Publication Information

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'July': [1], '2011Open': [2], 'Access': [3], 'Phosphorylation': [4], 'network': [5, 1047, 2567], 'rewiring': [6, 2227], 'by': [7, 52, 88, 124, 146, 195, 240, 276, 312, 334, 383, 638, 716, 720, 812, 831, 1295, 1388, 1396, 1418, 1466, 1484, 1756, 1800, 1901, 2131, 2235, 2283, 2401, 2421, 2560, 2661, 2707, 2897, 3582, 3793, 4126, 4210, 4296, 4307, 4340, 4376], 'gene': [8, 557, 678, 717, 1017, 1172, 2831, 3104], 'duplication': [9, 558, 592, 718, 763, 927, 1018, 1061, 3105], 'Luca': [10, 12, 198, 200, 388], 'Freschi': [11, 13, 199, 201], 'Département': [14, 59, 75, 95, 111, 133, 157, 202, 247, 263, 283, 299, 321, 345, 463], 'de': [15, 22, 60, 63, 71, 76, 79, 96, 99, 107, 112, 115, 134, 137, 158, 165, 203, 210, 248, 251, 259, 264, 267, 284, 287, 295, 300, 303, 322, 325, 346, 353, 403, 410, 437, 440, 448, 453, 456, 464, 467, 478], 'Biologie,': [16, 159, 204, 347, 404, 465], 'Université': [17, 29, 44, 70, 78, 106, 114, 136, 160, 172, 187, 205, 217, 232, 258, 266, 294, 302, 324, 348, 360, 375, 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1051, 1507, 1639, 1689, 1826, 1890, 1942, 2462, 2888, 3425, 3770, 4094, 4107, 4312], 'Quebec': [35, 178, 223, 366, 423], 'Research': [36, 179, 224, 367, 424], 'Network': [37, 180, 225, 368, 425], 'on': [38, 181, 226, 369, 426, 774, 779, 1257, 1521, 1682, 1720, 2617, 2711, 2784, 2978, 3014, 3023, 3197, 3482, 3541, 3669, 3951, 4010, 4159, 4244, 4255], 'Protein': [39, 182, 227, 370, 427, 821, 1460], 'Function,': [40, 183, 228, 371, 428], 'Structure': [41, 184, 229, 372, 429], 'and': [42, 185, 230, 373, 397, 430, 507, 525, 690, 709, 730, 748, 767, 778, 802, 816, 837, 842, 871, 897, 929, 961, 974, 992, 1025, 1069, 1091, 1096, 1105, 1129, 1136, 1142, 1160, 1182, 1189, 1200, 1277, 1318, 1354, 1391, 1394, 1450, 1499, 1577, 1751, 1883, 1923, 1975, 1979, 2137, 2203, 2280, 2489, 2500, 2538, 2584, 2626, 2670, 2690, 2703, 2730, 2793, 2799, 2815, 2826, 2837, 2843, 2864, 2876, 2900, 2912, 2996, 3078, 3101, 3201, 3288, 3359, 3427, 3433, 3463, 3530, 3598, 3644, 3758, 3765, 3773, 3797, 3838, 3852, 3866, 3893, 3902, 3922, 4199, 4265, 4283, 4326, 4356, 4374, 4399], 'Engineering,': [43, 186, 231, 374, 431], 'Search': [48, 84, 120, 142, 191, 236, 272, 308, 330, 379], 'for': [49, 85, 121, 143, 192, 237, 273, 309, 331, 380, 607, 637, 1240, 1335, 1436, 1452, 1741, 1919, 1972, 1989, 2024, 2183, 2249, 2261, 2297, 2375, 2425, 2434, 2496, 2554, 2576, 2728, 3004, 3147, 3178, 3280, 3618, 3632, 3655, 3881, 4056, 4090, 4110, 4248, 4322], 'more': [50, 86, 122, 144, 193, 238, 274, 310, 332, 381, 1112, 1403, 2192, 2704, 3090, 3232, 3681, 3992], 'papers': [51, 87, 123, 145, 194, 239, 275, 311, 333, 382], 'this': [53, 89, 125, 147, 196, 241, 277, 313, 335, 384, 671, 1037, 1253, 1411, 1537, 1973, 1983, 2497, 2926, 2970, 3084, 3700, 3724, 3923], 'author': [54, 90, 126, 148, 197, 242, 278, 314, 336, 385, 526], 'Mathieu': [55, 57, 243, 245, 390], 'Courcelles': [56, 58, 244, 246], 'Chimie,': [61, 97, 249, 285, 438], 'Recherche': [64, 100, 252, 288, 441], 'en': [65, 101, 253, 289, 442], 'Immunologie': [66, 102, 254, 290, 443], 'Cancérologie': [68, 104, 256, 292, 445], '(IRIC),': [69, 105, 257, 293, 446], 'Montréal,': [72, 80, 81, 108, 116, 117, 138, 139, 260, 268, 269, 296, 304, 305, 326, 327, 449, 457, 458], 'Biochimie,': [77, 113, 135, 265, 301, 323, 454], 'Pierre': [91, 93, 279, 281, 392], 'Thibault': [92, 94, 280, 282], 'Stephen': [127, 130, 315, 318, 394], 'W': [128, 131, 316, 319, 395], 'Michnick': [129, 132, 317, 320], 'Christian': [149, 154, 337, 342, 398], 'R': [150, 155, 338, 343, 399], 'Landry': [151, 156, 339, 344, 400], 'Corresponding': [152, 340], 'Author': [153, 341, 386], 'Information': [387], 'Freschi1,2,3,': [389], 'Courcelles4,5,': [391], 'Thibault4,5,': [393], 'Michnick5': [396], '1,2,3': [401], '1Département': [402], '2Institut': [409], '3PROTEO,': [421], '4Département': [436], '5Département': [452], '*Corresponding': [461], 'author.': [462], 'Integrative': [469], 'Systemes': [472], 'Universite': [474], '1030': [476], 'Avenue': [477], 'la': [479], 'Médecine,': [480], 'G1V': [483], '0A6.': [484], 'Tel.:': [485], '+1': [486, 491], '418': [487, 492], '656': [488, 493], '3954;': [489], 'Fax:': [490], '7176;': [494], 'E-mail:': [495], '[email': [496], 'protected]': [497], 'Molecular': [498], 'Systems': [499], 'Biology': [500], '(2011)7:504https://doi.org/10.1038/msb.2011.43': [501], 'PDFDownload': [502], 'PDF': [503], 'of': [504, 514, 551, 570, 581, 593, 602, 610, 641, 652, 663, 687, 701, 724, 744, 764, 768, 790, 798, 809, 828, 888, 936, 984, 996, 1008, 1027, 1033, 1081, 1093, 1144, 1184, 1212, 1232, 1236, 1245, 1265, 1337, 1370, 1382, 1480, 1493, 1501, 1509, 1517, 1543, 1563, 1565, 1588, 1595, 1604, 1635, 1641, 1647, 1662, 1668, 1711, 1737, 1744, 1753, 1764, 1778, 1796, 1811, 1854, 1874, 1892, 1930, 1936, 1947, 1993, 1996, 2000, 2011, 2030, 2037, 2043, 2056, 2092, 2104, 2111, 2143, 2151, 2211, 2238, 2256, 2272, 2278, 2322, 2349, 2456, 2465, 2468, 2534, 2590, 2595, 2607, 2624, 2628, 2640, 2659, 2666, 2685, 2692, 2714, 2721, 2733, 2788, 2828, 2835, 2839, 2871, 2890, 2903, 2925, 2939, 2960, 2964, 3032, 3061, 3075, 3111, 3120, 