{"id":"https://openalex.org/W4249235957","doi":"https://doi.org/10.1093/bib/bbl047","title":"Abstracts","display_name":"Abstracts","publication_year":2006,"publication_date":"2006-05-26","ids":{"openalex":"https://openalex.org/W4249235957","doi":"https://doi.org/10.1093/bib/bbl047"},"language":"nl","primary_location":{"id":"doi:10.1093/bib/bbl047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl047","pdf_url":"https://academic.oup.com/bib/article-pdf/8/1/60/738820/bbl047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"conference-abstract","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/8/1/60/738820/bbl047.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047756123","display_name":"I. K. Jordan","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"I. K. Jordan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5047756123"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":"1","first_page":"60","last_page":"64"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.21930000185966492,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.21930000185966492,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02889999933540821,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.02459999918937683,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44727662205696106}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44727662205696106}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bib/bbl047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl047","pdf_url":"https://academic.oup.com/bib/article-pdf/8/1/60/738820/bbl047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbl047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl047","pdf_url":"https://academic.oup.com/bib/article-pdf/8/1/60/738820/bbl047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4249235957.pdf","grobid_xml":"https://content.openalex.org/works/W4249235957.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Briefings":[0],"in":[1,35,44,135,144,311,490,496,530,612,647,669,778,797,823,891,914,925,929,958,1119,1191,1310,1406,1445,1484,1538,1611,1707,1775,1819,1940,1975,1985,1992,2003,2048,2057,2109,2150,2264,2290,2300,2332,2364,2375,2383,2426,2458,2471,2486,2508,2544,2892,2897,2968],"Bioinformatics":[2],"aims":[3],"to":[4,53,62,142,159,218,269,328,339,448,457,471,485,492,516,600,602,716,853,949,960,1007,1051,1062,1196,1213,1225,1313,1348,1490,1503,1518,1542,1606,1625,1705,1726,1799,1889,1903,1921,2012,2031,2131,2145,2167,2184,2226,2236,2257,2306,2318,2361,2404,2447,2597,2611,2658,2666,2676,2734,2746,2768,2792,2843,2852,2880,2887,2909,2916,2923,2937,2982,2998],"provide":[5],"working":[6],"biologists":[7],"with":[8,80,211,321,522,563,788,813,847,982,997,1254,1350,1558,1893,1916,2164,2335,2556,2868],"an":[9,42,81,1249,1478,1682,1732,1880,2481,2586,2715],"awareness":[10],"and":[11,20,88,94,117,167,188,207,234,306,489,573,625,732,735,795,850,947,1000,1012,1017,1123,1137,1150,1204,1219,1452,1466,1496,1561,1647,1672,1807,1896,1932,1946,1977,2014,2093,2205,2295,2366,2398,2450,2476,2519,2568,2575,2595,2624,2697,2706,2834,2894,2962,2988],"understanding":[12,656,1166,2587],"of":[13,25,29,31,41,71,133,175,183,186,190,205,223,236,263,281,284,318,331,343,359,370,414,479,507,527,541,577,642,657,676,686,702,709,719,752,762,811,856,870,887,894,911,917,931,941,974,1014,1020,1024,1041,1065,1090,1167,1176,1187,1199,1215,1238,1248,1258,1270,1286,1293,1300,1327,1359,1362,1375,1394,1424,1432,1440,1449,1455,1480,1493,1501,1521,1531,1533,1575,1587,1600,1629,1663,1676,1691,1694,1701,1713,1743,1777,1787,1853,1865,1882,1907,1934,1956,2061,2122,2178,2228,2275,2346,2350,2356,2373,2378,2389,2407,2416,2429,2432,2437,2454,2467,2474,2483,2488,2532,2