[{"article_processing_charge":"No","date_published":"2004-05-28T00:00:00Z","fulldoi":"https://doi.org/10.1074/jbc.M401539200","intvolume":"       279","publication_status":"published","year":"2004","pmid":1,"doi":"10.1074/jbc.M401539200","volume":279,"day":"28","publisher":"American Society for Biochemistry and Molecular Biology","month":"05","external_id":{"pmid":["15037611"]},"citation":{"apa":"Mamedova, A., Holt, P., Carroll, J., &#38; Sazanov, L. A. (2004). Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>","chicago":"Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2004. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>.","ieee":"A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational change in bacterial complex I,” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836, 2004.","ista":"Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.","short":"A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry 279 (2004) 23830–23836.","ama":"Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. 2004;279(22):23830-23836. doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>","mla":"Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22, American Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>."},"page":"23830 - 23836","date_updated":"2026-09-30T13:21:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","author":[{"first_name":"Aygun","last_name":"Mamedova","full_name":"Mamedova, Aygun"},{"full_name":"Holt, Peter","first_name":"Peter","last_name":"Holt"},{"full_name":"Carroll, Joe","last_name":"Carroll","first_name":"Joe"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"date_created":"2018-12-11T11:54:56Z","title":"Substrate-induced conformational change in bacterial complex I","_id":"1963","extern":"1","abstract":[{"text":"The mechanism coupling electron transfer and proton pumping in respiratory complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has been suggested that it involves conformational changes. Here, the influence of substrates on the conformation of purified complex I from Escherichia coli was studied by cross-linking and electron microscopy. When a zero-length cross-linking reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented the formation of cross-links between the hydrophilic subunits of the complex, including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral arm of the complex adopts a more open conformation, with increased distances between subunits. Single particle analysis showed the nature of this conformational change. The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly more open or expanded structure both in the peripheral arm and, unexpectedly, in the membrane domain also.","lang":"eng"}],"type":"journal_article","oa_version":"None","article_type":"original","OA_place":"publisher","OA_type":"gold","language":[{"iso":"eng"}],"publist_id":"5123","issue":"22","publication":"Journal of Biological Chemistry","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"acknowledgement":"This work was supported by the Medical Research Council and by a Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A. A. M.)"},{"page":"485 - 548","citation":{"ama":"Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. 2004;122(3):485-548. doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>","mla":"Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548, doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>.","ista":"Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons. Duke Mathematical Journal. 122(3), 485–548.","short":"T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004) 485–548.","ieee":"T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational instantons,” <i>Duke Mathematical Journal</i>, vol. 122, no. 3. Duke University Press, pp. 485–548, 2004.","chicago":"Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>. Duke University Press, 2004. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>.","apa":"Hausel, T., Hunsicker, E., &#38; Mazzeo, R. (2004). Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:26:24Z","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel","full_name":"Hausel, Tamas","orcid":"0000-0002-9582-2634"},{"last_name":"Hunsicker","first_name":"Eugénie","full_name":"Hunsicker, Eugénie"},{"first_name":"Rafe","last_name":"Mazzeo","full_name":"Mazzeo, Rafe"}],"date_created":"2018-12-11T11:52:08Z","status":"public","_id":"1456","title":"Hodge cohomology of gravitational instantons","abstract":[{"text":"We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory.","lang":"eng"}],"extern":"1","article_type":"original","oa_version":"None","type":"journal_article","OA_type":"green","OA_place":"repository","publist_id":"5737","language":[{"iso":"eng"}],"issue":"3","publication":"Duke Mathematical Journal","publication_identifier":{"issn":["0012-7094"],"eissn":["1547-7398"]},"acknowledgement":"Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.