3162, 3176, 3205, 3211, 3262, 3265, 3274, 3309, 3317, 3323, 3330, 3338, 3347, 3352, 3369, 3389, 3430, 3447, 3461, 3492, 3505, 3536, 3744, 3788, 3827, 3833, 3844, 3890, 3897, 3903, 3905, 3912, 3918, 3928, 3931, 3941, 3947, 3959, 3983, 4006, 4017, 4046, 4077, 4084, 4102, 4113, 4120, 4138, 4175, 4187, 4190, 4214, 4226, 4230, 4291, 4334, 4350, 4358, 4372, 4393], 'article': [505], 'text': [506], 'main': [508], 'figures.': [509], 'Peer': [510], 'ReviewDownload': [511], 'a': [512, 548, 582, 625, 699, 737, 903, 910, 913, 982, 1006, 1049, 1059, 1250, 1288, 1310, 1316, 1319, 1347, 1444, 1491, 1515, 1550, 1602, 1619, 1645, 1771, 1862, 1909, 1912, 1931, 1937, 2025, 2046, 2050, 2057, 2108, 2208, 2236, 2288, 2352, 2402, 2406, 2531, 2561, 2565, 2644, 2785, 2859, 2862, 2957, 2975, 2985, 3002, 3029, 3154, 3172, 3344, 3510, 3534, 3627, 3695, 3704, 3740, 3926, 3956, 4004, 4015, 4057, 4236, 4240], 'summary': [513], 'the': [515, 552, 567, 574, 587, 591, 608, 622, 639, 685, 702, 721, 725, 742, 756, 762, 769, 788, 791, 796, 807, 886, 926, 937, 941, 949, 953, 994, 1009, 1034, 1041, 1055, 1152, 1165, 1197, 1229, 1233, 1246, 1326, 1338, 1397, 1420, 1424, 1448, 1494, 1518, 1522, 1561, 1580, 1586, 1605, 1623, 1627, 1630, 1663, 1675, 1698, 1705, 1709, 1738, 1761, 1776, 1794, 1809, 1851, 1871, 1902, 1920, 1928, 1945, 1955, 1990, 1994, 1998, 2022, 2035, 2041, 2053, 2068, 2073, 2089, 2147, 2152, 2228, 2245, 2270, 2273, 2323, 2345, 2350, 2380, 2422, 2428, 2435, 2439, 2447, 2469, 2477, 2486, 2543, 2555, 2604, 2608, 2618, 2638, 2663, 2667, 2672, 2676, 2712, 2718, 2781, 2881, 2901, 2906, 2935, 2940, 2954, 2961, 2965, 2993, 3042, 3050, 3059, 3065, 3096, 3109, 3118, 3138, 3145, 3148, 3160, 3163, 3179, 3184, 3203, 3209, 3263, 3272, 3306, 3315, 3321, 3328, 3350, 3367, 3376, 3383, 3410, 3431, 3444, 3459, 3506, 3615, 3619, 3633, 3639, 3649, 3662, 3717, 3721, 3730, 3775, 3786, 3842, 3878, 3929, 3939, 3942, 3948, 3952, 3960, 3981, 3999, 4011, 4020, 4027, 4034, 4038, 4043, 4049, 4061, 4071, 4075, 4082, 4111, 4114, 4121, 4139, 4152, 4176, 4188, 4191, 4197, 4212, 4215, 4227, 4231, 4245, 4271, 4274, 4289, 4297, 4327, 4332, 4341, 4351, 4369, 4383, 4386, 4391, 4394, 4400], 'editorial': [516, 520], 'decision': [517, 521], 'process': [518], 'including': [519, 560], 'letters,': [522], 'reviewer': [523], 'comments': [524], 'responses': [527], 'to': [528, 531, 579, 613, 648, 661, 682, 735, 786, 795, 839, 885, 922, 931, 1054, 1114, 1167, 1226, 1274, 1281, 1343, 1364, 1471, 1487, 1674, 1821, 1849, 1887, 1953, 2020, 2140, 2160, 2206, 2287, 2344, 2373, 2472, 2557, 2572, 2593, 2643, 2650, 2675, 2688, 2695, 2739, 2762, 2773, 2809, 2851, 2932, 2945, 3092, 3131, 3144, 3170, 3234, 3268, 3271, 3438, 3442, 3457, 3502, 3587, 3614, 3694, 3702, 3752, 4172, 4178, 4196, 4224, 4239, 4390], 'feedback.': [529], 'ToolsAdd': [530], 'favoritesDownload': [532], 'CitationsTrack': [533], 'CitationsPermissions': [534], 'Figures': [535], '&': [536], 'Info': [537], 'Elucidating': [538], 'how': [539, 3854], 'complex': [540], 'regulatory': [541, 731, 765, 800, 962, 1131, 2230, 2566, 3385], 'networks': [542, 811, 1021, 1076, 2231, 2578, 3524], 'have': [543, 667, 736, 978, 988, 1098, 1178, 1193, 1469, 2049, 2098, 2190, 2483, 2551, 2599, 2736, 2931, 3168, 3341, 3374, 3418, 3749], 'assembled': [544], 'during': [545, 670, 714], 'evolution': [546, 640, 715, 743, 808], 'requires': [547], 'detailed': [549], 'understanding': [550], 'evolutionary': [553, 758, 793, 855], 'dynamics': [554], 'that': [555, 580, 584, 598, 659, 676, 691, 704, 760, 981, 999, 1011, 1072, 1224, 1321, 1340, 1373, 1399, 1401, 1429, 1442, 1477, 1548, 1844, 1870, 1904, 1906, 1914, 1935, 2019, 2048, 2067, 2071, 2087, 2114, 2129, 2146, 2167, 2180, 2240, 2313, 2326, 2339, 2382, 2446, 2476, 2479, 2529, 2569, 2683, 2746, 2856, 2929, 2934, 2943, 2987, 2997, 3020, 3028, 3058, 3087, 3103, 3117, 3122, 3219, 3365, 3393, 3465, 3496, 3521, 3664, 3679, 3748, 3818, 4194, 4249, 4293, 4303], 'follow': [556, 761], 'events,': [559], 'changes': [561, 1150, 2642], 'in': [562, 573, 618, 712, 741, 784, 851, 879, 909, 934, 948, 952, 1019, 1134, 1303, 1315, 1329, 1351, 1377, 1410, 1447, 1474, 1560, 1574, 1622, 1716, 1727, 1775, 1859, 1944, 2045, 2052, 2061, 2080, 2121, 2173, 2320, 2405, 2413, 2452, 2513, 2520, 2540, 2717, 2817, 2910, 2948, 2953, 3035, 3041, 3064, 3071, 3095, 3126, 3134, 3137, 3208, 3224, 3237, 3243, 3248, 3252, 3257, 3285, 3293, 3319, 3349, 3381, 3509, 3515, 3755, 3821, 3847, 3849, 3859, 3861, 3868, 3888, 3895, 3998, 4037, 4060, 4070, 4132, 4167, 4218, 4318, 4364, 4385], 'post-translational': [563, 688, 1482, 3370, 3474], 'modifications.': [564], 'We': [565, 596, 656, 751, 969, 1414, 1427, 2017, 2033, 2064, 2268, 2310, 2444, 2492, 2647, 2681, 2744, 2972, 3010, 3026, 3114, 3532, 3548, 3698, 3784, 3814, 3840, 3876, 3978, 4079, 4233, 4287, 4330, 4367, 4381], 'compared': [566, 2220, 3048, 3182], 'phosphorylation': [568, 611, 822, 985, 1046, 1485, 1779, 1872, 2605, 2946, 2962, 3539], 'profiles': [569], 'paralogous': [571, 645, 847, 1510, 1567, 1596, 1669, 1712, 1767, 2031, 2093, 2181, 2481, 2668, 3212, 3225, 3791, 3835], 'proteins': [572, 646, 680, 732, 766, 848, 1121, 1132, 1248, 1511, 2012, 2094, 2669, 2967, 3016, 3312, 3543, 3672, 