547,2562,2578,2622,2629,2642,2648,2671,2688,2694,2709,2717,2724,2731,2737,2762,2773,2862,2920,2931,2944,2970,2984,3030,3035],"the":[14,26,36,49,56,63,66,78,184,212,221,230,261,264,279,329,347,355,364,371,376,396,440,502,534,553,575,603,640,648,655,687,700,703,736,741,757,845,857,867,879,884,895,898,912,932,952,1009,1015,1021,1025,1063,1067,1072,1076,1087,1097,1154,1165,1174,1220,1239,1246,1255,1267,1275,1314,1324,1338,1351,1360,1376,1398,1407,1419,1446,1450,1462,1485,1491,1494,1508,1519,1522,1546,1593,1617,1627,1664,1673,1677,1709,1718,1740,1828,1925,1954,1964,1972,1981,2008,2022,2026,2036,2049,2058,2113,2120,2123,2143,2151,2206,2243,2265,2273,2311,2347,2371,2376,2387,2433,2442,2451,2472,2493,2511,2545,2548,2566,2668,2692,2722,2725,2729,2735,2738,2748,2754,2760,2769,2774,2786,2790,2793,2796,2801,2824,2849,2853,2869,2912,2918,3011,3032,3036],"computational":[15,208],"approaches":[16],"available":[17,1367],"for":[18,65,77,138,202,238,288,494,654,693,756,784,875,943,1114,1164,1266,1414,1565,1638,1669,1765,1801,1821,1851,1879,1905,1924,1953,1968,2119,2386,2413,2875,2956,2967,2993,3017,3027],"research":[19],"discovery.":[21],"The":[22,69,131,173,226,253,293,504,539,760,905,995,1055,1355,1885,1911,2410,2530,2627,2686,2711,2820,2857,2940],"Abstracts":[23],"section":[24,46],"journal":[27],"consists":[28],"summaries":[30],"bioinformatics":[32],"manuscripts":[33],"published":[34,1153],"preceding":[37],"two":[38,728,2037,2695],"months.":[39],"Inclusion":[40],"article":[43],"this":[45,487,517,888,1271,1584,1615,1808,1816,2197,2268,2438,2877,2921,2945],"indicates":[47,1084],"that":[48,155,215,301,353,387,426,499,555,580,596,608,645,695,749,766,865,909,951,988,1038,1058,1085,1159,1232,1264,1278,1323,1337,1370,1389,1409,1583,1685,1720,1803,1823,2025,2045,2127,2159,2213,2246,2286,2323,2354,2380,2419,2441,2456,2469,2495,2585,2616,2634,2651,2702,2805,2807,2816,2847,2860,2902,2948,3009],"editors":[50],"consider":[51],"it":[52,590,1244,2042],"be":[54,160,458,1052,1108,1563,1571,1581,1621,1727,1739,1772,1922,2032,2224,2227,2780,2812,2888,2965,2991,3007],"among":[55,723,2142,2327],"most":[57,542,598,1724,2434],"interesting":[58,1742,2435],"and/or":[59,992],"useful":[60],"contributions":[61,2670],"field":[64],"quarter":[67],"covered.":[68],"contents":[70],"these":[72,246,319,344,592,966,1091,1188,1569,1891,1935,2340,2357,2414,2863],"reports":[73],"are":[74,97,556,581,597,609,664,833,841,900,921,955,969,989,1048,1190,1404,1411,1426,1470,1555,1723,2019,2029,2155,2177,2182,2193,2214,2287,2324,2342,2359,2381,2721,2757],"briefly":[75],"distilled":[76],"readers":[79],"emphasis":[82,2207],"placed":[83,551,2209],"on":[84,220,229,248,363,439,546,552,639,1317,1708,1758,1791,1862,1888,2202,2210,2261,2272,2714,2823],"their":[85,412,511,962,1032,1197,1395,1898,2689,2900],"biological":[86,659,677,1926],"context":[87,2449],"potential":[89],"utility.":[90],"Publications":[91],"from":[92,971,1458,1731,1989,2250,2728,2789],"October":[93],"November":[95],"2006":[96],"reviewed":[98],"here.":[99],"Alan":[100],"M.":[101,1649],"Moses,":[102],"Daniel":[103],"A.":[104,107],"Pollard,":[105,2066],"David":[106,1138,2094,2139],"Nix,":[108],"Venky":[109],"N.":[110],"Iyer,":[111],"Xiao-Yong":[112],"Li,":[113],"Mark":[114,2515],"D.":[115,2073],"Biggin":[116],"Michael":[118],"B.":[119],"Eisen":[120],"PLoS":[121,2096],"Computational":[122],"Biology":[123,1141],"(2008)":[124],"Vol.":[125,630,1144,1653,2099,2524],"2,":[126,2100],"no.":[127,632,1655,2101,2526],"10,":[128,2102],"p.":[129,1146,2103],"e130":[130],"importance":[132,576,2372],"changes":[134,143,605,913,924,1118,1444,1483,2047,2126,2241,2374,2401,2468,2602,2679],"gene":[136,145,712,747,764,838,876,1120,1177,1222