\r\nHunsicker’s work partially supported by Stanford University.\r\nMazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and\r\nby the Mathematical Sciences Research Institute.","article_processing_charge":"No","date_published":"2004-04-15T00:00:00Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0207169"}],"fulldoi":"https://doi.org/10.1215/S0012-7094-04-12233-X","intvolume":"       122","year":"2004","publication_status":"published","doi":"10.1215/S0012-7094-04-12233-X","volume":122,"oa":1,"day":"15","month":"04","publisher":"Duke University Press","external_id":{"arxiv":["0207169"]}},{"OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}],"publist_id":"5736","issue":"3","publication":"Proceedings of the London Mathematical Society","publication_identifier":{"eissn":["1460-244X"],"issn":["0024-6115"]},"page":"632 - 658","citation":{"ama":"Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. 2004;88(3):632-658. doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>","mla":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>.","short":"T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88 (2004) 632–658.","ista":"Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical Society. 88(3), 632–658.","ieee":"T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli space of rank 2 higgs bundles,” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.","chicago":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>.","apa":"Hausel, T., &#38; Thaddeus, M. (2004). Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:24:04Z","status":"public","author":[{"first_name":"Tamas","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamas","orcid":"0000-0002-9582-2634"},{"full_name":"Thaddeus, Michael","first_name":"Michael","last_name":"Thaddeus"}],"date_created":"2018-12-11T11:52:10Z","_id":"1464","title":"Generators for the cohomology ring of the moduli space of rank 2 higgs bundles","abstract":[{"text":"The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle.\r\n\r\nThis paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes.\r\n\r\nThe spaces of Higgs bundles with values in K(n) for n &gt; 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). ","lang":"eng"}],"extern":"1","article_type":"original","oa_version":"None","type":"journal_article","doi":"10.1112/S0024611503014618","volume":88,"oa":1,"day":"01","month":"05","publisher":"Oxford University Press","external_id":{"arxiv":["0003093"]},"article_processing_charge":"No","date_published":"2004-05-01T00:00:00Z","arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/math/0003093","open_access":"1"}],"fulldoi":"https://doi.org/10.1112/S0024611503014618","intvolume":"        88","year":"2004","publication_status":"published"},{"main_file_link":[{"url":"http://arxiv.org/abs/cond-mat/0403240","open_access":"1"}],"arxiv":1,"fulldoi":"https://doi.org/10.1103/PhysRevA.70.023612","article_processing_charge":"No","date_published":"2004-08-01T00:00:00Z","intvolume":"        70","publication_status":"published","year":"2004","doi":"10.1103/PhysRevA.70.023612","volume":70,"publisher":"American Physical Society","month":"08","external_id":{"arxiv":["0403240"]},"oa":1,"day":"01","date_updated":"2026-09-30T13:13:48Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"023612 - 1-0236121-2","citation":{"chicago":"Aizenman, Michael, Élliott Lieb, Robert Seiringer, Jan Solovej, and Jakob Yngvason. “Bose-Einstein Quantum Phase Transition in an Optical Lattice Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2004. <a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">https://doi.org/10.1103/PhysRevA.70.023612</a>.","apa":"Aizenman, M., Lieb, É., Seiringer, R., Solovej, J., &#38; Yngvason, J. (2004). Bose-Einstein quantum phase transition in an optical lattice model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">https://doi.org/10.1103/PhysRevA.70.023612</a>","ama":"Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. Bose-Einstein quantum phase transition in an optical lattice model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2004;70(2):023612-1-0236121-2. doi:<a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">10.1103/PhysRevA.70.023612</a>","mla":"Aizenman, Michael, et al. “Bose-Einstein Quantum Phase Transition in an Optical Lattice Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 70, no. 2, American Physical Society, 2004, pp. 023612-1-0236121-2, doi:<a href=\"https://doi.org/10.1103/PhysRevA.70.023612\">10.1103/PhysRevA.70.023612</a>.","ieee":"M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, and J. Yngvason, “Bose-Einstein quantum phase transition in an optical lattice model,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 70, no. 2. American Physical Society, pp. 023612-1-0236121-2, 2004.","short":"M. Aizenman, É. Lieb, R. Seiringer, J. Solovej, J. Yngvason, Physical Review A - Atomic, Molecular, and Optical Physics 70 (2004) 023612-1-0236121-2.","ista":"Aizenman M, Lieb É, Seiringer R, Solovej J, Yngvason J. 2004. Bose-Einstein quantum phase transition in an optical lattice model. Physical Review A - Atomic, Molecular, and Optical Physics. 