Publication Information

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'abstract_inverted_index': {'Article6': [0], 'August': [1], '2018Open': [2], 'Access': [3], 'Transparent': [4], 'process': [5, 524, 2789], 'Metabolic': [6], 'oscillations': [7, 552, 722, 944, 1165, 1449, 1797, 2112, 2276, 2291, 2507, 2718, 3322, 3339, 3875, 3916, 3939, 4128], 'on': [8, 797, 968, 2333, 3220, 3940, 4092], 'the': [9, 521, 568, 572, 604, 684, 701, 729, 763, 784, 789, 793, 798, 806, 820, 852, 870, 889, 932, 999, 1014, 1077, 1172, 1184, 1189, 1206, 1239, 1249, 1310, 1314, 1358, 1384, 1396, 1425, 1433, 1444, 1480, 1500, 1556, 1585, 1593, 1696, 1701, 1716, 1734, 1752, 1755, 1767, 1772, 1786, 1818, 1827, 1836, 1856, 1863, 1911, 1937, 1940, 1988, 2002, 2015, 2056, 2071, 2092, 2119, 2125, 2156, 2159, 2182, 2185, 2200, 2209, 2212, 2223, 2264, 2270, 2421, 2447, 2470, 2499, 2537, 2558, 2567, 2570, 2573, 2604, 2608, 2656, 2661, 2714, 2733, 2769, 2803, 2814, 2838, 2858, 2875, 2893, 2904, 2907, 2930, 2936, 2959, 2983, 2997, 3034, 3060, 3085, 3088, 3121, 3148, 3185, 3237, 3291, 3369, 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4320, 4349, 4356, 4358], 'Drosophila': [14, 580, 608, 704, 717, 741, 755, 787, 842, 880, 1018, 1167, 1515, 1639, 2509, 3887, 3992, 4050, 4078, 4130, 4141, 4157, 4266], 'cells': [15, 582, 610, 682, 719, 743, 757, 840, 864, 908, 1020, 1029, 1036, 1050, 1101, 1169, 1252, 1312, 1675, 1722, 1737, 1770, 1816, 1831, 1993, 2487, 2511, 2774, 3547, 3889, 3994, 4022, 4143, 4178, 4223, 4259, 4353], 'lacking': [16], 'clock': [17, 795, 824, 845, 920, 969, 1089, 1119, 1533, 1941, 4016, 4070, 4084, 4099], 'genes': [18, 626, 825, 970, 1090, 1120, 1523, 1534, 1564, 2262, 4100], 'Guillaume': [19, 207, 397], 'Rey': [20, 208, 398], 'Corresponding': [21, 189, 209, 377], 'Author': [22, 190, 210, 378, 395], '[email': [23, 191, 211, 379, 493, 502], 'protected]': [24, 192, 212, 494, 503], 'orcid.org/0000-0001-7664-7052': [25, 213], 'The': [26, 42, 58, 73, 94, 118, 135, 173, 194, 214, 230, 246, 261, 282, 306, 323, 361, 382, 1179, 2280, 3542, 3609, 3952, 4211], 'Francis': [27, 43, 59, 74, 95, 119, 136, 174, 195, 215, 231, 247, 262, 283, 307, 324, 362, 383, 428], 'Crick': [28, 44, 60, 75, 96, 120, 137, 175, 196, 216, 232, 248, 263, 284, 308, 325, 363, 384, 429], 'Institute,': [29, 45, 61, 76, 97, 121, 138, 176, 197, 217, 233, 249, 264, 285, 309, 326, 364, 385, 430], 'London,': [30, 46, 62, 77, 83, 98, 104, 122, 139, 177, 198, 218, 234, 250, 265, 271, 286, 292, 310, 327, 365, 386, 431, 437], 'UK': [31, 47, 63, 78, 84, 99, 105, 123, 140, 162, 178, 199, 219, 235, 251, 266, 272, 287, 293, 311, 328, 350, 366, 387, 432, 438, 451], 'Search': [32, 48, 64, 85, 106, 124, 141, 163, 179, 200, 220, 236, 252, 273, 294, 312, 329, 351, 367, 388], 'for': [33, 49, 65, 86, 107, 125, 142, 152, 164, 180, 201, 221, 237, 253, 274, 295, 313, 330, 340, 352, 368, 389, 441, 470, 571, 1045, 1436, 1492, 1567, 1869, 2124, 2285, 2441, 2449, 2473, 2624, 2777, 2943, 2945, 2996, 3033, 3047, 3059, 3073, 3330, 3617, 3625, 3777, 3904, 4192, 4234, 4382, 4400], 'more': [34, 50, 66, 87, 108, 126, 143, 165, 181, 202, 222, 238, 254, 275, 296, 314, 331, 353, 369, 390, 2090, 2729, 2734, 3209, 3731], 'papers': [35, 51, 67, 88, 109, 127, 144, 166, 182, 203, 223, 239, 255, 276, 297, 315, 332, 354, 370, 391], 'by': [36, 52, 68, 89, 110, 128, 145, 167, 183, 204, 224, 240, 256, 277, 298, 316, 333, 355, 371, 392, 662, 1065, 1210, 2565, 2636, 2922, 3236, 3343, 3500, 3848, 4300], 'this': [37, 53, 69, 90, 111, 129, 146, 168, 184, 205, 225, 241, 