,1913,2501,2741,2837],"regulation":[137,157,937,1042,2377,2388],"organismic":[139],"evolution\u2014as":[140],"opposed":[141],"coding":[146,165,690,1121],"sequences":[147,154,166,287,310,554,571,579,595,832,851,1178,1388,1736,1850,1874,1983,2158,2176,2322,2341,2485],"per":[148,2765],"se\u2014has":[149],"long":[150,1284,2620,2640,3028],"been":[151,428,550,1391,1698,2054,2186,2200,2952],"recognized.":[152],"However,":[153,873,1243,1730,2006,2256],"control":[156,493,942],"tend":[158],"less":[161,401],"well":[162,277,422,515,1180,2479],"characterized":[163,1282,1392,2638],"than":[164,393,403,584,1117,1364,1434,1846,2218,2814,2896,2959],"hence":[168],"not":[169,775,804,1028,1412,1748,3023],"as":[170,276,278,421,423,863,1005,1029,1031,1179,1181,1373,1475,1573,1624,1693,1762,1835,1838,2478,2480,2499,2759],"intensively":[171],"studied.":[172],"paper":[174,1810],"Moses":[176],"et":[177,680,1813,2662],"al.":[178,681,1814,2663],"presents":[179],"a":[180,239,249,282,322,350,406,523,683,972,985,1109,1429,1497,1529,1635,1660,1689,1784,1839,1857,1863,1962,1997,2259,2303,2395,2423,2465,2506,2579,2619,2655,2682,2844,2873,2906,2974,3014],"large-scale":[181,637,711,1251,2683],"evaluation":[182,2716],"rate":[185,1431],"gain":[187],"loss":[189],"Drosophila":[191,291,297,315],"cis-regulatory":[192],"transcription":[193,241,1766,2365],"factor":[194,242,1767],"binding":[195,335,345,367,397,469,1768],"sites":[196,272,361,389,417,420,425,470,532],"(TFBS).":[197],"This":[198,462,560,636,935,1083,1307,1868,1948,2135,2369,2491,2559,2605],"work":[199,2946],"is":[200,216,591,882,1027,1094,1100,1171,1223,1233,1245,1281,1329,1590,1681,2043,2208,2282,2418,2422,2636,2654,2691,2947],"notable":[201],"its":[203,1205,2203],"combination":[204,1247],"experimental":[206,267],"analyses":[209],"along":[210,562,699,981,1075,1253,2242,2310,2510,2785],"analytical":[213],"rigor":[214],"brought":[217],"bear":[219],"question":[222,1684],"TFBS":[224,237,379,442,508,570,594],"evolution.":[225,613,1867,2430,2710,2939,2972],"authors":[227,294,348,906,1056,1276,1356,1829,1886,1965,2023,2443,2858,2913,3012],"focused":[228],"evolutionary":[231,341,357,671,1018,1262,1468,1510,1548,1733,2059,2124,2173,2230,2313,2513,2534,3003],"turnover":[232,342,506,529],"(gain":[233],"loss)":[235],"single":[240],"Zeste,":[243],"but":[244,400],"considered":[245],"dynamics":[247,672],"whole":[250],"genome":[251,254,286,1666,2157,2267],"scale.":[252],"scale":[255],"comparative":[256,684,1702],"analysis":[257,512,685,1252],"was":[258,445,454,803,1919,2141,2440,2583,2618],"facilitated":[259],"by":[260,274,304,395,405,510,923,977,1283,1297,1331,1428,1472,1477,1592,1811,2138,2162,2188,2639,2645,2680],"use":[262,2693],"high-throughput":[265],"ChIP-chip":[266],"technique":[268],"identify":[270,717,2146,2283],"genomic":[271,299,1715,1873,2106,2211,2284,2321,2677],"bound":[273,303],"Zeste":[275,305,323,334,360,378,388,416,441,452,468,531],"availability":[280,1628],"number":[283,478,973,1530,2761,2833],"complete":[285],"closely":[289,314,2252],"related":[290,1195,2253],"species.":[292,316,781,826,1755,2063,2255,2581,2604],"identified":[295,381,746,1834,1984,1991],"294":[296],"melanogaster":[298],"regions":[300,320,1448,1488,1712,1722,1802,1806,1822,1832,1892,1918,1970,2010,2212,2222,2263,2285,2358,2487],"were":[302,382,483,1371,1527,1937,1987,2160,2316,2554,2592,2744,2840,2866,2935],"had":[307],"corresponding":[308],"orthologous":[309,763,786,808],"three":[312],"other":[313,410,564,828,1386,1463,2165,2251,2291,2328,2336,2390,2393,2496,2825,3033],"Evaluation":[317],"position":[324],"weight":[325],"matrix":[326],"led":[327,2130,2137],"identification":[330,2121],"1,406":[332],"putative":[333,377,415,467