70(2), 023612-1-0236121-2."},"extern":"1","abstract":[{"lang":"eng","text":"An optical lattice model developed that is similar to the Bose-Hubbard model to describe the transition between Bose-Einstein condensation (BEC) and a Mott insulator state was analyzed. It was found that the system was a hard core lattice gas at half of the maximum density and the optical lattice was modeled by a periodic potential of strength λ. It was also observed that the interparticle interaction was essential for this transition that occurred even in the ground state. The results show that all the essential features could be proved rigorously such as the existence of BEC for small λ and its suppression for a large λ."}],"type":"journal_article","oa_version":"None","article_type":"original","date_created":"2018-12-11T11:57:12Z","author":[{"full_name":"Aizenman, Michael","last_name":"Aizenman","first_name":"Michael"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"},{"last_name":"Yngvason","first_name":"Jakob","full_name":"Yngvason, Jakob"}],"status":"public","title":"Bose-Einstein quantum phase transition in an optical lattice model","_id":"2360","publist_id":"4567","language":[{"iso":"eng"}],"OA_place":"repository","OA_type":"green","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"issue":"2","publication":"Physical Review A - Atomic, Molecular, and Optical Physics"},{"volume":115,"doi":"10.1023/B:JOSS.0000019811.15510.27","external_id":{"arxiv":["0210027"]},"publisher":"Springer Nature","month":"04","day":"01","oa":1,"fulldoi":"https://doi.org/10.1023/B:JOSS.0000019811.15510.27","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math-ph/0210027"}],"arxiv":1,"date_published":"2004-04-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","year":"2004","intvolume":"       115","language":[{"iso":"eng"}],"publist_id":"4568","OA_place":"repository","OA_type":"green","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"publication":"Journal of Statistical Physics","issue":"1-2","date_updated":"2026-09-30T13:15:37Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"185 - 190","citation":{"ama":"Lieb É, Seiringer R.  Equivalent forms of the Bessis-Moussa-Villani conjecture. <i>Journal of Statistical Physics</i>. 2004;115(1-2):185-190. doi:<a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">10.1023/B:JOSS.0000019811.15510.27</a>","mla":"Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani Conjecture.” <i>Journal of Statistical Physics</i>, vol. 115, no. 1–2, Springer Nature, 2004, pp. 185–90, doi:<a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">10.1023/B:JOSS.0000019811.15510.27</a>.","short":"É. Lieb, R. Seiringer, Journal of Statistical Physics 115 (2004) 185–190.","ieee":"É. Lieb and R. Seiringer, “ Equivalent forms of the Bessis-Moussa-Villani conjecture,” <i>Journal of Statistical Physics</i>, vol. 115, no. 1–2. Springer Nature, pp. 185–190, 2004.","ista":"Lieb É, Seiringer R. 2004.  Equivalent forms of the Bessis-Moussa-Villani conjecture. Journal of Statistical Physics. 115(1–2), 185–190.","chicago":"Lieb, Élliott, and Robert Seiringer. “ Equivalent Forms of the Bessis-Moussa-Villani Conjecture.” <i>Journal of Statistical Physics</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">https://doi.org/10.1023/B:JOSS.0000019811.15510.27</a>.","apa":"Lieb, É., &#38; Seiringer, R. (2004).  Equivalent forms of the Bessis-Moussa-Villani conjecture. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1023/B:JOSS.0000019811.15510.27\">https://doi.org/10.1023/B:JOSS.0000019811.15510.27</a>"},"oa_version":"None","type":"journal_article","article_type":"original","extern":"1","abstract":[{"lang":"eng","text":"The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace transform of a positive measure, is shown to be equivalent to two other statements: (i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive measure for A, B ≥ 0, p &gt; 0."