257, 278, 299, 317, 334, 356, 372, 393, 484, 578, 988, 1009, 1159, 1882, 1908, 1970, 2080, 2870, 3258, 3990, 4117], 'author': [38, 54, 70, 91, 112, 130, 147, 169, 185, 206, 226, 242, 258, 279, 300, 318, 335, 357, 373, 394, 532], 'Nikolay': [39, 227, 400], 'B': [40, 187, 228, 375, 401, 424], 'Milev': [41, 229], 'Utham': [55, 243, 403], 'K': [56, 244, 404], 'Valekunja': [57, 245], 'Ratnasekhar': [71, 259, 406], 'Ch': [72, 260], 'UCL': [79, 100, 267, 288], 'Institute': [80, 101, 151, 268, 289, 339, 434, 440], 'of': [81, 102, 269, 290, 435, 455, 461, 475, 510, 520, 556, 574, 625, 686, 697, 700, 765, 792, 808, 822, 839, 888, 902, 957, 1002, 1079, 1174, 1191, 1198, 1212, 1225, 1233, 1238, 1251, 1274, 1305, 1343, 1360, 1365, 1395, 1427, 1446, 1502, 1509, 1558, 1588, 1596, 1660, 1720, 1736, 1754, 1769, 1781, 1829, 1835, 1859, 1875, 1884, 1929, 1939, 2014, 2049, 2058, 2122, 2161, 2184, 2202, 2211, 2259, 2272, 2307, 2392, 2428, 2457, 2498, 2501, 2526, 2536, 2544, 2555, 2557, 2575, 2581, 2584, 2603, 2607, 2716, 2797, 2817, 2840, 2857, 2860, 2878, 2929, 2968, 2975, 2985, 2992, 3000, 3028, 3041, 3054, 3067, 3087, 3123, 3129, 3141, 3170, 3254, 3278, 3371, 3423, 3431, 3444, 3496, 3505, 3545, 3550, 3567, 3579, 3587, 3596, 3611, 3627, 3632, 3643, 3705, 3787, 3834, 3843, 3896, 3969, 4000, 4110, 4123, 4126, 4237, 4288, 4308], 'Neurology,': [82, 103, 270, 291, 436], 'Sandipan': [92, 280, 408], 'Ray': [93, 281], 'Mariana': [113, 301, 410], 'Silva': [114, 302, 411], 'Dos': [115, 303, 412], 'Santos': [116, 304], 'orcid.org/0000-0003-2404-8490': [117, 305], 'Andras': [131, 319, 414], 'D': [132, 320, 415], 'Nagy': [133, 321], 'orcid.org/0000-0003-1759-4039': [134, 322], 'Robin': [148, 336, 417], 'Antrobus': [149, 337], 'Cambridge': [150, 338], 'Medical': [153, 341, 442, 463], 'Research': [154, 342, 443], '(CIMR),': [155, 343, 444], 'Wellcome': [156, 344, 445], 'Trust/MRC': [157, 345, 446], 'Building,': [158, 346, 447], "Addenbrooke's": [159, 347, 448], 'Hospital,': [160, 348, 449], 'Cambridge,': [161, 349, 450], 'James': [170, 358, 419], 'I': [171, 359, 420, 4401], 'MacRae': [172, 360], 'Akhilesh': [186, 374, 423], 'Reddy': [188, 376, 425], 'orcid.org/0000-0003-3328-1470': [193, 381], 'protected]b.net': [380], 'Information': [396], '*,1,†,‡,': [399], 'Milev1,†,‡,': [402], 'Valekunja1,': [405], 'Ch1,2,': [407], 'Ray1,2,': [409], 'Santos1,': [413], 'Nagy1,': [416], 'Antrobus3,': [418], 'MacRae1': [421], 'and': [422, 458, 513, 531, 619, 627, 630, 647, 653, 675, 705, 712, 726, 768, 778, 803, 810, 829, 847, 860, 927, 1005, 1061, 1094, 1135, 1256, 1323, 1334, 1389, 1418, 1420, 1467, 1520, 1570, 1604, 1655, 1683, 1741, 1746, 1757, 1776, 1842, 1849, 1886, 1905, 2065, 2089, 2129, 2137, 2167, 2171, 2199, 2236, 2248, 2313, 2350, 2387, 2399, 2423, 2479, 2515, 2572, 2639, 2653, 2655, 2663, 2687, 2781, 2799, 2819, 2842, 2863, 2887, 2897, 2932, 2970, 2977, 2988, 3013, 3019, 3030, 3056, 3093, 3113, 3152, 3176, 3280, 3287, 3316, 3359, 3389, 3417, 3457, 3461, 3481, 3510, 3522, 3534, 3536, 3573, 3604, 3667, 3682, 3708, 3722, 3753, 3805, 3832, 3852, 3871, 3920, 3956, 3985, 4007, 4023, 4037, 4113, 4131, 4137, 4150, 4169, 4209, 4222, 4249, 4273, 4282, 4341, 4361, 4368, 4385], '*,1': [426], '1The': [427], '2UCL': [433], '3Cambridge': [439], '†Present': [452, 467], 'address:': [453, 468], 'Department': [454], 'Genetic': [456], 'Medicine': [457], 'Development,': [459], 'University': [460, 474], 'Geneva': [462], 'School,': [464], 'Geneva,': [465], 'Switzerland': [466, 478], 'Center': [469], 'Integrative': [471, 710, 770], 