],"sites.":[336,1781],"In":[337,409,782,827,1273,1507,1614,2039,2392,2882],"order":[338],"detect":[340,2307,2319],"sites,":[346,1769],"developed":[349],"probabilistic":[351],"model":[352,399,1860,2305,2712,2803,2846],"represents":[354],"position-specific":[356,372],"rates":[358,2428],"based":[362,438,1861],"factors":[365],"known":[366],"specificity.":[368],"Observation":[369],"variation":[373,2958],"observed":[374,2854],"when":[375,831,1763,2551,2994],"they":[380,744,1035,1410,1746,1843,1994,2181,2192,2233,2280,2315,2463,3021],"compared":[383],"across":[384,1553],"genomes":[385,1369,2166],"showed":[386,1996],"evolve":[390,572,1226],"more":[391,455,1049,1102,1111,1363,1845,2216,2781,2809,2890,2954],"rapidly":[392,402,569,1227,1825,2217],"predicted":[394,404],"site":[398,453],"neutral":[407],"model.":[408],"words,":[411,829,2394],"population":[413],"includes":[418],"conserved":[419,459,557,585,835,848,1711,1759,1792,1837,1848,2187,2289,2326,2338],"nonconserved":[424,475,593],"have":[427,696,776,1079,1152,1346,1390,1543,1697,1797,1830,2053,2129,2168,2185],"lost":[429],"or":[430,460,860,984,2539,2782],"gained":[431],"over":[432,533,586,1081,2172,2928],"time.":[433,587,1082,2174],"A":[434,477],"likelihood":[435],"ratio":[436,1500],"test,":[437],"evolution":[443,641,692,1157,1280,1302,1326,1589,1955,2617,2885,2904,2987],"model,":[444,2606,2822],"then":[446],"applied":[447],"test":[449,463],"whether":[450],"each":[451],"likely":[456,599,1050,1725,2030,2183],"nonconserved.":[461],"revealed":[464,509,2353],"215":[465],"(>15%)":[466],"show":[472,820,1036,1289,1597,1804,2464],"statistically":[473,1876],"significant":[474,1877,1998,2308],"signals.":[476],"additional":[480],"statistical":[481,1858,2304,2845],"tests":[482],"used":[484,1572,1831,1897,2745],"validate":[486],"result":[488,2470],"particular,":[491,930],"errors":[495],"sequence":[497,548,691,1122,1400,1680,1703,1716,2107,2125,2400,2448,2678,2742,2838,2910,2925,2933,2957],"alignment":[498],"could":[500,1570,2402,2572],"confound":[501],"analysis.":[503],"rapid":[505,1259,1301,1325,1467,1509,1547,2649],"holds":[513,2633],"up":[514,521,1634],"scrutiny.":[518],"They":[519,706],"come":[520],"fairly":[524],"conservative":[525],"estimate":[526,2917,2999],"5%":[528],"last":[535],"10":[536],"million":[537],"years.":[538],"focus":[540,1790],"evolutionarily":[543,1779],"informed":[544],"studies":[545,2417],"regulatory":[547,578,604,688,1098,1105,2408],"has":[549,651,1160,1686,1950,2199,2951],"between":[558,606,836,1382,1754,1826,2035,2238,2576,2603,2704,2831,3002],"genomes.":[559],"manuscript,":[561],"recent":[565],"studies,":[566],"shows":[567],"how":[568,658,1168,2567],"underscores":[574,2370],"diverged":[582],"rather":[583],"After":[588],"all,":[589],"contribute":[601],"species":[607,1827,2292],"so":[610,1622,2989],"important":[611,1030,1564,1780,2056,2955],"Lars":[614],"Juhl":[615],"Jensen,":[616,619],"Thomas":[617],"Sk\u00f8t":[618],"Ulrik":[620],"de":[621],"Lichtenberg,":[622],"S\u00f8ren":[623],"Brunak":[624],"Peer":[626],"Bork":[627],"Nature":[628],"(2006)":[629,1143,1652,2098,2523],"443,":[631],"7111,":[633],"pp.":[634,1657,2528],"594\u2013597":[635],"study":[638,1158,2439],"molecular":[643,1069,1092,1156,2971,2986,2996,3019],"complexes":[644,946,954,968,1070,1093],"function":[646,1013],"cell":[649,704,858,896,918,944,1077,1930,1942],"cycle":[650,859,897,919,945,1078],"profound":[652],"implications":[653,1163,1952],"systems":[660],"evolve.":[661],"Apparently,":[662],"there":[663,2778],"very":[665,1752,2170],"different":[666,674,1039,1060,1459,1539,2034,2787],"rules":[667],"involved":[668,1939,2002,2363],"governing":[670],"at":[673,768,789,814,1071,1173],"levels":[675,1