}],"title":" Equivalent forms of the Bessis-Moussa-Villani conjecture","_id":"2355","date_created":"2018-12-11T11:57:11Z","author":[{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"status":"public"},{"title":"New constructions of weak ε-nets","_id":"2425","status":"public","author":[{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:57:35Z","type":"journal_article","oa_version":"None","article_type":"original","extern":"1","abstract":[{"text":"A finite set N ⊂ Rd is a weak ε-net for an n-point set X ⊂ Rd (with respect to convex sets) if N intersects every convex set K with |K ∩ X| ≥ εn. We give an alternative, and arguably simpler, proof of the fact, first shown by Chazelle et al., that every point set X in Rd admits a weak ε-net of cardinality O(ε-dpolylog(1/ε)). Moreover, for a number of special point sets (e.g., for points on the moment curve), our method gives substantially better bounds. The construction yields an algorithm to construct such weak ε-nets in time O(n ln(1/ε)).","lang":"eng"}],"page":"195 - 206","citation":{"ama":"Matoušek J, Wagner U. New constructions of weak ε-nets. <i>Discrete &#38; Computational Geometry</i>. 2004;32(2):195-206. doi:<a href=\"https://doi.org/10.1007/s00454-004-1116-4\">10.1007/s00454-004-1116-4</a>","mla":"Matoušek, Jiří, and Uli Wagner. “New Constructions of Weak ε-Nets.” <i>Discrete &#38; Computational Geometry</i>, vol. 32, no. 2, Springer, 2004, pp. 195–206, doi:<a href=\"https://doi.org/10.1007/s00454-004-1116-4\">10.1007/s00454-004-1116-4</a>.","ista":"Matoušek J, Wagner U. 2004. New constructions of weak ε-nets. Discrete &#38; Computational Geometry. 32(2), 195–206.","ieee":"J. Matoušek and U. Wagner, “New constructions of weak ε-nets,” <i>Discrete &#38; Computational Geometry</i>, vol. 32, no. 2. Springer, pp. 195–206, 2004.","short":"J. Matoušek, U. Wagner, Discrete &#38; Computational Geometry 32 (2004) 195–206.","chicago":"Matoušek, Jiří, and Uli Wagner. “New Constructions of Weak ε-Nets.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2004. <a href=\"https://doi.org/10.1007/s00454-004-1116-4\">https://doi.org/10.1007/s00454-004-1116-4</a>.","apa":"Matoušek, J., &#38; Wagner, U. (2004). New constructions of weak ε-nets. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-004-1116-4\">https://doi.org/10.1007/s00454-004-1116-4</a>"},"date_updated":"2026-09-30T13:08:52Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Discrete & Computational Geometry","issue":"2","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"OA_type":"closed access","language":[{"iso":"eng"}],"publist_id":"4500","publication_status":"published","year":"2004","intvolume":"        32","date_published":"2004-07-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/s00454-004-1116-4","day":"01","publisher":"Springer","month":"07","volume":32,"doi":"10.1007/s00454-004-1116-4"},{"month":"01","publication_identifier":{"issn":["0271-4132"]},"publisher":"American Mathematical Society","publication":"Towards a Theory of Geometric Graphs","day":"01","doi":"10.1090/conm/342","language":[{"iso":"eng"}],"publist_id":"4508","volume":342,"extern":"1","intvolume":"       342","year":"2004","oa_version":"None","type":"book_chapter","publication_status":"published","author":[{"full_name":"Lovász, László","last_name":"Lovász","first_name":"László"},{"first_name":"Katalin","last_name":"Vesztergombi","full_name":"Vesztergombi, Katalin"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emo","last_name":"Welzl","full_name":"Welzl, Emo"}],"status":"public","date_created":"2018-12-11T11:57:32Z","_id":"2417","editor":[{"full_name":"Pach, János","first_name":"János","last_name":"Pach"}],"title":"Convex quadrilaterals and k-sets ","fulldoi":"https://doi.org/10.1090/conm/342","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:11:01Z","article_processing_charge":"No","page":"139 - 148","citation":{"ista":"Lovász L, Vesztergombi K, Wagner U, Welzl E. 2004.Convex quadrilaterals and k-sets . In: Towards a Theory of Geometric Graphs. Contemporary Mathematics , vol. 342, 139–148.","short":"L. Lovász, K. Vesztergombi, U. Wagner, E. Welzl, in:, J. Pach (Ed.), Towards a Theory of Geometric Graphs, American Mathematical Society, 2004, pp. 139–148.","ieee":"L. Lovász, K. Vesztergombi, U. Wagner, and E. Welzl, “Convex quadrilaterals and k-sets ,” in <i>Towards a Theory of Geometric Graphs</i>, vol. 342, J. Pach, Ed. American Mathematical Society, 2004, pp. 139–148.","ama":"Lovász L, Vesztergombi K, Wagner U, Welzl E. Convex quadrilaterals and k-sets . In: Pach J, ed. <i>Towards a Theory of Geometric Graphs</i>. Vol 342. American Mathematical Society; 2004:139-148. doi:<a href=\"https://doi.org/10.1090/conm/342\">10.1090/conm/342</a>","mla":"Lovász, László, et al. “Convex Quadrilaterals