3792], 'budding': [575, 588, 1042, 1056, 2619], 'yeast': [576, 589, 1043, 1057, 1237, 2153, 2257, 2281, 2299, 2620, 3384, 4192, 4328], 'Saccharomyces': [577, 1044, 1884], 'cerevisiae': [578, 1885, 2950, 2991, 3044, 3053, 3082, 3098, 3128, 3239, 3270, 3671], 'species': [583, 1959, 2986], 'diverged': [585, 1170, 1205, 1470, 2552, 2988], 'from': [586, 1536, 1684, 2305, 2388, 2498, 2655, 2775, 2880, 2989, 3544, 3553, 3593, 3601, 3608, 3803, 4142, 4260, 4316], 'before': [590, 2992], 'those': [594, 2641], 'genes.': [595], 'found': [597, 658, 1428, 2018, 2066, 2086, 2179, 2312, 2338, 2493, 2682, 3027, 3116, 3130, 3343, 3846, 3858], '100': [599, 1063, 1475, 2588, 3497, 4100], 'million': [600, 1064], 'years': [601, 1065], 'post-duplication': [603], 'divergence': [604, 723, 1500, 3161, 3210, 3351], 'are': [605, 695, 733, 782, 858, 946, 964, 1012, 1272, 1307, 1341, 1374, 1376, 1407, 1680, 1835, 2233, 2316, 2342, 2393, 2431, 2517, 2760, 2770, 2806, 2846, 2857, 3038, 3123, 3221, 3231, 3242, 3780, 3809, 4148], 'sufficient': [606, 3501], 'majority': [609], 'sites': [612, 923, 932, 986, 1339, 1372, 1643, 1780, 1905, 2039, 2044, 2133, 2341, 2392, 2437, 2451, 2458, 2474, 2482, 2535, 2686, 2693, 2716, 2879, 2937, 2947, 3121, 3247, 3256, 3266, 3284, 3292, 3435, 3540, 3817, 3845, 3886, 4025, 4086, 4089], 'be': [614, 634, 1115, 1323, 1365, 1488, 1822, 1888, 1898, 2021, 2558, 2999, 3093, 3132, 3235, 3408, 3439, 3455, 3479, 3500, 3691, 3753], 'lost': [615, 933, 965, 1015, 1916, 2872, 3094, 3223], 'or': [616, 621, 881, 1002, 1014, 1031, 1228, 1671, 1808, 1878, 2145, 2398, 2657, 3651, 3991, 4397], 'gained': [617, 2874], 'one': [619, 863, 880, 935, 1227, 1244, 1275, 1344, 1352, 1405, 2101, 3146, 3666, 3683, 3990, 4068, 4310, 4349], 'paralog': [620, 864, 1276, 1331, 1353, 1625, 4041, 4063, 4073], 'other,': [623], 'with': [624, 1423, 1598, 1861, 2157, 2221, 2849, 2916, 3049, 3183, 3277, 3517, 3626, 3641, 3733, 4118], 'strong': [626], 'bias': [627], 'toward': [628], 'losses.': [629, 2696], 'However,': [630], 'some': [631, 2141], 'losses': [632, 1026, 1183, 2656, 2748, 2827, 2838, 2892, 3207, 4357, 4375], 'may': [633, 666, 849, 865, 877, 987, 2126, 2598, 3373, 3406, 3478, 3499], 'partly': [635], 'compensated': [636], 'other': [642, 1230, 1624, 3484, 3776], 'phosphosites,': [643, 1997, 3722], 'as': [644, 1048, 1088, 1101, 1117, 1260, 1514, 1601, 1613, 1644, 2040, 2753, 2764, 2778, 3001, 3412, 3476, 3580, 3976, 4104, 4156, 4362], 'tend': [647, 681, 1820, 1886, 2205], 'preserve': [649], 'similar': [650, 2521, 2571, 2802, 3070], 'numbers': [651, 1573, 4371], 'phosphosites': [653, 694, 1028, 1169, 1185, 1214, 1259, 1532, 1564, 1670, 1797, 1834, 1948, 2193, 2279, 2360, 2629, 2660, 2755, 2791, 2829, 3013, 3033, 3088, 3220, 3230, 3417, 3747, 3789, 4035, 4103, 4122, 4177, 4206, 4359, 4384], 'over': [654, 1895, 2355, 4087], 'time.': [655], 'also': [657, 1395, 1829, 2204, 2518, 2771, 2807, 3039, 3115, 3342, 3454, 3857, 3894], 'up': [660, 1263, 2592], '50%': [662, 2455, 2594], 'kinase–substrate': [664, 950, 997, 1191, 1718, 2502, 2515, 2596, 3507, 4256], 'relationships': [665, 1192, 2274, 2516, 2597, 3508], 'been': [668, 1099, 1179, 1194, 1950, 1969, 2600, 2737, 3375, 3419, 3750, 3762], 'rewired': [669], 'period.': [672], 'Our': [673, 1208, 2804, 3187, 3362, 3799], 'results': [674, 2769, 2805, 3189, 3363], 'suggest': [675, 2127, 2528, 3364], 'after': [677, 925, 1016, 1151, 1171, 1206, 1703, 2225, 2830], 'duplication,': [679, 1173], 'subfunctionalize': [683], 'at': [684, 1242, 1285, 1590, 1908, 2099, 2113, 2741, 3327, 3366, 3468, 3648, 4066, 4308, 4347], 'level': [686, 1763, 2110, 3329, 3368], 'regulation': [689, 1483, 3340], 'even': [692], 'when': [693, 1793, 1831, 1927, 2219, 3397], 'preserved,': [696], 'there': [697, 1177, 1617, 1769, 1967, 2185, 3808, 4064], 'is': [698, 1249, 1313, 1349, 1358, 1384, 1433, 1528, 1611, 1618, 1650, 1692, 1701, 1770, 1798, 1828, 1847, 1858, 1915, 1940, 1987, 2075, 2119, 2134, 2138, 2166, 2186, 2357, 2419, 2536, 2570, 2574, 2893, 2928, 3141, 3392, 3495, 3514, 4151], 'turnover': [700, 1758, 1891, 1985, 2568, 3973], 'kinases': [703, 1095, 1128, 1468, 1707, 2239, 2263, 2282, 2300, 2325, 2478, 4116, 4141, 4282], 'phosphorylate': [705, 2480], 'them.': [706], 'Introduction': [707], 'Genomes': [708], 'organisms': [710, 781], 'gain': [711, 3063], 'complexity': [713, 746], 'followed': [719], 'functional': [722, 2188, 3445], 'duplicates': [726], '(Hurles,': [727], '2004).': [728, 1157], 'Signaling': [729], 'thought': [734], 'particularly': [738, 1926], 'important': [739, 3378], 'role': [740], 'organismal': [745], '(Gough': [747], 'Wong,': [749], '2010).': [750, 844, 1125, 1981, 2309, 2491, 2586], 'know': [752], 'very': [753], 'little': [754], 'about': [755, 2076, 3720], 'early': [757], 'steps': [759], 'substrates': [770], 'they': [771, 1261, 3241, 3688], 'regulate.': [772], 'Studies': [773], 'short': [775], 'time': [776, 1896, 3725], 'scales': [777], 'well-characterized': [780], 'needed': [783], 'order': [785, 4171], 'estimate': [787, 1542, 3443, 3958], 'contribution': [789, 3346], 'different': [792, 1742, 2403, 2407, 2562, 2742, 4281], 'forces': [794], 'assembly': [797], 'novel': [799], 'pathways': [801, 1879], 'networks.': [803], 