040],"organization.":[678],"Jensen":[679],"performed":[682],"versus":[689,1260,2673],"genes":[694,722,755,861,899,920,980,996,1047,1895,1936,2001,2018,2352,2362,2379],"periodic":[697,821,880,915,998],"expression":[698,713,801,822,839,849,881,916,999],"stages":[701],"cycle.":[705],"took":[707,1357],"advantage":[708,1358,1700],"numerous":[710],"data":[714,1340,1401,1704,2864,2997],"sets":[715,748,765,787,846,877,2865],"hundreds":[718],"periodically":[720,753,771,792,817,990,1045],"expressed":[721,754,772,793,818,979,991,1046,2758],"four":[724,758,780,799,825],"divergent":[725,2299,2331],"eukaryotes:":[726],"human,":[727,1993],"yeasts":[729],"Saccharomyces.":[730],"cerevisiae":[731],"S.":[733,2065,2082],"pombe":[734],"plant":[737],"Arabidopsis":[738],"thaliana.":[739],"At":[740],"same":[742,1068,1973],"time,":[743],"also":[745,907,1345,1528,1556,1966,2504],"contain":[750,767],"orthologs":[751,777,796],"organisms.":[759],"majority":[761],"least":[769,790,815,1741],"one":[770,791,816,983],"member":[773,794],"do":[774,1349,1747,2281,3022],"all":[779,798,824,1744],"addition,":[783,2883],"those":[785,1990,2111],"species,":[800],"periodicity":[802],"conserved.":[805],"Only":[806,1659],"five":[807],"sets,":[809],"out":[810,1607,2665],"381":[812],"member,":[819],"even":[830,874,2613],"demonstrably":[834],"lineages,":[837],"patterns":[840],"not.":[842],"Less":[843],"surprisingly,":[844],"correspond":[852],"essential":[854],"regulators":[855],"such":[862,1721,1735,1761,2262,2498,2588,2829,2977],"histones":[864],"encode":[866],"building":[868],"blocks":[869],"eukaryotic":[871],"chromatin.":[872],"where":[878],"conserved,":[883,1096],"actual":[885,2452],"timing":[886,1011],"expression,":[889],"i.e.":[890],"which":[892,1288,1321,1596,2607,2632,2720],"phase":[893],"expressed,":[901],"can":[902,2223],"often":[903],"differ.":[904],"reveal":[908],"many":[910,1059,1385,1933,2355],"accompanied":[922],"post-translational":[926,936,1001],"regulation,":[927],"phosphorylation":[928],"encoded":[933,976],"proteins.":[934],"adds":[938],"another":[939],"layer":[940],"helps":[948],"ensure":[950,1008],"appropriate":[953,1073],"assembled":[956,970],"\u2018just":[957],"time\u2019":[959],"play":[961,2505],"functional":[963,967,1674,1909,2348],"role.":[964],"Often":[965],"proteins":[975],"constitutively":[978],"few":[986,1785,2396],"members":[987],"post-transcriptionally":[993],"modified.":[994],"modifications":[1002],"may":[1003,1107,1344,1562,1620,1737,1770,2052,2128,2234,2247,2503],"act":[1004],"triggers":[1006,1026],"proper":[1010],"complexes,":[1016],"conservation":[1019],"specific":[1022,1908,2011,2399],"identity":[1023],"existence.":[1033],"Furthermore,":[1034],"evidence":[1037,1292,1599,1852,1878,3026],"co-evolved,":[1043],"since":[1044,1568,2232],"post-translationally":[1053],"regulated.":[1054],"conclude":[1057],"solutions":[1061],"problem":[1064],"assembling":[1066],"point":[1074],"evolved":[1080],"while":[1086,1980,3010],"protein-coding":[1088],"component":[1089],"highly":[1095,1836,2288,2298,2325,2337],"part":[1099,1374,3034],"far":[1101,2953],"dynamic.":[1103],"Thus,":[1104,1756],"innovations":[1106],"much":[1110,1347,2889],"viable":[1112],"substrate":[1113],"adaptive":[1115],"divergence":[1116,3000],"protein":[1124,1451,1670],"structure.":[1125],"Yuri":[1126,1148],"I.":[1127],"Wolf,":[1128],"Cecile":[1129],"Viboud,":[1130],"Edward":[1131,1648],"C.":[1132],"Holmes,":[1133],"Eugene":[1134],"V.":[1135],"Koonin":[1136],"J.":[1139],"Lipman":[1140],"Direct":[1142],"1,":[1145],"34":[1147],"Wolf":[1149],"colleagues":[1151],"rare":[1155],"both":[1161,2062,2593],"fundamental":[1162,2656],"natural":[1169,2189,2420],"selection":[1170,1231,1474,1560