and K-Sets .” <i>Towards a Theory of Geometric Graphs</i>, edited by János Pach, vol. 342, American Mathematical Society, 2004, pp. 139–48, doi:<a href=\"https://doi.org/10.1090/conm/342\">10.1090/conm/342</a>.","apa":"Lovász, L., Vesztergombi, K., Wagner, U., &#38; Welzl, E. (2004). Convex quadrilaterals and k-sets . In J. Pach (Ed.), <i>Towards a Theory of Geometric Graphs</i> (Vol. 342, pp. 139–148). American Mathematical Society. <a href=\"https://doi.org/10.1090/conm/342\">https://doi.org/10.1090/conm/342</a>","chicago":"Lovász, László, Katalin Vesztergombi, Uli Wagner, and Emo Welzl. “Convex Quadrilaterals and K-Sets .” In <i>Towards a Theory of Geometric Graphs</i>, edited by János Pach, 342:139–48. American Mathematical Society, 2004. <a href=\"https://doi.org/10.1090/conm/342\">https://doi.org/10.1090/conm/342</a>."},"alternative_title":["Contemporary Mathematics "],"date_published":"2004-01-01T00:00:00Z"},{"issue":"5","publication":"Genome Research","acknowledgement":"We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada.\r\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.","publication_identifier":{"issn":["1088-9051"],"eissn":["1549-5469"]},"OA_type":"closed access","publist_id":"6750","language":[{"iso":"eng"}],"author":[{"last_name":"Castillo Davis","first_name":"Cristian","full_name":"Castillo Davis, Cristian"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"first_name":"Daniel","last_name":"Hartl","full_name":"Hartl, Daniel"},{"first_name":"Rob","last_name":"Kulathinal","full_name":"Kulathinal, Rob"}],"date_created":"2018-12-11T11:49:06Z","status":"public","_id":"902","title":"The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint","abstract":[{"text":"We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.","lang":"eng"}],"extern":"1","article_type":"original","oa_version":"None","type":"journal_article","page":"802 - 811","citation":{"apa":"Castillo Davis, C., Kondrashov, F., Hartl, D., &#38; Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>","chicago":"Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2004. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>.","short":"C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.","ista":"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. 14(5), 802–811.","ieee":"C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” <i>Genome Research</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.","ama":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. 2004;14(5):802-811. doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>","mla":"Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:33:40Z","day":"01","month":"05","publisher":"Cold Spring Harbor Laboratory Press","external_id":{"pmid":["15123580"]},"doi":"10.1101/gr.2195604","volume":14,"intvolume":"        14","pmid":1,"year":"2004","publication_status":"published","article_processing_charge":"No","date_published":"2004-05-01T00:00:00Z","fulldoi":"https://doi.org/10.1101/gr.2195604"},{"publication":"Nature Genetics","issue":"11","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"acknowledgement":"We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes","OA_type":"closed access","language":[{"iso":"eng"}],"publist_id":"6759","_id":"889","title":"Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs","status":"public","date_created":"2018-12-11T11:49:02Z","author":[{"full_name":"Kern, Andrew","first_name":"Andrew","last_name":"Kern"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"article_type":"original","oa_version":"None","type":"journal_article","extern":"1","abstract":[{"text":"The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.","lang":"eng"}],"citation":{"chicago":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>.","apa":"Kern, A., &#38; Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>","mla":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>.","ama":"Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. 2004;36(11):1207-1212. doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>","ista":"Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.","ieee":"A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” <i>Nature Genetics</i>, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004.","short":"A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212."