'Genomics,': [472], 'Geńopode,': [473], 'Lausanne,': [476, 477], '‡These': [479], 'authors': [480], 'contributed': [481, 1699], 'equally': [482], 'to': [483, 534, 537, 673, 868, 872, 879, 935, 941, 976, 996, 1075, 1187, 1349, 1382, 1404, 1443, 1554, 1618, 1631, 1645, 1700, 1714, 1792, 1794, 1803, 1862, 1921, 2046, 2070, 2101, 2222, 2300, 2322, 2365, 2420, 2551, 2701, 2731, 2759, 2802, 2828, 2958, 3184, 3289, 3357, 3367, 3784, 3901, 3918, 3936, 4054, 4064, 4181], 'work': [485], '*Corresponding': [486, 495], 'author.': [487, 496], 'Tel:': [488, 497], '+44': [489, 498], '203': [490, 499], '7963351;': [491], 'E-mail:': [492, 501], '7963426;': [500], 'Mol': [504], 'Syst': [505], 'Biol': [506], '(2018)14:e8376https://doi.org/10.15252/msb.20188376': [507], 'PDFDownload': [508], 'PDF': [509], 'article': [511], 'text': [512], 'main': [514, 4351], 'figures.': [515], 'Peer': [516], 'ReviewDownload': [517], 'a': [518, 554, 639, 695, 736, 773, 837, 899, 937, 980, 1046, 1072, 1260, 1303, 1339, 1375, 1475, 1507, 1575, 1635, 1724, 1778, 1974, 2219, 2334, 2347, 2355, 2425, 2454, 2756, 2787, 2792, 2822, 2846, 3102, 3126, 3138, 3167, 3264, 3275, 3353, 3420, 3429, 3699, 3796, 3840, 3865, 3946, 3962, 3976, 3997, 4069, 4083], 'summary': [519], 'editorial': [522, 526], 'decision': [523, 527], 'including': [525, 826, 922, 1091, 1573, 3519], 'letters,': [528], 'reviewer': [529], 'comments': [530], 'responses': [533], 'feedback.': [535], 'ToolsAdd': [536], 'favoritesDownload': [538], 'CitationsTrack': [539], 'CitationsPermissions': [540], 'ShareFacebookTwitterLinked': [541], 'InMendeleyWechatReddit': [542], 'Figures': [543], '&': [544, 815, 946, 1042, 1109, 1464, 1470, 3474], 'Info': [545], 'Abstract': [546], 'Circadian': [547], 'rhythms': [548, 761, 859, 875, 1968, 3345], 'are': [549, 567, 583, 635, 657, 865, 886, 909, 1122, 1402, 2113, 2728, 2915, 2949, 3190, 3634, 3646, 3958, 3995], 'cell-autonomous': [550], 'biological': [551], 'with': [553, 1037, 1105, 1302, 1329, 1506, 1817, 2061, 2208, 2288, 2495, 3037, 3049, 3063, 3075, 3107, 3162, 3166, 3260, 3295, 3403, 3447, 3484, 3637, 3648, 3702, 3961, 3975, 4163, 4197, 4240, 4269, 4285, 4372], 'period': [555, 827, 1304, 1938, 2023, 2048, 2082], 'about': [557, 3171], '24': [558, 1307, 4248, 4301, 4314], 'h.': [559, 2067, 4251, 4315], 'Current': [560], 'models': [561, 699, 791], 'propose': [562], 'that': [563, 607, 623, 649, 668, 716, 731, 754, 855, 954, 960, 1087, 1121, 1147, 1357, 1391, 1399, 1704, 1751, 1785, 1910, 2005, 2097, 2110, 2254, 2324, 2352, 2389, 2485, 2644, 2744, 2768, 2807, 2892, 2953, 3187, 3324, 3337, 3816, 3884, 3927, 3954, 4004, 4021, 4028, 4077], 'transcriptional': [564, 739, 1796, 2275, 2798, 3231, 3279, 3897], 'feedback': [565, 939, 3898], 'loops': [566, 3899], 'primary': [569, 900], 'mechanism': [570], 'generation': [573, 2271, 3906], 'oscillations.': [576, 986, 2050], 'Within': [577], 'framework,': [579], 'S2': [581, 609, 718, 742, 756, 1019, 1028, 1100, 1125, 1168, 1545, 1674, 1815, 1966, 1992, 2278, 2486, 2510, 2773, 3375, 3546, 3624, 3888, 3993, 4142, 4177, 4258], 'regarded': [584, 850, 910], 'as': [585, 588, 851, 911, 1278, 1895, 2179, 2181, 2786, 3105, 3556, 3846, 3978, 4035, 4102], '"non-rhythmic"': [586], 'cells,': [587, 884, 1438], 'they': [589, 732, 914, 2913, 3910], 'do': [590, 611, 733, 744, 915, 929, 1676, 3890, 4029], 'not': [591, 734, 745, 866, 916, 930, 965, 1097, 1138, 1156, 1677, 1761, 1790, 1879, 1915, 1943, 1995, 2228, 3011, 3021, 3147, 3891, 3933, 4012, 4030, 4067, 4089], 'express': [592, 735, 746, 917, 