,1602,2190,2421],"manifest":[1172],"level":[1175],"urgent":[1182],"human":[1183,1201,1665,1894,1912,1958,2013,2133,2152,2156,2244,2266,2312,2512],"health":[1184],"significance.":[1185],"Both":[1186],"accomplishments":[1189],"no":[1192,1291,1437,1598,2828],"small":[1193],"way":[1194],"choice":[1198],"study\u2014the":[1200],"influenza":[1202,1318,1368,1387,1421],"virus":[1203,1319],"hemagglutinin":[1206],"(HA)":[1207],"encoding":[1208],"gene.":[1209],"Influenza":[1210,1377],"epidemics":[1211],"lead":[1212,1517,2235,2403,2981],"thousands":[1214],"deaths":[1216],"every":[1217],"year,":[1218],"HA":[1221,1240,1279,1328,1441,1486],"thought":[1224,2961],"via":[1228],"positive":[1229,1294,1305,1333,1473,1559,1601],"Darwinian":[1230,2557],"predicated":[1234],"upon":[1235],"changing":[1236,2215],"antigenicity":[1237],"epitope":[1241,1447,1487],"regions.":[1242,2277,2460],"impressively":[1250],"judicious":[1256],"distinction":[1257],"static":[1261],"regimes":[1263],"allowed":[1265],"heterodox":[1268],"conclusions":[1269,1353],"work.":[1272],"short,":[1274],"find":[1277],"periods":[1285,1299,1423,2641,3029],"stasis,":[1287,3031],"basically":[1290],"selection,":[1295],"followed":[1296,2644],"short":[1298,1465,1809,2646],"under":[1303,1717,2751,2776],"strong":[1304,3015],"selection.":[1306,1334],"finding":[1308,1949,2901],"stands":[1309],"stark":[1311],"contrast":[1312],"prevailing":[1315],"views":[1316],"evolution,":[1320,3020],"emphasize":[1322],"driven":[1330],"continuous":[1332],"It":[1335,1579,2582,3005],"seems":[1336],"particular":[1339,2110,2240,2770],"set":[1341,1914,2664],"analyzed":[1342,1402,2841],"here":[1343,1403],"novel":[1352,1416],"reached.":[1354],"existence":[1361],"1,000":[1365],"publicly":[1366],"sequenced":[1372],"Genome":[1378],"Sequencing":[1379],"Project":[1380],"(IGSP)":[1381],"1995\u20132005.":[1383],"Unlike":[1384],"because":[1393,1745,2007,2180,2191],"seriological":[1396],"novelty,":[1397],"IGSP":[1399],"unbiased":[1405],"sense":[1408],"enriched":[1413,1923],"antigenically":[1415],"isolates.":[1417],"For":[1418,2461],"H3N2":[1420,1609,1618],"subtype,":[1422],"stasis":[1425,2643],"marked":[1427],"higher":[1430],"synonymous":[1433],"non-synonymous":[1435],"substitutions,":[1436],"demonstrable":[1438],"overrepresentation":[1439,2482],"amino":[1442,1481,1535],"acid":[1443,1482,1536],"slow":[1453],"extinction":[1454,1520],"co-circulating":[1456],"viruses":[1457],"lineages.":[1460,1525,2038,3004],"On":[1461,2973],"hand,":[1464,2826],"phases":[1469],"dominated":[1471],"demonstrated":[1476],"excess":[1479,1881],"relative":[1489,2669],"rest":[1492],"protein,":[1495],"relatively":[1498],"lower":[1499],"synonyomous":[1502],"nonsynonymous":[1504],"substitution":[1505],"rate.":[1506],"phase,":[1511],"newly":[1512],"arisen":[1513],"dominant":[1514,1577],"lineages":[1515,1540,1554,1610,1619],"quickly":[1516,2608],"previously":[1523,1833,2960],"coexisting":[1524],"There":[1526],"cases":[1532],"parallel":[1534,1551],"substitutions":[1537,1552,1855,2455,2764,2934],"shown":[1541],"occurred":[1544],"during":[1545],"phase.":[1549],"Independent":[1550],"consistent":[1557,2867],"vaccine":[1566],"development":[1567],"predictors":[1574],"new":[1576,1636],"strains.":[1578],"should":[1580,2811,2964,2990,3006],"noted":[1582,3008],"clear":[1585],"case":[1586],"punctuated":[1588,2630,2674,2802,2850,2870,2884,2903,2938,2949,2978,3018,3037],"complicated":[1591],"H1N1":[1594],"strains,":[1595],"yet":[1603,2297,2330],"manage":[1604],"somehow":[1605],"compete":[1608],"some":[1612,2612],"seasons.":[1613],"case,":[1616,2041],"successful":[1623],"limit":[1626],"susceptible":[1630],"hosts":[1631],"thus":[1632,2963],"opening":[1633],"niche":