'Here,': [804], 'we': [805, 901, 1039, 1163, 1174, 1255, 2008, 2085, 2178, 2337, 2779, 2800, 2930, 3021, 3166, 3394, 3589, 3623, 3637, 3659, 3711, 3726, 3738, 3829, 4002, 4031, 4184], 'address': [806], 'phosphoregulatory': [810], 'directly': [813], 'studying': [814], 'phosphoproteins': [815, 1109, 1188, 1203, 1672, 2722, 3985], 'their': [817, 833, 1130, 1481, 4179, 4200], 'associated': [818, 4117], 'protein': [819, 829, 911, 1094, 1317, 1406, 1467, 1677, 1801, 1876, 2047, 2262, 2324, 2547, 2563, 3331, 3472, 3684, 4115, 4237], 'kinases.': [820], 'regulates': [823], 'several': [824, 2750, 3413], 'if': [825, 1530, 1616, 2007, 2359, 3240, 4055], 'not': [826, 859, 1362, 1408, 2318, 2385, 2395, 2409, 2636, 2858, 3407, 3645, 3690, 3728], 'most': [827, 3377, 4180], 'functions': [830, 868, 890, 991, 1137, 3006, 3332], 'affecting': [832], 'stability,': [834], 'localization,': [835], 'activity': [836], 'ability': [838], 'interact': [840], '(Moses': [841, 2488], 'Landry,': [843, 1980, 2490, 2585], 'When': [845], 'maintained,': [846], 'diverge': [850, 1302], 'function': [852, 914, 958, 1603, 1646, 3308, 3322, 3760], 'following': [853, 3616], 'two': [854, 938, 1247, 1304, 3073, 3831, 3883, 3916, 3943, 4352], 'paths,': [856], 'which': [857, 906, 1168, 1241, 1818, 2184, 2514, 2735, 3405, 3588], 'mutually': [860], 'exclusive.': [861], 'First,': [862], 'evolve': [866, 2740, 2763, 3525], 'new': [867, 944, 957], '(neofunctionalization)': [869], '(Conant': [870], 'Wolfe,': [872, 1106], '2008).': [873], 'Second,': [874, 1346, 2336], 'degenerative': [875], 'mutations': [876], 'accumulate': [878], 'both': [882, 1819, 2096, 2541, 3822, 3987, 4305, 4336], 'paralogs': [883, 1118, 1239, 1432, 1782, 2003, 2097, 2315, 2365, 3046, 3100, 3140, 3325, 3353, 3934, 3963, 3988, 4292, 4302, 4337], 'leading': [884, 1053], 'loss': [887, 1755, 1921, 2611], 'redundant': [889], '(subfunctionalization)': [891], '(Force': [892], 'al,': [894, 917, 972, 1124, 1140, 1156, 1724, 1733, 1867, 1962, 2266, 2308, 2507, 2511, 2581, 2632, 2758, 2983, 3356, 3423, 3487, 3558, 3562, 3566, 3570, 3574, 3578], '1999;': [895], 'Lynch': [896], 'Force,': [898], '2000).': [899, 2267, 3424], 'If': [900, 1982], 'assume': [902, 2933], 'model': [904, 1986], 'under': [905], 'each': [907, 2285, 2917, 3399, 3483, 3825, 3995, 4091, 4119, 4219, 4225], 'phosphosite': [908, 1754, 1893, 2051, 2286, 3062, 3112, 3157, 3206, 3400, 3972, 3996, 4059, 4069, 4198], 'has': [912, 959, 1949, 1968, 3106, 3313, 3401, 3761], '(Holmberg': [915], '2002),': [918], 'neofunctionalization': [919, 1032, 2625, 3348, 3462], 'would': [920, 1022, 2968, 3167], 'correspond': [921, 1280, 2687, 2694, 2944, 4195], 'acquired': [924], 'event': [928, 2995], 'subfunctionalization': [930, 1030, 2627, 2751, 3318, 3372, 3464], 'paralogs.': [939, 1505, 1825, 3823], 'In': [940, 1036, 1252, 4170, 4270], 'first': [942, 2065, 2311, 2417, 3705, 4000, 4062, 4272], 'case,': [943, 955, 3411, 4273], 'connections': [945], 'created': [947, 1013], 'network;': [951], 'second': [954, 4040, 4072, 4313], 'no': [956, 989], 'evolved': [960, 1000], 'links': [963, 1010], 'rather': [966, 1933, 2013, 4164], 'than': [967, 1119, 1293, 1404, 1934, 2014, 2438, 2705, 2895, 3251, 3682, 4165], 'created.': [968], '(Landry': [970, 1960, 2756], '2009)': [973, 1868, 2759], 'others': [975], '(Lienhard,': [976], '2008)': [977, 1141], 'recently': [979], 'suggested': [980], 'fraction': [983, 1007, 1640, 1691, 1700, 2533, 3175, 4290], 'specific': [990, 1938, 2139, 2242], 'represent': [993, 1023, 2749, 4276], 'result': [995, 1857, 2125, 2387, 2774, 3085, 3513], 'interactions': [998, 1719, 1730, 4257, 4278, 4323], 'neutrally': [1001], 'nearly': [1003], 'neutrally.': [1004], 'Accordingly,': [1005], 'these': [1020, 1187, 1269, 1416, 1591, 1695, 2526, 2747, 3072, 3448, 3477, 3609, 3882, 4146], 'gains': [1024, 1181, 2658, 2689, 2836, 2904, 3158, 3177, 4373], 'without': [1029], 'proteins.': [1035, 1568, 2176], 'study,': [1038], 'used': [1040, 3000, 3549, 3699, 4109], 'cerevisae': [1045], 'model.': [1050, 2646], 'lineage': [1052, 3068], 'underwent': [1058], 'whole-genome': [1060], '(WGD)': [1062], '(My)': [1066], 'ago': [1067], '(Wolfe': [1068], 'Shields,': [1070], '1997)': [1071], 'affected': [1073], 'its': [1074, 1330, 1355, 2062], 'signaling': [1075], 'significantly:': [1077], 'while': [1078, 1697, 2530, 2602, 3935, 3964], 'only': [1079, 1440, 1478, 1832, 2172, 3815, 4301], '10%': [1080], 'all': [1082, 1266, 1456, 1531, 1555, 2222, 3656, 3661, 3774, 3980, 4023, 4033, 4088, 4174, 4186, 4344], 'genes': [1083, 2259, 3076], '(∼500': [1084], 'pairs)': [1085], 'were': [1086, 1110, 1533, 2361, 2951, 3089, 3611, 3685, 3819, 3856, 4123, 4207, 4258, 4294, 4304, 4338, 4360], 'maintained': [1087], 'duplicates,': [1089, 1102], '30': [1090], '33%': [1092], 'phosphatases': [1097], 'retained': [1100, 1116], 'respectively': [1103], '(Seoighe': [1104], '1999).': [1107], 'Furthermore,': [1108], 'significantly': [1111, 2006, 2191, 2432, 2701, 3107, 3173], 'likely': [1113, 3091, 3233, 4181], 'nonphosphorylated': [1120, 2440, 2449, 2457], '(Amoutzias': [1122, 2630], 'Finally,': [1126, 3737], 'duplicated': [1127, 3310], 'differ': [1133], 'sequence': [1135, 2819, 2942, 