},"page":"1207 - 1212","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:35:39Z","day":"01","external_id":{"pmid":["15502829"]},"month":"11","publisher":"Nature Publishing Group","volume":36,"doi":"10.1038/ng1451","year":"2004","pmid":1,"publication_status":"published","intvolume":"        36","date_published":"2004-11-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/ng1451"},{"external_id":{"pmid":["15175752"]},"publisher":"Nature Publishing Group","month":"06","day":"03","volume":429,"doi":"10.1038/nature02601","publication_status":"published","pmid":1,"year":"2004","intvolume":"       429","fulldoi":"https://doi.org/10.1038/nature02601","date_published":"2004-06-03T00:00:00Z","article_processing_charge":"No","acknowledgement":"We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","issue":"6991","publist_id":"6746","language":[{"iso":"eng"}],"OA_type":"closed access","oa_version":"None","type":"journal_article","article_type":"original","extern":"1","abstract":[{"text":"New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement.","lang":"eng"}],"title":"Positive selection at sites of multiple amino acid replacements since rat-mouse divergence","_id":"898","status":"public","author":[{"last_name":"Bazykin","first_name":"Georgii","full_name":"Bazykin, Georgii"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aleksey","last_name":"Ogurtsov","full_name":"Ogurtsov, Aleksey"},{"full_name":"Sunyaev, Shamil","first_name":"Shamil","last_name":"Sunyaev"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey"}],"date_created":"2018-12-11T11:49:05Z","date_updated":"2026-09-30T13:31:32Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"558 - 562","citation":{"mla":"Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>.","ama":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. 2004;429(6991):558-562. doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>","ista":"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. 429(6991), 558–562.","short":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.","ieee":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” <i>Nature</i>, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.","chicago":"Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>.","apa":"Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., &#38; Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>"}},{"day":"01","external_id":{"pmid":["15010543"]},"publisher":"Wiley-Blackwell","month":"04","volume":13,"doi":"10.1110/ps.03465504","publication_status":"published","pmid":1,"year":"2004","intvolume":"        13","date_published":"2004-04-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1110/ps.03465504","publication":"Protein Science","issue":"4","acknowledgement":"We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport.","publication_identifier":{"eissn":["1469-896X"],"issn":["0961-8368"]},"OA_type":"closed access","publist_id":"6786","language":[{"iso":"eng"}],"title":"Prediction of functional sites by analysis of sequence and structure conservation","_id":"864","date_created":"2018-12-11T11:48:55Z","status":"public","author":[{"last_name":"Panchenko","first_name":"Anna","full_name":"Panchenko, Anna"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"first_name":"Stephen","last_name":"Bryant","full_name":"Bryant, Stephen"}],"type":"journal_article","oa_version":"None","article_type":"original","abstract":[{"lang":"eng","text":"We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites."}],"extern":"1","page":"884 - 892","citation":{"chicago":"Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>. Wiley-Blackwell, 2004. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>.","apa":"Panchenko, A., Kondrashov, F., &#38; Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>","ama":"Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. 2004;13(4):884-892. doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>","mla":"Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>.","short":"A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.","ista":"Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.","ieee":"A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” <i>Protein Science</i>, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004."},"date_updated":"2026-09-30T13:44:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"citation":{"chicago":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>.","apa":"Kondrashov, F., &#38; Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>","ama":"Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. 2004;20(7):287-291. doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>","mla":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>.","short":"F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.","ista":"Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291.","ieee":"F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” <i>Trends in Genetics</i>, vol. 20, no. 7. Elsevier, pp. 287–291, 2004."