3892, 4031], 'several': [593, 747, 823, 955, 1088], 'canonical': [594, 748, 1118, 2260, 3929, 4014], 'components.': [596, 750], 'Using': [597, 3795], 'an': [598, 992, 1363, 1808, 2255, 2305, 2548, 2621, 3703, 3738, 3771, 3979], 'unbiased': [599, 993], 'multi-omics': [600, 994], 'approach,': [601], 'we': [602, 973, 990, 1048, 1297, 1400, 1423, 1454, 1498, 1548, 1591, 1705, 1764, 1811, 1853, 1972, 2006, 2054, 2074, 2154, 2226, 2340, 2363, 2413, 2616, 2741, 2835, 2873, 2919, 3214, 3250, 3335, 3351, 3433, 3449, 3685, 3799, 4327], 'made': [603], 'surprising': [605], 'discovery': [606, 1386], 'fact': [613, 730, 3186, 3953, 4081], 'display': [614, 758], 'widespread': [615, 759], 'daily': [616, 721, 760, 857, 1000, 1015, 1038, 1448, 1658, 1795, 2281, 2804, 3321, 3618, 4043], 'rhythms.': [617, 664, 4044], 'Transcriptomics': [618], 'proteomics': [620, 713, 2376, 2971, 3668], 'analyses': [621, 643, 714, 752, 771, 1553], 'revealed': [622, 2296, 2845], 'hundreds': [624], 'their': [628, 1063, 1933, 3163, 3638, 3649], 'products,': [629], 'particular': [632, 2942], 'metabolic': [633, 659, 670, 777, 1006, 1571, 1589, 2301, 2315, 2745, 2779, 3331, 3338, 3683, 3915, 3984, 4006], 'enzymes,': [634], 'rhythmically': [636, 1407, 1559, 2243, 2372, 2395], 'expressed': [637, 1080, 1098, 1123, 1192, 1408, 1560, 1633, 2244, 2396, 3159, 3191], '24-h': [640, 669, 874, 943, 985, 1140, 1537, 1731, 1922, 2020, 2072, 2111, 2274, 2335, 2489, 2954, 3292, 3344, 3873, 3914], 'cycle.': [641, 1872, 3608], 'Metabolomics': [642], 'extended': [644], 'these': [645, 844, 1805, 2251, 2393, 2482, 2765, 3272, 3862], 'findings': [646, 1806], 'demonstrate': [648, 667], 'central': [650, 3478, 3497, 3809], 'carbon': [651, 3314, 3479, 3498, 3810], 'metabolism': [652, 656, 1580, 2785, 3315, 3319, 3480, 3487, 3499, 3811], 'amino': [654, 3317, 3485], 'acid': [655, 3318, 3486, 3512, 3524, 3606], 'core': [658, 3894], 'pathways': [660, 3482], 'driven': [661, 3342], 'protein': [663, 676, 767, 1132, 1568, 2311, 2314, 2328, 2344, 2577, 2582, 2618, 2717, 2820, 2886, 2898, 2908, 2933, 2978, 3014, 3020, 3031, 3057, 3114, 3130, 3248, 3680, 3869, 3921, 4112], 'We': [665, 1021, 1070, 1373, 1613, 1691, 1707, 1825, 2010, 2117, 2379, 2630, 3082, 3377, 3493, 3689, 3881, 4019], 'thus': [666, 2782, 3925, 3996], 'oscillations,': [671, 3684], 'coupled': [672, 3917], 'gene': [674, 724, 779, 1003, 1024, 1176, 1538, 1876, 1923, 2490, 3405, 3919, 3986, 4008, 4017], 'cycles,': [677], 'take': [678], 'place': [679], 'nucleated': [681], 'without': [683, 1530], 'contribution': [685], 'any': [687, 1148, 1531, 1918], 'known': [688, 1149, 1532], 'regulators.': [690], 'These': [691, 818, 907], 'results': [692, 2133, 2252, 2483, 2649, 2766, 3273, 3863, 3924, 4075], 'therefore': [693, 928, 1692], 'suggest': [694, 2253, 2767, 3864, 4076], 'reconsideration': [696], 'existing': [698], 'clockwork': [702], 'other': [706, 863, 4133], 'eukaryotic': [707, 3947, 4134], 'systems.': [708, 4135], 'Synopsis': [709], 'transcriptomics': [711, 2969], 'show': [715, 720, 753], 'expression': [725, 780, 1004, 1025, 1177, 1207, 1539, 1587, 1877, 1924, 2491, 3406, 3681, 3987, 4009, 4115], 'metabolism,': [727], 'despite': [728], 'functional': [737], 'clockwork.': [740], 'Multi-omics': [751], 'at': [762, 1051, 1283, 1332, 1392, 1952, 1980, 1984, 2115, 2165, 2465, 2821, 4153, 4186, 4190, 4193, 4204, 4217, 4232, 4244, 4256, 4262, 4293, 4297, 4303, 4311, 4363], 'level': [764], 'transcripts,': [766, 1590, 1885, 2141, 2451], 'metabolites.': [769, 3492, 3514, 3592], 'indicate': [772, 959, 