[1637],"H1N1.":[1639],"Shyam":[1640],"Prabhakar,":[1641],"James":[1642],"P.":[1643],"Noonan,":[1644],"Svante":[1645],"P\u00e4\u00e4bo,":[1646],"Rubin":[1650],"Science":[1651,2522],"314,":[1654,2525],"5800,":[1656],"786":[1658],"tiny":[1661],"fraction":[1662],"actually":[1667,1738,1771],"codes":[1668],"sequences,":[1671,1760],"relevance":[1675],"remaining":[1678],"noncoding":[1679,1714,1793,1849],"open":[1683],"attracted":[1687],"quite":[1688,2020,2033],"bit":[1690],"attention":[1692,2446],"late.":[1695],"Investigators":[1696],"taking":[1699],"hone":[1706],"anomalously":[1710],"rationale":[1719],"functionally":[1728,2194],"germane.":[1729],"perspective":[1734],"change":[1749,1751,1824,2573,2650,2675,2950,2979],"(or":[1750],"little)":[1753],"focusing":[1757],"looking":[1764,1820],"positively":[1773],"misleading":[1774],"terms":[1776],"identifying":[1778],"Fortunately,":[1782],"after":[1783,2872],"years":[1786],"almost":[1788],"exclusive":[1789,2699],"regions,":[1794,2339],"several":[1795],"groups":[1796],"begun":[1798],"look":[1800],"accelerated":[1805,1917,1969,1982,2009,2221,2459,2484],"Prabhakar":[1812],"exemplifies":[1815],"approach.":[1817,2685],"Interestingly,":[1818,1979],"starting":[1840],"point.":[1841],"Specifically,":[1842,2278],"evaluated":[1844],"100,000":[1847],"human-specific":[1854,1883],"using":[1856,1971,2681,2995],"null":[1859],"pattern":[1864,2772],"constrained":[1866],"approach":[1869,1974,2690],"yielded":[1870],"992":[1871],"distinct":[1872,1988],"showing":[1875],"substitutions.":[1884],"went":[1887],"associate":[1890],"Gene":[1899],"Ontology":[1900],"(GO)":[1901],"annotations":[1902,2349],"check":[1904],"enrichment":[1906,1999],"categories.":[1910],"associated":[1915],"found":[1920,2859],"process":[1927,2621],"GO":[1928],"term":[1929,2600],"adhesion,":[1931,1943],"specifically":[1938],"neuronal":[1941,2004,2016],"e.g.":[1944],"cadherins":[1945],"neuroligins.":[1947],"obvious":[1951],"uniquely":[1957,2132],"cognitive":[1959],"traits.":[1960],"As":[1961,2334],"control,":[1963],"looked":[1967],"mouse":[1976,2294],"chimpanzee.":[1978],"chimpanzees":[1986],"too":[1995],"near":[2000],"adhesion.":[2005],"chimpanzee":[2015,2116],"adhesion":[2017],"different,":[2021],"argue":[2024],"phenotypic":[2027],"effects":[2028],"any":[2040,3025],"intriguing":[2044],"independent":[2046],"nervous":[2050],"system":[2051],"particularly":[2055],"diversification":[2060],"Katherine":[2064],"Sofie":[2067],"R.":[2068,2089],"Salama,":[2069],"Bryan":[2070],"King,":[2071],"Andrew":[2072,2520],"Kern,":[2074],"Tim":[2075],"Dreszer,":[2076],"Sol":[2077],"Katzman,":[2078],"Adam":[2079],"Siepel,":[2080],"Jakob":[2081],"Pedersen,":[2083],"Gill":[2084],"Bejerano,":[2085],"Robert":[2086],"Baertsch,":[2087],"Kate":[2088],"Rosenbloom,":[2090],"Jim":[2091],"Kent":[2092],"Haussler":[2095,2140],"Genetics":[2097],"e168":[2104],"Comparative":[2105],"analyses,":[2108],"involving":[2112],"recently":[2114],"completed":[2115],"sequence,":[2117],"allow":[2118],"characteristics.":[2134],"group":[2136],"first":[2144],"so-called":[2147,2536],"\u2018ultra-conserved\u2019":[2148],"elements":[2149],"genome.":[2153],"These":[2154,2220],"inferred":[2161,2225],"comparison":[2163],"changed":[2169],"little":[2171],"Such":[2175],"interest":[2179,2231],"important.":[2195],"Now":[2196],"idea":[2198],"turned":[2201],"head":[2204],"others.":[2219],"outstanding":[2229],"differences":[2237],"lineages\u2014in":[2239],"lineage":[2245],"distinguish":[2248],"us":[2249],"primate":[2254],"get":[2258],"handle":[2260],"team":[2269],"still":[2270],"relies":[2271],"presence":[2274],"ultra-conserved":[2276],"what":[2279],"(chimp,":[2293],"rat)":[2296],"human.":[2301],"Using