3199], '(Musso': [1138], 'many': [1143, 2250, 3855], 'them': [1145, 2105, 2328], 'show': [1146], 'accelerated': [1147, 1180, 3108, 3159], 'amino': [1148, 2078, 3650, 4228], 'acid': [1149], 'WGD': [1153, 1207, 1238, 1504, 1566, 2314, 2487, 2994, 3045, 3099, 3139, 3164, 3311, 3324, 3984], '(Kellis': [1154], 'Using': [1158], 'computational': [1159], 'experimental': [1161], 'analyses,': [1162], 'examined': [1164, 2269, 3853, 4003], 'extent': [1166, 1473, 2639, 3930], 'addressed': [1175, 2410, 3440], 'whether': [1176, 1190, 2652], 'among': [1186, 1503, 1708, 1958, 2088, 3416, 4343], 'modified': [1195], 'since': [1196, 2485], 'WGD.': [1198], 'Results': [1199, 2909], 'discussion': [1201], 'Paralogous': [1202], 'substantially': [1204], 'data': [1209, 1412, 1576, 2810, 2883, 3621, 3635, 3657, 3701, 3706, 3714, 3719, 3742, 3772, 3777, 3800, 4147, 4275, 4314], 'set': [1210, 2277, 2303, 2720, 2884, 3535, 3636, 3707, 3715, 3743, 3801], 'consists': [1211], '2726': [1213], '(serines': [1215], '(S),': [1216], '82%;': [1217], 'threonines': [1218, 2844], '(T),': [1219], '16%;': [1220], 'tyrosines': [1221], '(Y),': [1222], '2%)': [1223], 'belong': [1225], 'member': [1231], '352': [1234], 'pairs': [1235, 1597, 1710, 2091, 2182, 3982], 'least': [1243, 2100, 4067, 4309, 4348], 'phosphoprotein.': [1251], 'work,': [1254], 'focused': [1256], 'S/T': [1258, 1311, 1348, 2450, 3820, 4379], 'make': [1262], '98%': [1264], 'phosphosites.': [1267, 1855, 2840, 3993], 'Among': [1268], 'sites,': [1270, 2377, 2427], '2445': [1271], 'unique': [1273, 1342, 3267], '118': [1278], '(that': [1279], '236': [1282], 'phosphosites)': [1283], 'occur': [1284], 'homologous': [1286, 1327, 1356, 1371, 2054], 'positions,': [1287], 'number': [1289, 1562, 1587, 1777, 1795, 1853, 1995, 2029, 2371, 2787, 2889, 2902, 3264, 3273, 3843, 4333], '7.4': [1290], 'times': [1291, 4335], 'higher': [1292, 2433, 3174], 'expected': [1294, 1529, 1664, 1699, 2358, 2706, 2761, 2896, 3169, 4370], 'chance': [1296, 2708, 2898], '(P≪0.001;': [1297], 'Supplementary': [1298, 2333, 2796], 'Figure': [1299, 1497, 1787, 2122, 2334, 2368, 2460, 2797, 2813, 2822, 2824, 3214, 3874, 4252, 4365], 'S1).': [1300], 'Phosphosites': [1301, 2232], 'ways.': [1305], 'First': [1306], 'cases': [1308, 2623, 4345], 'where': [1309, 2095, 3156, 3986, 4346], 'residue': [1312, 1320, 1939, 4395], 'phosphorylated': [1314, 1324, 1350, 1366, 1375, 1620, 2175, 2234, 2397, 2400, 2436, 2539, 2867, 2952, 3040, 3125, 3133, 3236, 3754, 4295, 4306, 4339], 'cannot': [1322], 'occupies': [1325], 'position': [1328, 1357, 1446, 1894, 1910, 1946, 2293], '(site-divergence).': [1332], 'Site-divergence': [1333], 'accounts': [1334], '69%': [1336], 'paralog.': [1345, 2063], 'conserved': [1359, 1489, 1615, 1642, 2519, 2537, 2877, 4054, 4085], '(S/T)': [1360, 2938], 'but': [1361, 1964, 2027, 2634, 3723], 'observed': [1363, 1653, 1690, 2575, 2673, 2801, 2891], '(state-divergence).': [1367], 'Eighty-six': [1368], 'percent': [1369], 'fact': [1378, 1398, 1903, 2381, 2423], 'state-diverged.': [1379], 'This': [1380, 1789, 1841, 1856, 2124, 2370, 2416, 2725, 3512], 'measure': [1381, 3927], 'state-divergence': [1383, 2383, 3787], 'strongly': [1385], 'upwardly': [1386], 'biased': [1387, 2319], 'false-negative': [1389], '(FN)': [1390], 'false-positive': [1392], 'identifications': [1393], 'phosphopeptides': [1400, 1441, 1547, 3552, 3592, 3600, 3607], 'match': [1402, 1443, 1549], 'included': [1409], 'set.': [1413], 'considered': [1415, 1612, 1836, 2847, 3624, 3816, 3830], 'issues': [1417], 'comparing': [1419, 2671, 3794], 'cross-study': [1421, 1425, 1519, 1523, 3795, 3919, 3949, 3953], 'conservation': [1422, 1492, 1520, 1600, 1992, 2001, 2112, 2271, 3796, 3932, 3950], 'reproducibility.': [1426, 1524, 3798], 'state-conservation': [1430, 1508, 3961], 'between': [1431, 1766, 1781, 1824, 1880, 2002, 2275, 2364, 3790, 3885, 3933, 3962, 4279, 4324], 'around': [1434, 2252], '36%': [1435], 'filtered': [1437, 3612], 'peptides': [1438, 1454, 3625, 3640, 3663], '(considering': [1439, 1455], 'single': [1445, 1551, 3696], 'proteome)': [1449], '54%': [1451], 'unfiltered': [1453, 1553], 'phosphopeptides)': [1457], '(Figure': [1458, 2082, 2442, 2523, 2679, 2723, 3055, 3151, 3969], '1A).': [1459, 3970], 'sequence,': [1461], 'function,': [1462, 3404, 3473], 'localization': [1463, 2550], 'and/or': [1464, 2546, 2549], 'recognition': [1465], 'such': [1472, 2168], 'My': [1476, 2589, 3498], '36–54%': [1479], 'appears': [1486], 'despite': [1490, 1760], 'actual': [1495, 1581, 2015], 'residues.': [1496, 4204], '1.Conservation': [1498], 'phosphoregulation': [1502], '(A)': [1506, 2833, 3227], 'was': [1512, 3069, 3974, 4053, 4065, 4097, 4353], 'estimated': [1513, 1702, 2445, 3785, 4098, 4288, 4368], 'regression': [1516, 3946], 'A': [1525, 1609, 2614, 2923, 3302, 3945, 4051], '1:1': [1526, 1538, 3051, 3149, 3185, 3244, 3281], 'relationship': [1527, 1539], 'state-conserved.': [1534], 'Deviation': [1535], 'provides': [1540, 3955], 'an': [1541, 3402, 4317], 'state-divergence.': [1544], 'Filtered': [1545], 'data:': [1546, 1554], 'protein;': [1552], 'phosphopeptides.': [1556], '(B)': [1557, 2869, 3260], 'Positive': [1558], 'correlation': [1559, 1774, 1790, 1827, 1842], 'Red': [1569], 