2484, 3926], 'strong': [774], 'coupling': [775], 'between': [776, 1479, 2063, 2135, 2158, 2569, 2658, 2895, 2938, 3044, 3070, 3095, 3228, 3659, 3678, 3719, 3803, 3868, 3983, 4207, 4247], 'cycles.': [781, 3922], 'Introduction': [782], 'In': [783, 1295, 1496, 1801, 1851, 2068, 2152, 2218, 3401, 3767, 3989], 'fruit': [785], 'fly': [786, 893, 4027], 'melanogaster,': [788], 'recognised': [790], 'centre': [796], 'transcription': [799, 821, 1703, 3959], 'factors': [800, 3960], 'CYCLE': [801], '(CYC)': [802], 'CLOCK': [804, 811], '(CLK),': [805], 'homologs': [807], 'BMAL1': [809], 'mammals': [813, 2705], '(Young': [814], 'Kay,': [816], '2001).': [817], 'control': [819], '(per)': [828], 'timeless': [830], '(tim)': [831], '(Panda': [832], 'et': [833, 950, 1113, 1318, 1370, 1379, 1517, 1666, 1822, 1960, 2707, 2711, 3302, 3306, 3310], 'al,': [834, 951, 1114, 1319, 1371, 1380, 1518, 1667, 1823, 1961, 2708, 2712, 3303, 3307, 3311], '2002).': [835], 'Only': [836], 'subset': [838, 3430], 'expresses': [843], 'components': [846, 1151, 3241, 3895], 'it': [848, 2353], 'is': [849, 964, 1760, 1789, 1932, 2267, 2283, 2775, 2899, 2909, 3181, 3973, 4046], 'principal': [853, 1576, 3216], 'pacemaker': [854], 'drives': [856], 'activity': [858], 'physiology.': [861], 'All': [862], 'thought': [867, 3900, 4053], 'have': [869, 931, 1362, 1441, 3882, 4051, 4082], 'capacity': [871], 'generate': [873, 2488, 3937], 'autonomously.': [876], 'This': [877, 1145, 2108, 2319, 2890, 3178, 3814, 4045], 'extends': [878], 'Schneider': [881], '2': [882, 1608, 3575, 4286], '(S2)': [883], 'which': [885, 1085, 1355, 1439, 1473, 1651, 2642, 2844, 2918, 2946, 3145, 3382, 3439, 3448, 3696, 3965], 'one': [887], 'most': [890, 1670, 2462, 3188, 3197, 3734, 3817], 'commonly': [891], 'used': [892, 1071, 1374, 1435, 1647, 1812, 4328], 'cell': [894, 1160, 1672, 1697, 1717, 1758, 1787, 1837, 1864, 1871, 1889, 1912, 1967, 2233, 2240, 2265, 4321], 'lines,': [895, 1673], 'originally': [896], 'derived': [897], 'from': [898, 3570, 3576, 3581, 3598, 3662, 4061, 4146], 'culture': [901, 1682, 4140], 'late-stage': [903], 'embryos': [904], '(Schneider,': [905], '1972).': [906], 'non-rhythmic': [912], 'because': [913], 'key': [918, 2788, 3089, 3517], 'components,': [921, 4010], 'PER,': [923], 'TIM': [924], 'or': [925, 1155, 1285, 1367, 1946, 1955, 2263, 2906, 2911, 3165, 4096, 4104], 'CLK,': [926], 'necessary': [933], 'apparatus': [934], 'form': [936], 'transcription–translation': [938], 'loop': [940], 'drive': [942], '(Saez': [945, 1108], 'Young,': [947, 1110], '1996;': [948, 1111], 'Darlington': [949, 1112], '1998).': [952, 1115], 'Given': [953, 2361, 2806, 3323], 'lines': [956], 'evidence': [958], 'oscillatory': [962], 'behaviour': [963], 'fully': [966], 'dependent': [967], '(Lakin-Thomas,': [971], '2006),': [972], 'set': [974, 1078, 1190, 1501, 1883, 3466, 3584], 'out': [975], 'investigate': [977], 'whether': [978, 1695, 1965, 2367, 3206], 'such': [979, 4034, 4101], '"clock-less"': [981], 'system': [982, 1820, 3948, 4335], 'could': [983, 1440, 1656, 2007, 3450], 'exhibit': [984, 1139, 1678, 3320, 3912, 4041], 'To': [987, 1583, 1963, 2051, 2337, 2832, 2867, 3204, 3348, 3426, 3674, 4316], 'end,': [989], 'adopted': [991], 'approach': [995, 1654], 'comprehensively': [997], 'determine': [998, 1964, 2366, 3205, 3368, 3675], 'dynamics': [1001], 'state': [1007], 'cellular': [1010, 2784, 4001], 'model.': [1011], 'Results': [1012], 'Defining': [1013], 'transcriptome': [1016, 1064, 1512], 'first': [1022, 2341, 2836, 3238, 3690], 'characterised': [1023], 