},"page":"287 - 291","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:38:03Z","_id":"875","title":"A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications","date_created":"2018-12-11T11:48:58Z","status":"public","author":[{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Koonin","first_name":"Eugene","full_name":"Koonin, Eugene"}],"article_type":"original","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis."}],"extern":"1","OA_type":"closed access","publist_id":"6775","language":[{"iso":"eng"}],"publication":"Trends in Genetics","issue":"7","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"date_published":"2004-07-01T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.tig.2004.05.001","year":"2004","pmid":1,"publication_status":"published","intvolume":"        20","volume":20,"doi":"10.1016/j.tig.2004.05.001","day":"01","external_id":{"pmid":["15219392"]},"month":"07","publisher":"Elsevier"},{"citation":{"apa":"Kondrashov, F., Ogurtsov, A., &#38; Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>","chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.","ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” <i>Nucleic Acids Research</i>, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004.","ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. 2004;32(5):1731-1737. doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>","mla":"Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>."},"page":"1731 - 1737","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-30T13:42:52Z","author":[{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ogurtsov, Aleksey","last_name":"Ogurtsov","first_name":"Aleksey"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey"}],"date_created":"2018-12-11T11:48:56Z","status":"public","_id":"870","title":"Bioinformatical assay of human gene morbidity","abstract":[{"text":"Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates.","lang":"eng"}],"extern":"1","article_type":"original","type":"journal_article","oa_version":"None","OA_place":"publisher","OA_type":"gold","publist_id":"6780","language":[{"iso":"eng"}],"issue":"5","publication":"Nucleic Acids Research","publication_identifier":{"eissn":["1362-4962"],"issn":["0305-1048"]},"article_processing_charge":"No","date_published":"2004-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1093/nar/gkh330","intvolume":"        32","pmid":1,"year":"2004","publication_status":"published","doi":"10.1093/nar/gkh330","volume":32,"day":"01","month":"01","publisher":"Oxford University Press","external_id":{"pmid":["15020709"]}},{"date_updated":"2026-09-30T13:59:49Z","fulldoi":"https://doi.org/10.1007/s00222-004-0360-9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2004-03-17T00:00:00Z","page":"553 - 573","citation":{"chicago":"Browning, Timothy D, and Roger Heath Brown. “Equal Sums of Three Powers.” <i>Inventiones Mathematicae</i>. Unknown, 2004. <a href=\"https://doi.org/10.1007/s00222-004-0360-9\">https://doi.org/10.1007/s00222-004-0360-9</a>.","apa":"Browning, T. D., &#38; Heath Brown, R. (2004). Equal sums of three powers. <i>Inventiones Mathematicae</i>. Unknown. <a href=\"https://doi.org/10.1007/s00222-004-0360-9\">https://doi.org/10.1007/s00222-004-0360-9</a>","ama":"Browning TD, Heath Brown R. Equal sums of three powers. <i>Inventiones Mathematicae</i>. 2004;157(3):553-573. doi:<a href=\"https://doi.org/10.1007/s00222-004-0360-9\">10.1007/s00222-004-0360-9</a>","mla":"Browning, Timothy D., and Roger Heath Brown. “Equal Sums of Three Powers.” <i>Inventiones Mathematicae</i>, vol. 157, no. 3, Unknown, 2004, pp. 553–73, doi:<a href=\"https://doi.org/10.1007/s00222-004-0360-9\">10.1007/s00222-004-0360-9</a>.","ieee":"T. D. Browning and R. Heath Brown, “Equal sums of three powers,” <i>Inventiones Mathematicae</i>, vol. 157, no. 3. Unknown, pp. 553–573, 2004.","short":"T.D. Browning, R. Heath Brown, Inventiones Mathematicae 157 (2004) 553–573.","ista":"Browning TD, Heath Brown R. 2004. Equal sums of three powers. Inventiones Mathematicae. 157(3), 553–573."},"article_processing_charge":"No","publication_status":"published","oa_version":"None","type":"journal_article","article_type":"original","year":"2004","intvolume":"       157","extern":"1","title":"Equal sums of three powers","_id":"209","date_created":"2018-12-11T11:45:13Z","status":"public","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"first_name":"Roger","last_name":"Heath Brown","full_name":"Heath Brown, Roger"}],"volume":157,"language":[{"iso":"eng"}],"publist_id":"7703","doi":"10.1007/s00222-004-0360-9","OA_type":"closed access","publisher":"Unknown","month":"03","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"publication":"Inventiones Mathematicae","day":"17","issue":"3"}]