richard"},{"first_name":"Marinete","last_name":"Povoa","full_name":"Povoa, Marinete"}],"type":"journal_article","_id":"3439","article_processing_charge":"No","issue":"4","publication":"Molecular Ecology Notes","oa_version":"None","date_created":"2018-12-11T12:03:20Z","status":"public","volume":1,"title":"Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi","day":"01","publisher":"Wiley-Blackwell","publist_id":"2961","date_updated":"2023-05-15T13:58:49Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","date_published":"2001-12-01T00:00:00Z","month":"12","article_type":"original","acknowledgement":"For support in Brazil we thank D. Galiza, R.N.L. Lacerda,E.P. Santa Rosa, M.N.O. Segura, and R.T.L. de Souza. We also thankM.J. Braun for allowing work on the library construction at theLaboratory of Molecular Systematics, Washington. Supported byNIH AI 40116 to JEC and Instituto Evandro Chagas, Belém, Brazil.","extern":"1","doi":" 10.1046/j.1471-8278.2001.00078.x","citation":{"ista":"Conn J, Bollback JP, Onyabe D, Robinson T, Wilkerson R, Povoa M. 2001. Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes. 1(4), 223–225.","ieee":"J. Conn, J. P. Bollback, D. Onyabe, T. Robinson, R. Wilkerson, and M. Povoa, “Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi,” Molecular Ecology Notes, vol. 1, no. 4. Wiley-Blackwell, pp. 223–225, 2001.","mla":"Conn, Jan, et al. “Isolation of Polymorphic Microsatellite Markers from the Malaria Vector Anopheles Darlingi.” Molecular Ecology Notes, vol. 1, no. 4, Wiley-Blackwell, 2001, pp. 223–25, doi: 10.1046/j.1471-8278.2001.00078.x.","apa":"Conn, J., Bollback, J. P., Onyabe, D., Robinson, T., Wilkerson, R., & Povoa, M. (2001). Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes. Wiley-Blackwell. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x","chicago":"Conn, Jan, Jonathan P Bollback, David Onyabe, Tessa Robinson, Richard Wilkerson, and Marinete Povoa. “Isolation of Polymorphic Microsatellite Markers from the Malaria Vector Anopheles Darlingi.” Molecular Ecology Notes. Wiley-Blackwell, 2001. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x.","short":"J. Conn, J.P. Bollback, D. Onyabe, T. Robinson, R. Wilkerson, M. Povoa, Molecular Ecology Notes 1 (2001) 223–225.","ama":"Conn J, Bollback JP, Onyabe D, Robinson T, Wilkerson R, Povoa M. Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes. 2001;1(4):223-225. doi: 10.1046/j.1471-8278.2001.00078.x"},"quality_controlled":"1","intvolume":" 1","publication_identifier":{"issn":["1471-8278"]},"language":[{"iso":"eng"}],"year":"2001","page":"223 - 225","abstract":[{"lang":"eng","text":"High molecular weight DNA was extracted from the primary Neotropical malaria vector, Anopheles darlingi from Capanema, Pará, Brazil, to create a small insert genomic library, and then a phagemid library. Enriched sublibraries were constructed from the phagemid library using a microsatellite oligo primed second strand synthesis protocol. The resulting 242 760 individual clones were screened. The mean clone size of the positive clones was 302 bp. Flanking primers were designed for each suitable microsatellite sequence. Eight polymorphic loci were optimized and characterized. The allele size ranges are based on 253 samples of A. darlingi from eastern Amazonian and central Brazil."}]},{"article_type":"original","month":"05","date_published":"2001-05-01T00:00:00Z","publication_status":"published","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publist_id":"2960","date_updated":"2023-05-15T13:54:01Z","publisher":"Oxford University Press","date_created":"2018-12-11T12:03:20Z","oa_version":"None","publication":"Systematic Biology","article_processing_charge":"No","_id":"3440","type":"journal_article","issue":"3","author":[{"full_name":"Huelsenbeck, John","first_name":"John","last_name":"Huelsenbeck"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"day":"01","title":"Empirical and hierarchical Bayesian estimation of ancestral states","volume":50,"status":"public","page":"351 - 366","external_id":{"pmid":["12116580"]},"abstract":[{"lang":"eng","text":"Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.