'patterns': [1026, 1874, 2955], 'using': [1030, 1245, 1313, 1457, 1641, 1711, 1807, 1839, 1866, 2373, 2518, 2547, 2620, 2694, 4392], 'RNA': [1031, 2450, 2883, 2931, 2976, 2987, 3010, 3017, 3112, 4339, 4342, 4375], 'Sequencing': [1032], '(RNA-Seq).': [1033], 'After': [1034], 'synchronising': [1035], 'temperature': [1039, 1430, 2003, 2040, 2043, 4182, 4289], 'cycles': [1040, 1540, 1759, 2492, 4183, 4290], '(Glaser': [1041], 'Stanewsky,': [1043], '2007)': [1044, 1519], 'week,': [1047, 4196], 'sampled': [1049], '3-h': [1052, 4245], 'intervals': [1053, 4246], 'constant': [1055, 1281, 1953], 'conditions': [1056, 1282], '(at': [1057], '25°C': [1058, 2126, 2224, 4154, 4233], 'darkness)': [1060], 'measured': [1062, 1592, 1766, 1826, 2018], 'RNA-Seq': [1066, 1351, 1620, 1976, 4254, 4380], '(Appendix': [1067, 1082, 1142, 1345, 1450, 1482, 1526, 1622, 1798, 1846, 2105, 2215, 2245, 2358, 2431, 2627, 2650, 2669, 2925, 2962, 3117, 3242, 3267, 3711, 3745, 3949], 'Fig': [1068, 1083, 1143, 1321, 1346, 1416, 1451, 1483, 1527, 1623, 1748, 1799, 1847, 1903, 2034, 2106, 2150, 2173, 2197, 2216, 2246, 2359, 2401, 2432, 2628, 2651, 2670, 2926, 2963, 3118, 3243, 3268, 3391, 3459, 3712, 3746, 3859, 3950], 'S1A).': [1069], 'mixture': [1073], 'model': [1074, 3999, 4059, 4118], 'define': [1076, 1188, 1715], 'transcripts': [1081, 1215, 1227, 1276, 1301, 1337, 1361, 1398, 1505, 1860, 1891, 2017, 2060, 2078, 2163, 2204, 2235, 2242, 2308, 2474, 2761, 2808, 2841, 2862, 3029, 3055, 3124, 3164, 3189], 'S1B),': [1084], 'established': [1086], 'clk,': [1092], 'per': [1093, 1196, 1200, 1267, 4036, 4103], 'tim': [1095], 'were': [1096, 1152, 1541, 1565, 1684, 1878, 1892, 2099, 2370, 2394, 2563, 2747, 3099, 3115, 3158, 3208, 3233, 3327, 3385, 3410, 3488, 3820, 4144, 4151, 4179, 4224, 4230, 4260, 4277, 4283, 4354, 4370, 4389], '(Fig': [1102, 1581, 1744, 2169, 2317, 2377, 2397, 2459, 2467, 2477, 2698, 2722, 2738, 2753, 2762, 2849, 2865, 2916, 3150, 3174, 3194, 3202, 3333, 3387, 3415, 3455, 3532, 3761, 3812], '1A),': [1103], 'consistent': [1104, 3294, 3974], 'previous': [1106, 1350, 2702, 3296], 'studies': [1107, 1352, 1513, 2703, 3297], 'Moreover,': [1116, 1763], 'four': [1117, 2876, 3229], 'cells—clockwork': [1126], 'orange': [1127], '(cwo),': [1128], 'cyc,': [1129], 'par': [1130], 'domain': [1131], '1': [1133, 3572, 4195], '(pdp1)': [1134], 'vrille': [1136], '(vri)—did': [1137], 'rhythmicity': [1141, 1456, 2021, 2123, 3619, 3870], 'S1C).': [1144], 'verified': [1146], 'either': [1153, 2695, 2903], 'absent': [1154], 'rhythmic': [1157, 1214, 1240, 1279, 1300, 1397, 1504, 1563, 1586, 1702, 1896, 2059, 2162, 2356, 2429, 2496, 2528, 2609, 2726, 2751, 2760, 2770, 2861, 2882, 2885, 2986, 3038, 3050, 3064, 3076, 3116, 3156, 3325, 3386, 3408, 3491, 3528, 3557, 3568, 3591, 3679], 'line.': [1161], 'Figure': [1162, 2504, 2965, 3540], '1.': [1163], 'Transcriptional': [1164], 'Histogram': [1170], 'showing': [1171, 1205, 1248, 2982, 3263, 3655], 'distribution': [1173, 1224, 2456, 2535, 3140, 3701], 'mean': [1175, 1270], 'levels.': [1178], 'dashed': [1180], 'vertical': [1181], 'line': [1182], 'represents': [1183, 3614], 'cut-off': [1185], 'chosen': [1186], 'transcripts.': [1193, 1241, 1561, 3039, 3051], 'FPKM,': [1194], 'fragments': [1195], 'kilobase': [1197], 'transcript': [1199, 2896, 2905], 'million': [1201], 'mapped': [1202], 'reads.': [1203], 'Heatmap': [1204, 2524, 3026, 3052, 3548, 3654], 'profiles': [1208, 1617, 1858, 2634, 2693, 2816, 2934, 2948, 3631, 3710, 3760], '(ordered': [1209], 'phase)': [1211], '482': [1213, 