'dots': [1570, 1579], 'indicate': [1571, 1585], 'average': [1572, 1661], 'binned': [1575], 'green': [1578], 'data.': [1582], 'Green': [1583], 'intensities': [1584], 'points': [1589], 'positions.': [1592, 2016, 4078], '(C)': [1593, 2887], 'Proportion': [1594], 'significant': [1599, 1773, 1792, 1830, 2026, 2109, 2162, 2187, 2532, 3345], 'window': [1606, 1628, 1648, 2059, 2069, 2115, 4005, 4092], 'size': [1607, 1649, 2060, 2070], 'considered.': [1608], 'site': [1610, 1621, 1913, 4052, 4242, 4250], 'being': [1614, 2396, 2399, 3646], 'within': [1626, 4048], '(excluding': [1629], 'exact': [1631, 3667, 4028], 'position).': [1632], '(D)': [1633], 'Case': [1634], 'putative': [1636, 2622], 'local': [1637, 1984], 'compensation.': [1638, 2163], 'shown.': [1651], 'Blue:': [1652], 'value;': [1654], 'Grey:': [1655], '95th': [1656], 'quantile': [1657], '(100': [1658], 'permutations);': [1659], 'Red:': [1660], 'distribution.': [1665], '(E)': [1666], 'Fraction': [1667], 'assigned': [1673, 1706, 2343, 2429, 3692, 4235], 'same': [1676, 2346, 2470, 2719, 2782, 3718, 3879, 4029, 4298], 'kinase.': [1678, 4311], 'Assignments': [1679], 'based': [1681, 2710, 3195, 4243], 'PWMs': [1683], 'Mok': [1685, 2306, 4127], 'al': [1687, 3585, 3596, 3604, 4129, 4263, 4268], '(2010).': [1688], 'calculated': [1693, 4331], 'using': [1694, 2290, 3673, 3716, 4099, 4136], 'assignments': [1696], 'shuffling': [1704], 'sites.': [1713, 1745, 4380], 'Ptacek:': [1714], 'large-scale': [1715, 2499, 3546], 'vitro': [1717, 1728, 4133, 4319], 'microarrays': [1721], '(Ptacek': [1722], '2005).': [1725, 3009], 'Ubersax:': [1726], 'Cdc28–substrate': [1729], '(Ubersax': [1731, 2505], '2003).': [1734], '(F)': [1735], 'Distributions': [1736], 'PWM': [1739, 4108, 4221], 'scores': [1740, 2430], 'classes': [1743, 4388], 'Download': [1746, 1748, 2919, 2921, 3296, 3298], 'figure': [1747, 2920, 3297], 'PowerPoint': [1749, 2922, 3299], 'Conservation': [1750], 'compensation': [1752, 2130, 2169, 2189], 'site-position': [1757], 'Surprisingly,': [1759], 'low': [1762, 2463], 'site-conservation': [1765, 1957], 'proteins,': [1768, 2144, 2734, 3836], 'highly': [1772, 2174], '(ρ=0.35,': [1783], 'P-value<2.2': [1784], '×': [1785, 1806, 1816, 1839, 2201, 2331], '10−16;': [1786, 2332], '1B).': [1788], 'remains': [1791, 2726], 'normalized': [1799], 'length': [1802, 1810, 2081, 2116, 4007], '(ρ=0.32': [1803], 'P-value': [1804], '<6.9': [1805], '10−14)': [1807], 'disordered': [1812, 2212, 2731, 2913], 'regions': [1813, 2010, 2732, 2914], '(ρ=0.27': [1814], 'P-value<3.8': [1815], '10−10),': [1817], 'preserved': [1823], 'site-diverged': [1833], '(ρ=0.28,': [1837], 'P-value=2.0': [1838], '10−11).': [1840], 'suggests': [1843, 2475], 'stabilizing': [1845], 'selection': [1846], 'acting': [1848, 3326], 'maintain': [1850], 'overall': [1852, 1991], 'agreement': [1860, 3516], 'recent': [1863, 2615], 'study': [1864, 2616, 3304, 3494, 3850, 3862, 3869, 3891, 3898, 3906], '(Beltrao': [1865], 'reporting': [1869], 'levels': [1873, 3470], 'orthologous': [1875], 'complexes': [1877], 'Candida': [1881], 'albicans': [1882], 'conserved.': [1889], 'could': [1897, 3689], 'made': [1899], 'possible': [1900, 3811], 'appear': [1907], 'nearby': [1911, 2132], 'can': [1917, 2998], 'compensate': [1918], '(Serber': [1922], 'Ferrell,': [1924], '2007),': [1925], 'charge': [1929], 'region': [1932, 2055], 'important.': [1941], 'redundancy': [1943], 'previously': [1951], 'proposed': [1952], 'explain': [1954], 'weak': [1956], '2009),': [1963, 2984], 'so': [1965, 2411, 3807], 'far': [1966, 2412], 'limited': [1970, 2028, 2149, 2158], 'evidence': [1971], '(Ba': [1974, 2792, 3764], 'Moses,': [1976, 2794, 3766], '2010;': [1977, 2795], 'Moses': [1978, 2583], 'responsible': [1988], 'proportion': [1999, 2036, 2042, 2210, 3031, 3119], 'should': [2004], 'increase': [2005, 2354], 'consider': [2009, 2745, 3395], 'case': [2023], 'pairs.': [2032, 2223], 'reconsidered': [2034], 'state-conserved': [2038, 2340, 2473, 4024], 'given': [2058, 4058], 'maximizes': [2072], 'signal': [2074], '33': [2077], 'acids': [2079, 4229], '1C).': [2083], 'Then,': [2084], '167': [2090], 'phosphosite,': [2102], '11': [2103], '(6.6%)': [2106], 'showed': [2107], '(an': [2117], 'example': [2118], 'shown': [2120, 2738, 3314, 3751], '1D).': [2123], 'either': [2128, 2394], 'relatively': [2135, 2148], 'uncommon': [2136], 'types': [2142], 'coverage': [2150], 'phosphoproteome': [2154], 'leaves': [2155], 'us': [2156], 'power': [2159], 'detect': [2161], 'Another': [2164, 3489], 'possibility': [2165], 'takes': [2170], 'place': [2171, 3467], 'Indeed,': [2177], '(mean:': [2194, 2214], '9.28': [2195], 'versus': [2196, 2216], '3.87;': [2197], 'Wilcoxon': [2198], 'test:': [2199], 'P-value<9.5': [2200], '10−11)': [2202], 'contain': [2207], 'larger': [2209], 'residues': [2213, 2855], '53': [2215], '42%,': [2217], 'P=0.01)': [2218], 'Life': [2224], 'WGD:': [2226], 'cellular': [2229], 'variety': [2237], 'recognize': [2241], 'motifs': [2243, 4163], 'surrounding': [2244], 'phosphorylatable': [2246, 2715, 2936], 'residue.': [2247], 'As': [2248], 'eukaryotes,': [2251], '2%': [2253], '(120': [2254], 'total)': [2255], 'protein-coding': [2258], 'code': [2260], '(Zhu': [2264], 'our': [2276, 