\r\n"}],"quality_controlled":"1","citation":{"apa":"Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150119871","chicago":"Huelsenbeck, John, and Jonathan P Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology. Oxford University Press, 2001. https://doi.org/10.1080/10635150119871.","short":"J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.","ista":"Huelsenbeck J, Bollback JP. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 50(3), 351–366.","ieee":"J. Huelsenbeck and J. P. Bollback, “Empirical and hierarchical Bayesian estimation of ancestral states,” Systematic Biology, vol. 50, no. 3. Oxford University Press, pp. 351–366, 2001.","mla":"Huelsenbeck, John, and Jonathan P. Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology, vol. 50, no. 3, Oxford University Press, 2001, pp. 351–66, doi:10.1080/10635150119871.","ama":"Huelsenbeck J, Bollback JP. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 2001;50(3):351-366. doi:10.1080/10635150119871"},"doi":"10.1080/10635150119871","extern":"1","year":"2001","publication_identifier":{"issn":["0039-7989"]},"language":[{"iso":"eng"}],"intvolume":" 50","pmid":1},{"publication_status":"published","publisher":"Elsevier","publist_id":"2940","date_updated":"2021-01-12T07:43:31Z","month":"11","date_published":"2001-11-14T00:00:00Z","title":"Weighted quantified computation tree logic","status":"public","day":"14","year":"2001","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Pallab","last_name":"Dasgupta","full_name":"Dasgupta, Pallab"},{"full_name":"Chakrabarti, Partha P","last_name":"Chakrabarti","first_name":"Partha"}],"conference":{"name":"CIT: Conference on Information Technology"},"citation":{"mla":"Chatterjee, Krishnendu, et al. Weighted Quantified Computation Tree Logic. Elsevier, 2001.","ieee":"K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “Weighted quantified computation tree logic,” presented at the CIT: Conference on Information Technology, 2001.","ista":"Chatterjee K, Dasgupta P, Chakrabarti P. 2001. Weighted quantified computation tree logic. CIT: Conference on Information Technology.","chicago":"Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “Weighted Quantified Computation Tree Logic.” Elsevier, 2001.","short":"K. Chatterjee, P. Dasgupta, P. Chakrabarti, in:, Elsevier, 2001.","apa":"Chatterjee, K., Dasgupta, P., & Chakrabarti, P. (2001). Weighted quantified computation tree logic. Presented at the CIT: Conference on Information Technology, Elsevier.","ama":"Chatterjee K, Dasgupta P, Chakrabarti P. Weighted quantified computation tree logic. In: Elsevier; 2001."},"date_created":"2018-12-11T12:03:23Z","quality_controlled":0,"_id":"3447","type":"conference","extern":1},{"title":"Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists","volume":81,"status":"public","day":"01","author":[{"last_name":"Jones","first_name":"M.V","full_name":"Jones, M.V"},{"last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"},{"last_name":"Sahara","first_name":"Y.","full_name":"Sahara, Y."},{"full_name":"Westbrook, G.","first_name":"G.","last_name":"Westbrook"}],"date_created":"2018-12-11T12:03:37Z","oa_version":"Published Version","_id":"3493","article_processing_charge":"No","type":"journal_article","issue":"5","publication":"Biophysical Journal","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","publisher":"Biophysical Society","date_updated":"2023-05-15T13:50:21Z","publist_id":"2894","date_published":"2001-11-01T00:00:00Z","month":"11","article_type":"original","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1301733/","open_access":"1"}],"pmid":1,"intvolume":" 81","year":"2001","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-3495"]},"citation":{"ama":"Jones M., Jonas PM, Sahara Y, Westbrook G. Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists. Biophysical Journal. 2001;81(5):2660-2670. doi:10.1016/S0006-3495(01)75909-7 ","mla":"Jones, M. .., et al. “Microscopic Kinetics and Energetics Distinguish GABAA Receptor Agonists from Antagonists.” Biophysical Journal, vol. 81, no. 5, Biophysical Society, 2001, pp. 2660–70, doi:10.1016/S0006-3495(01)75909-7 .","ieee":"M. . Jones, P. M. Jonas, Y. Sahara, and G. Westbrook, “Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists,” Biophysical Journal, vol. 81, no. 5. Biophysical Society, pp. 2660–2670, 2001.","ista":"Jones M., Jonas PM, Sahara Y, Westbrook G. 2001. Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists. Biophysical Journal. 81(5), 2660–2670.","short":"M.. Jones, P.M. Jonas, Y. Sahara, G. Westbrook, Biophysical Journal 81 (2001) 2660–2670.","chicago":"Jones, M.V, Peter M Jonas, Y. Sahara, and G. Westbrook. “Microscopic Kinetics and Energetics Distinguish GABAA Receptor Agonists from Antagonists.” Biophysical Journal. Biophysical Society, 2001. https://doi.org/10.1016/S0006-3495(01)75909-7 .","apa":"Jones, M. ., Jonas, P. M., Sahara, Y., & Westbrook, G. (2001). Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/S0006-3495(01)75909-7 "},"doi":"10.1016/S0006-3495(01)75909-7 ","quality_controlled":"1","extern":"1","oa":1,"abstract":[{"text":"Although agonists and competitive antagonists presumably occupy overlapping binding sites on ligand-gated channels, these interactions cannot be identical because agonists cause channel opening whereas antagonists do not. One explanation is that only agonist binding performs enough work on the receptor to cause the conformational changes that lead to gating. This idea is supported by agonist binding rates at GABAA and nicotinic acetylcholine receptors that are slower than expected for a diffusion-limited process, suggesting that agonist binding involves an energy-requiring event. This hypothesis predicts that competitive antagonist binding should require less activation energy than agonist binding. To test this idea, we developed a novel deconvolution-based method to compare binding and unbinding kinetics of GABAA receptor agonists and antagonists in outside-out patches from rat hippocampal neurons. Agonist and antagonist unbinding rates were steeply correlated with affinity. Unlike the agonists, three of the four antagonists tested had binding rates that were fast, independent of affinity, and could be accounted for by diffusion- and dehydration-limited processes. In contrast, agonist binding involved additional energy-requiring steps, consistent with the idea that channel gating is initiated by agonist-triggered movements within the ligand binding site. Antagonist binding does not appear to produce such movements, and may in fact prevent them.","lang":"eng"}],"page":"2660 - 2670","external_id":{"pmid":["11606279"]}},{"main_file_link":[{"url":"ncbi.nlm.nih.gov/pmc/articles/PMC6762544/","open_access":"1"}],"date_published":"2001-04-15T00:00:00Z","month":"04","article_type":"original","publisher":"Society for Neuroscience","publist_id":"2893","date_updated":"2023-05-15T13:47:04Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication_status":"published","issue":"8","_id":"3494","article_processing_charge":"No","type":"journal_article","publication":"Journal of Neuroscience","date_created":"2018-12-11T12:03:37Z","oa_version":"Published Version","author":[{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"},{"last_name":"Vida","first_name":"Imre","full_name":"Vida, Imre"},{"last_name":"Frotscher","first_name":"Michael","full_name":"Frotscher, Michael"},{"full_name":"Geiger, Jörg","first_name":"Jörg","last_name":"Geiger"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"day":"15","status":"public","title":"Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network.","volume":21,"external_id":{"pmid":["11306622"]},"page":"2687 - 2698","oa":1,"abstract":[{"text":"Mutual synaptic interactions between GABAergic interneurons are thought to be of critical importance for the generation of network oscillations and for temporal encoding of information in the hippocampus. However, the functional properties of synaptic transmission between hippocampal interneurons are largely unknown. We have made paired recordings from basket cells (BCs) in the dentate gyrus of rat hippocampal slices, followed by correlated light and electron microscopical analysis. Unitary GABAAreceptor-mediated IPSCs at BC–BC synapses recorded at the soma showed a fast rise and decay, with a mean decay time constant of 2.5 ± 0.2 msec (32°C). Synaptic transmission at BC–BC synapses showed paired-pulse depression (PPD) (32 ± 5% for 10 msec interpulse intervals) and multiple-pulse depression during repetitive stimulation. Detailed passive cable model simulations based on somatodendritic morphology and localization of synaptic contacts further indicated that the conductance change at the postsynaptic site was even faster, decaying with a mean time constant of 1.8 ± 0.6 msec. Sequential triple recordings revealed that the decay time course of IPSCs at BC–BC synapses was approximately twofold faster than that at BC–granule cell synapses, whereas the extent of PPD was comparable. To examine the consequences of the fast postsynaptic conductance change for the generation of oscillatory activity, we developed a computational model of an interneuron network. The model showed robust oscillations at frequencies >60 Hz if the excitatory drive was sufficiently large. Thus the fast conductance change at interneuron–interneuron synapses may promote the generation of high-frequency oscillations observed in the dentate gyrusin vivo. ","lang":"eng"}],"extern":"1","citation":{"apa":"Bartos, M., Vida, I., Frotscher, M., Geiger, J., & Jonas, P. M. (2001). Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.21-08-02687.2001","short":"M. Bartos, I. Vida, M. Frotscher, J. Geiger, P.M. Jonas, Journal of Neuroscience 21 (2001) 2687–2698.","chicago":"Bartos, Marlene, Imre Vida, Michael Frotscher, Jörg Geiger, and Peter M Jonas. “Rapid Signaling at Inhibitory Synapses in a Dentate Gyrus Interneuron Network.” Journal of Neuroscience. Society for Neuroscience, 2001. https://doi.org/10.1523/JNEUROSCI.21-08-02687.2001.","ista":"Bartos M, Vida I, Frotscher M, Geiger J, Jonas PM. 2001. Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network. Journal of Neuroscience. 21(8), 2687–2698.","ieee":"M. Bartos, I. Vida, M. Frotscher, J. Geiger, and P. M. Jonas, “Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network.,” Journal of Neuroscience, vol. 21, no. 8. Society for Neuroscience, pp. 2687–2698, 2001.","mla":"Bartos, Marlene, et al. “Rapid Signaling at Inhibitory Synapses in a Dentate Gyrus Interneuron Network.” Journal of Neuroscience, vol. 21, no. 8, Society for Neuroscience, 2001, pp. 2687–98, doi:10.1523/JNEUROSCI.21-08-02687.2001.","ama":"Bartos M, Vida I, Frotscher M, Geiger J, Jonas PM. Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network. Journal of Neuroscience. 2001;21(8):2687-2698. doi:10.1523/JNEUROSCI.21-08-02687.2001"},"doi":"10.1523/JNEUROSCI.21-08-02687.2001","quality_controlled":"1","acknowledgement":"This work was supported by grants of the Deutsche Forschungsgemeinschaft (SFB 505/C6) and the Human Frontiers Science Program Organization (RG0017/1998-B). We thank Drs. M. V. Jones, J. Bischofberger, and U. Kraushaar for critically reading this manuscript. We also thank B. Taskin and A. Roth for advice in the use of reconstruction and modeling software, and S. Nestel, M. Winter, and A. Blomenkamp for technical assistance.","publication_identifier":{"issn":["0270-6474"]},"language":[{"iso":"eng"}],"year":"2001","pmid":1,"intvolume":" 21"}]