1299, 1503], '(JTK-Cycle,': [1216, 1287, 1897, 2022, 2084, 2530], 'P': [1217, 1288, 1489, 2438, 2531, 2598, 2676, 3559], '<': [1218, 1289, 1327, 1490, 1900, 2028, 2087, 2144, 2406, 2439, 2532, 2599, 2677, 3396, 3471, 3560], '0.05,': [1219, 2145, 2407, 3561], 'FDR': [1220, 2030, 2093, 2146, 2408, 3398, 3562], '=': [1221, 1265, 1410, 1413, 2031, 2147, 2409, 2591, 3399, 3563, 3765, 3793, 4219, 4313], '0.31).': [1222], 'Phase': [1223, 2534], 'shown': [1228, 2540, 3635, 3647, 3883], '(B).': [1230, 2542], 'Scatterplot': [1231, 2601], 'representation': [1232, 2525, 2602, 3549], 'Gene': [1234, 1550, 2292], 'Ontology': [1235, 1551, 2293], '(GO)': [1236, 1552, 2294], 'analysis': [1237, 1244, 2121, 2606, 3218, 3454, 3504, 3586, 3595], 'Cell': [1242, 4139, 4332], 'cycle': [1243, 1698, 1718, 1788, 1838, 1890, 1913, 2241, 3513, 3525], 'flow': [1246, 1709, 1840], 'cytometry': [1247, 1710, 1841], 'fraction': [1250, 1828, 2201], 'G1,': [1254, 1739], 'S': [1255, 1740], 'G2': [1257, 1742], 'phases': [1258, 1331, 1743, 2458, 3414, 3580], 'over': [1259, 2346, 2383, 3530, 4323], 'course': [1262, 1774, 1978, 2128, 2349, 3356], 'experiment': [1263, 1775, 1979, 4255], '(n': [1264, 2590], '3': [1266], 'point,': [1269], '±': [1271], 'SEM).': [1272], 'Example': [1273], 'six': [1275, 2239], 'detected': [1277, 1298, 1401, 1894, 2164, 3378, 3555], 'under': [1280], '25': [1284, 2166, 4384], '28°C': [1286, 1981, 2168, 4263, 4386], '0.05).': [1290, 2533], 'Download': [1291, 1293, 2611, 2613, 3078, 3080, 3670, 3672], 'figure': [1292, 2612, 3079, 3671], 'PowerPoint': [1294, 2614, 3081, 3673], 'contrast,': [1296, 3155, 3768], 'approximately': [1306], 'h': [1308, 3173, 4185, 4189, 4292, 4296, 4302], 'same': [1311, 2120, 3827], 'JTK-Cycle': [1315], 'algorithm': [1316, 2187, 2214], '(Hughes': [1317, 1369], '2010;': [1320], '1B': [1322, 2478], 'C;': [1324], 'adjusted': [1325, 1898, 2026, 2085, 2142, 2404, 3394], 'P-value': [1326, 1899, 2027, 2086, 2143, 2405, 3395, 3470, 3616], '0.05),': [1328, 2088], 'peak': [1330, 2471, 3199], 'CT0': [1333, 2466, 3201], 'CT12.': [1335], 'Most': [1336], 'had': [1338, 2295, 3737], 'relatively': [1340, 2720], 'low': [1341, 1428, 1956, 2289, 2721], 'amplitude': [1342, 1364, 1429, 2290, 2715, 3092], 'oscillation': [1344, 4097], 'S1D),': [1347], 'similarly': [1348], 'Drosophila,': [1354], 'showed': [1356, 1474, 2891], 'majority': [1359], 'two-fold': [1366], 'less': [1368], '2012).': [1372], 'permutation-based': [1376], 'method': [1377, 2550, 2697, 4395], '(Xie': [1378], '2005)': [1381], 'estimate': [1383], 'false': [1385, 2103], 'rate': [1387], '(FDR)': [1388], 'found': [1390, 1521, 1614, 1630, 1777, 2011, 2075, 2237, 2351, 2424, 2743, 3824], 'least': [1393, 4194], 'two-thirds': [1394], 'likely': [1403, 1791, 2100, 2730, 3182], 'be': [1405, 1632, 2102, 2331, 2732, 2810, 2826, 2829, 3137, 3341, 3902, 3934, 4055], 'truly': [1406], '(FDR': [1409], '0.31,': [1411], 'n': [1412], '10,000;': [1414], 'Appendix': [1415, 1747, 1902, 2033, 2149, 2172, 2196, 2400, 3390, 3458, 3462, 3537, 3622, 3858], 'S1E': [1417], 'Materials': [1419, 4136], 'Methods).': [1421], 'Importantly,': [1422], 'excluded': [1424], 'presence': [1426, 4094], 'fluctuations': [1431], 'incubators': [1434], 'culturing': [1437], 'led': [1442, 2320], 'appearance': [1445], 'artefactual': [1447], 'S1F).': [1452], 'Furthermore,': [1453], 'validated': [1455, 2617, 2920, 3494], 'two': [1458, 2415, 3239, 3413], 'alternative': [1459, 2549, 2622, 2640], 'detection': [1460, 2418], 'methods': [1461, 2419], '[RAIN': [1462], '(Thaben': [1463], 