3024, 3192, 3390, 3493], 'assigning': [2284], 'kinase': [2289, 2347, 2404, 2471, 4220, 4238, 4342], 'empirically': [2291, 4125, 4160], 'derived': [2292, 4124, 4161], 'weight': [2294], 'matrices': [2295], '(PWM)': [2296], '61': [2298, 4137], '(Supplementary': [2301, 2459, 2812, 2821, 3017, 3873, 4251], 'Data': [2302, 4254], 'S1': [2304], 'generally': [2317], 'terms': [2321], 'regulate': [2327], '(ρ=0.99,': [2329], 'P-value<2': [2330], 'S2).': [2335], '44%': [2348], 'time,': [2351], '20-fold': [2353], 'what': [2356, 2573], 'randomly': [2362, 2765, 4377], 'matched': [2363, 3665, 3680], '(P-value': [2366], '<0.0001;': [2367], '1E).': [2369, 2524], 'drops': [2372], '23%': [2374], 'state-diverged': [2376, 2426, 2448], 'again': [2378], 'supporting': [2379], 'does': [2384], 'entirely': [2386], 'FN': [2389], 'identifications.': [2390], 'These': [2391, 2697, 2768], 'condition': [2408], 'phosphoproteomics': [2414, 2976, 3188, 3217], 'studies.': [2415, 3547, 3944], 'hypothesis': [2418], 'supported': [2420], 'that,': [2424, 3396], 'ones': [2441, 3276], '1F).': [2443], 'reality': [2453], 'comprise': [2454], 'S3).': [2461], 'percentage': [2464], 'assignment': [2466], '(44%)': [2467], 'changed': [2484], 'independent': [2494, 3403], 'support': [2495, 3191], 'small-scale': [2501, 3756], 'interaction': [2503, 3523], 'experiments': [2504, 3757], '2003;': [2508, 3357], 'Ptacek': [2509, 4261], '2005)': [2512], 'proportions': [2522, 2674, 2698], 'Overall,': [2525], 'analyses': [2527, 2783, 3194, 3452], 'paralogs,': [2542, 3165], 'flanking': [2544, 4202], 'sequences': [2545, 2665], 'structure': [2548], 'enough': [2553], 'substrate': [2556], 'regulated': [2559], 'kinase,': [2564, 4299], 'transcriptional': [2577, 3339], '(Gasch': [2579], '2004;': [2582], 'After': [2587], 'evolution,': [2591], 'rewired,': [2601], 'preserving': [2603], 'status': [2606], 'substrates.': [2609, 4286], 'Phosphosite': [2610], 'dominates': [2612], 'site-divergence': [2613, 2653], 'reported': [2621, 3420], '2010),': [2633], 'did': [2635, 3727, 3877], 'compare': [2637], 'null': [2645], 'therefore': [2648, 2973, 3190, 3914], 'sought': [2649], 'quantify': [2651], 'resulted': [2654], 'reconstructing': [2662], 'ancestral': [2664, 2818, 2941, 2966, 3005, 3198, 3307], 'neutral': [2677], 'expectations': [2678], '2A–C).': [2680], '25%': [2684], '31%': [2691], 'are,': [2699], 'respectively,': [2700], 'less': [2702], 'alone,': [2709], 'resampling': [2713], '2C).': [2724], 'true': [2727], 'ordered': [2729, 2911], 'rates.': [2743], 'events': [2752], 'nonfunctional': [2754], 'selected': [2766, 3638, 3660], 'S/T.': [2767, 2868], 'unlikely': [2772], 'false': [2776], 'positives,': [2777], 'performed': [2780, 2974], 'smaller': [2786, 3030], 'manually': [2789, 3745], 'curated': [2790, 2882, 3746], 'S4)': [2798], 'results.': [2803], 'robust': [2808], 'filtering': [2811, 3731], 'S5)': [2814], 'variation': [2816], 'reconstruction': [2820, 3200], 'S6).': [2823], '2.Gains': [2825], 'duplication.': [2832], 'Inference': [2834], 'Serines': [2841], '(S)': [2842], '(T)': [2845], 'equivalent': [2848], 'respect': [2850], 'phosphorylation.': [2852], '!S/!T': [2853], 'indicates': [2854, 2866], 'S': [2860], 'nor': [2861], 'T,': [2863], 'pS/pT': [2865], 'Examples': [2870], '(S72),': [2873], '(T121)': [2875], '(S103)': [2878], '(Dataset': [2885, 3708, 3735, 3768], '2).': [2886, 3736], 'greater': [2894], 'alone': [2899], 'shows': [2905], 'opposite': [2907], 'result.': [2908], 'agree': [2915], 'other.': [2918], 'limitation': [2924, 3388], 'analysis': [2927, 3391], 'S.': [2949, 2990, 3043, 3052, 3097, 3127, 3238, 3269, 3670, 4143], 'ancestor.': [2955], 'Only': [2956], 'direct': [2958], 'observation': [2959], 'state': [2963], 'alleviate': [2969], 'problem.': [2971], 'experiment': [2977, 4320], 'Lachancea': [2979], 'kluyveri': [2980, 3037, 3067, 3216, 3229, 3279], '(Souciet': [2981], 'proxy': [3003], '(van': [3007, 3333], 'Hoof,': [3008, 3334], 'identified': [3011, 3034, 3887], '855': [3012], '429': [3015], 'information': [3018], 'S1)': [3019], 'mapped': [3022], 'alignments.': [3025], 'L.': [3036, 3066, 3080, 3135, 3228, 3278], '(1:2)': [3047], 'orthologs': [3054, 3150, 3181, 3245, 3254, 3282, 3290], '3A).': [3056], 'Assuming': [3057], 'rate': [3060, 3110], 'categories': [3074], '(1:1': [3077], '1:2': [3079, 3253], 'kluyveri–S.': [3081], 'orthologs),': [3083], 'confirms': [3086, 3218], 'thus': [3102, 4013], 'divergence.': [3113], 'uniquely': [3124], '(not': [3129], 'kluyveri)': [3136], 'actually': [3142], 'comparable': [3143], '3B).': [3152], 'Under': [3153], 'scenario': [3155], 'see': [3171], '2:1': [3180, 3289], 'ones.': [3186], 'bioinformatics': [3193], 'solely': [3196], 'confirm': [3202], 'prevalence': [3204], 'phosphoproteins.': [3213, 3226], '3.L.': [3215], 'preferentially': [3222], '(142/469': [3246], '108': [3249, 3286], 'proteins)': [3250, 3287], '(31/181': [3255], '45': [3258, 3294], 'proteins).': [3259, 3295], 'Ratios': [3261], 'shared': [3275], '(142/6644': [3283], '(62/2681': [3291], 'Concluding': [3300], 'remarks': [3301], 'previous': [3303, 3518], 'considering': [3305, 4300], 'importance': [3316, 3460], 'shaping': [3320, 3382], '2005),': [3335], 'whereas': [3336], 