":[2302],"accelerations":[2309,2509],"lineage,":[2314],"able":[2317],"202":[2320],"vertebrates":[2329],"humans.":[2333],"mostly":[2343],"noncoding.":[2344],"Analysis":[2345],"nearby":[2351],"close":[2360,2445],"DNA":[2367,2932],"binding.":[2368],"themselves":[2382],"turn":[2384],"responsible":[2385],"genes.":[2391],"pointed":[2397],"complex":[2405],"cascades":[2406],"effects.":[2409],"general":[2411],"assumption":[2412],"types":[2415],"major":[2424],"player":[2425],"determining":[2427],"One":[2431],"aspects":[2436],"played":[2444],"kinds":[2453],"occur":[2457],"instance,":[2462],"preponderance":[2466],"creation":[2473],"guanine":[2475],"cytosine":[2477],"high":[2489],"recombination.":[2490],"suggests":[2492],"possibility":[2494],"forces,":[2497],"biased":[2500],"conversion,":[2502],"role":[2507],"lineage.":[2514],"Pagel,":[2516],"Chris":[2517],"Venditti":[2518],"Meade":[2521],"5796,":[2527],"119\u2013121":[2529],"foundations":[2531],"modern":[2533],"theory\u2014the":[2535],"\u2018New":[2537],"Synthesis\u2019":[2538],"\u2018Neo-Darwinian":[2540],"Synthesis\u2019\u2014were":[2541],"laid":[2542],"down":[2543],"middle":[2546],"20th":[2549],"century":[2550],"Mendelian":[2552],"genetics":[2553],"united":[2555],"theory.":[2558],"elaborate":[2560],"body":[2561],"formal":[2563],"theory":[2564,2628],"detailed":[2565],"why":[2569],"allele":[2570],"frequencies":[2571],"within":[2574,2590],"populations":[2577],"given":[2580],"assumed":[2584],"microevolutionary\u2014i.e.":[2589],"species\u2014changes":[2591],"necessary":[2594],"sufficient":[2596],"explain":[2598],"longer":[2599,2813],"macroevolutionary":[2601],"became":[2609],"orthodoxy\u2014and":[2610],"dogma\u2014strongly":[2614],"implied":[2615],"steady":[2623],"gradual":[2625,2672,2705,2821],"change.":[2626],"equilibrium,":[2631],"macroevolution":[2635],"better":[2637],"bursts":[2647],"accompany":[2652],"speciation,":[2653],"challenge":[2657],"Neo-Darwinian":[2659],"orthodoxy.":[2660],"Pagel":[2661],"assess":[2667],"phylogenetic":[2684,2700,2732,2749],"strength":[2687],"simple":[2696],"mutually":[2698],"models":[2701,2969],"discriminate":[2703],"punctual":[2707],"modes":[2708],"rests":[2713],"path":[2718,2755,2835,2855],"lengths,":[2719],"sums":[2723],"branch":[2726],"lengths":[2727,2756],"roots":[2730,2791],"trees":[2733,2750],"tips":[2736],"trees.":[2739],"Since":[2740,2795],"alignments":[2743,2839],"build":[2747],"consideration":[2752],"here,":[2753],"nucleotide":[2763],"site.":[2766],"According":[2767],"branching":[2771],"phylogeny":[2775],"consideration,":[2777],"will":[2779,2980],"fewer":[2783,2818],"nodes":[2784,2797,2810],"paths":[2788,2806,2815],"tips.":[2794],"represent":[2798],"speciation":[2799],"events,":[2800],"predicts":[2804,2827],"cross":[2808],"traverse":[2817],"nodes.":[2819],"correlation":[2830],"node":[2832],"length.122":[2836],"according":[2842],"evaluates":[2848],"contribution":[2851,2908,2922],"lengths.":[2856],"47%":[2861],"model;":[2871],"correction":[2874],"artifacts":[2876],"figure":[2878],"fell":[2879],"35%.":[2881],"appears":[2886],"common":[2891],"plants":[2893],"fungi":[2895],"animals.":[2898],"Given":[2899],"makes":[2905],"substantial":[2907],"changes,":[2911],"next":[2914],"tried":[2915],"extent":[2919],"overall":[2924],"diversity.":[2926],"Just":[2927],"one-fifth":[2929],"(22%)":[2930],"attributed":[2936],"take":[2941],"home":[2942],"message":[2943],"accounted":[2966,2992],"technical":[2975],"note,":[2976],"violations":[2983],"clock-like":[2985],"times":[3001],"observe":[3013],"signal":[3016],"see":[3024],"equilibrium":[3038],"picture.":[3039]},"counts_by_year":[],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2022-05-12T00:00:00"}