'investigations': [3337], '(Papp': [3354], 'Tirosh': [3358], 'Barkai,': [3360], '2007).': [3361], 'regulation,': [3371], 'driving': [3379], 'force': [3380], 'network.': [3386], 'One': [3387], 'functional,': [3398], 'necessarily': [3409], 'cooperative': [3414], 'effects': [3415, 3429, 3446], '(Kapoor': [3421], 'combined': [3426], 'individual': [3428], 'subfunctionalized': [3432], 'neofunctionalized': [3434], 'will': [3436, 3453], 'need': [3437], 'experimentally': [3441], 'divergences.': [3449], 'Further': [3450], 'integrative': [3451], 'required': [3456], 'elucidate': [3458], 'take': [3466], 'multiple': [3469], '(transcription,': [3471], 'modifications),': [3475], 'largely': [3480], 'dependent': [3481], '(Jensen': [3485], '2006).': [3488], 'key': [3490], 'finding': [3491], 'rewire': [3503], 'half': [3504], 'cell.': [3511], 'studies': [3519, 3555, 3610, 3828, 3884, 3913], 'showing': [3520], 'protein–protein': [3522], 'rapidly': [3526], '(Wagner,': [3527], '2001).': [3528], 'Materials': [3529], 'methods': [3531], 'compiled': [3533, 3581, 3712, 3739, 3771], '20': [3537], '342': [3538], '2688': [3542], 'eight': [3545, 3804], '21': [3550], '068': [3551], 'six': [3554], '(Gruhler': [3556], '2005;': [3559], 'Bodenmiller': [3560], '2007;': [3563, 3567, 3571, 3575], 'Chi': [3564], 'Li': [3568], 'Reinders': [3572], 'Albuquerque': [3576], '2008),': [3579], 'Amoutzias': [3583], '(2010)': [3586, 4130], 'added': [3590], '3616': [3591], 'Beltrao': [3594, 3634], '(2009)': [3597], '3620': [3599], 'Gnad': [3602, 3620], '(2009).': [3605], 'Raw': [3606], 'according': [3613, 4389], 'criteria:': [3617], 'set,': [3622], 'probability': [3628], 'score': [3629, 3642, 4247], 'above': [3630], '0.95;': [3631], '>0.02': [3643], 'acetylated': [3647], 'carboxy': [3652], 'terminus;': [3653], 'then': [3654, 4080, 4208, 4234], 'sets': [3658, 3832], 'hit': [3668], 'Blat': [3674, 3734], 'searches': [3675], '(Kent,': [3676], '2002).': [3677], 'Peptides': [3678], 'eliminated': [3686], 'because': [3687], 'unambiguously': [3693], 'protein.': [3697], 'assemble': [3703], '1).': [3709], 'Thus,': [3710], 'another': [3713], 'apply': [3729], 'step': [3732], 'third': [3741], 'whose': [3759], 'determined': [3763, 4081], '2010)': [3767], '3).': [3769], 'described': [3778, 4105, 4363], 'below': [3779], 'available': [3781, 4155], 'at:': [3782], 'http://www.bio.ulaval.ca/landrylab/download/.': [3783], 'comes': [3802, 4315], 'distinct': [3805], 'studies,': [3806], '28': [3810], 'pairwise': [3812], 'comparisons.': [3813], 'For': [3824, 3994], 'pair': [3826, 3911], 'concatenated': [3834], 'para.1': [3837, 3848, 3860, 3904], 'para.2.': [3839], 'counted': [3841, 4032], '1': [3851, 3892], '2': [3863, 3870, 3899, 3907], '(cross-study': [3864, 3871, 3900, 3908], 'reproducibility)': [3865, 3901], 'para.2': [3867, 3889, 3896], 'conservation)': [3872], 'S7).': [3875], 'comparison': [3880], 'conservation).': [3909], 'Each': [3910], 'yields': [3915], 'ratios': [3917], 'conservation/cross-study': [3920], 'reproducibility': [3921, 3940, 3954, 3966], 'ratio': [3924, 4083], 'gives': [3925], 'taking': [3936, 3965], 'into': [3937, 3967], 'account': [3938, 3968], 'rough': [3957], 'Local': [3971], 'tested': [3975], 'follows.': [3977], 'took': [3979], 'had': [3989], 'present': [3997, 4036, 4217], 'paralog,': [4001], 'l': [4008], 'centered': [4009], 'site,': [4012], 'defining': [4014], 'range': [4016, 4045, 4076], 'positions': [4018, 4047], 'along': [4019], 'sequence.': [4021], 'Excluding': [4022], '(at': [4026], 'position),': [4030], 'aligned': [4039], 'inside': [4042, 4074], 'corresponding': [4044, 4182, 4223], 'window.': [4050], 'size.': [4093], 'random': [4095], 'expectation': [4096], 'randomizations': [4101], 'below.': [4106], 'prediction': [4112], 'through': [4131], 'peptide': [4134], 'screening': [4135], '122': [4140], 'cerevisiae.': [4144], 'While': [4145], 'incomplete,': [4149], 'it': [4150, 4157], 'best': [4153], 'currently': [4154], 'relies': [4158], 'consensus': [4162], 'completely': [4166], 'silico': [4168], 'predictions.': [4169], 'assign': [4173], 'kinases,': [4183], 'extracted': [4185], '15-mers': [4189], 'proteome': [4193], '14': [4201], '(±7)': [4203], 'All': [4205], 'scored': [4209], 'summing': [4211], 'logarithm': [4213], 'values': [4216], 'matrix': [4222], '15-mer.': [4232], 'particular': [4241], 'highest': [4246], 'S8).': [4253], 'obtained': [4259], '(2005)': [4264], 'Ubersax': [4266], '(2003).': [4269], 'microarray': [4277], '87': [4280], '>4000': [4284], 'potential': [4285], 'testing': [4321], 'Cdc28': [4325], 'proteome.': [4329], 'phosphorylated.': [4354], 'Gains': [4355], 'inferred': [4361], '2A.': [4366], 'sampling': [4378], 'divided': [4382], 'four': [4387], 'type': [4392], '(S': [4396], 'T)': [4398], 'typ': [4401]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2101991263', 'counts_by_year': [{'year': 2023, 'cited_by_count': 2}, {'year': 2022, 'cited_by_count': 1}, {'year': 2018, 'cited_by_count': 1}, {'year': 2017, 'cited_by_count': 4}, {'year': 2015, 'cited_by_count': 3}, {'year': 2014, 'cited_by_count': 8}, {'year': 2013, 'cited_by_count': 3}, {'year': 2012, 'cited_by_count': 13}], 'updated_date': '2024-12-24T14:20:15.364218', 'created_date': '2016-06-24'}