'Westermark,': [1465], '2014)': [1466], 'ARSER': [1468], '(Yang': [1469], 'Su,': [1471], '2010)],': [1472], 'highly': [1476, 2667, 2830, 3133, 3706, 4047], 'significant': [1477, 1919, 2178, 2668], 'overlap': [1478, 2157, 2176, 2657, 2856, 2984], 'groups': [1481, 2999], 'S1G;': [1484], 'two-sided': [1485, 2434, 2672], "Fisher's": [1486, 2193, 2435, 2673], 'exact': [1487, 2194, 2436, 2674], 'test,': [1488, 2195, 2437, 2597, 2675], '10−16': [1491, 2440], 'every': [1493, 2442, 4072, 4086, 4201], 'pairwise': [1494, 2443], 'comparison).': [1495, 2444], 'addition,': [1497, 1852, 2153], 'compared': [1499], 'meta-analysis': [1508], 'five': [1510], '(Keegan': [1516], '18': [1522, 2066, 2138, 2384], 'common': [1525], 'S1H).': [1528], 'Thus,': [1529], 'being': [1535], 'rhythmic,': [1536, 2910, 2950], 'readily': [1542], 'apparent': [1543, 1880], 'cells.': [1546, 2279, 3376], 'Next,': [1547, 2615], 'performed': [1549, 1708, 1973, 2118, 3215, 3361, 3435, 4216, 4371], 'identify': [1555, 2783, 3428], 'functions': [1557], 'Strikingly,': [1562], 'enriched': [1566, 2284, 2776, 3329, 3489], 'biosynthesis': [1569], 'processes': [1572, 2316, 2746, 3332], 'glycolysis,': [1574, 3506, 3599], 'pathway': [1577, 3452, 3509, 3602, 3776, 3838], 'glucose': [1579], '1D).': [1582, 2318, 2763], 'validate': [1584, 1804], 'mRNA': [1594, 1857, 2818, 3285], 'accumulation': [1595, 3529], 'three': [1597, 3261], 'glycolytic': [1598], 'genes—lactate': [1599], 'dehydrogenase': [1600, 1607, 3751], '(ImpL3),': [1601], 'enolase': [1602], '(eno)': [1603], 'glyceraldehyde': [1605], '3-phosphate': [1606], '(Gapdh2)—using': [1609], 'quantitative': [1610, 2375], 'PCR': [1611], '(qPCR).': [1612], 'similar': [1615, 1844, 2132, 2220, 2426, 2757, 3103, 3252, 3354, 3797, 4042], 'temporal': [1616, 2633, 2815, 2923, 3212, 3226, 3424, 3630], 'our': [1619, 1649, 1653, 1688, 2637, 3404, 4121], 'data': [1621, 2422, 2972, 3222], 'S1I).': [1624], 'Of': [1625, 3515], 'note,': [1626, 3516], 'ImpL3': [1627], 'was': [1628, 1729, 2038, 2094, 2188, 2304, 2446, 2453, 2475, 2666, 2719, 2854, 3125, 3146, 3725, 3729, 3782, 4215], 'recently': [1629], 'pattern': [1637, 2357], 'heads': [1640], 'identical': [1642, 2692], 'statistical': [1643], 'criteria': [1644], 'those': [1646, 3048, 3074, 3445, 3823], 'study,': [1650], 'substantiates': [1652], 'imply': [1657], 'regulation': [1659, 2497, 3495], 'glycolysis': [1661], 'whole': [1663], 'animals': [1664], '(Kuintzle': [1665], '2017).': [1668], 'Unlike': [1669], 'mammalian': [1671, 3299], 'contact': [1679], 'inhibition': [1680], 'actively': [1685], 'dividing': [1686], 'during': [1687, 1771], 'courses.': [1690], 'next': [1693, 3083, 3434], 'determined': [1694, 2055, 2155, 2388], 'observed.': [1706], 'DAPI': [1712], 'staining': [1713], 'status': [1719], 'temperature-synchronised': [1721], '2-day': [1725], 'course.': [1727], 'There': [1728], 'no': [1730, 2039], 'variation': [1732], 'proportion': [1735, 2207], '1E': [1745], 'S2A),': [1749], 'indicating': [1750, 1784, 3419], 'phasing': [1753], 'correlated.': [1762], 'also': [1765, 1854], 'density': [1768, 2580, 4322], 'doubling': [1779], '37': [1782], 'h,': [1783, 2025, 2139, 4221], 'contribute': [1793, 1916, 2956], 'S2B).': [1800], 'order': [1802], 'independent': [1809, 2258], 'method,': [1810], 'stably': [1813], 'transfected': [1814], 'Fly-FUCCI': [1819], '(Zielke': [1821], '2014).': [1824, 3312], 'fixed': [1830], 'each': [1833, 2576, 3221, 3612, 3660, 3720], 'phase': [1834, 2472, 3042, 3068, 3122, 3142, 3161, 3168, 3179], 'reached': [1843], 'conclusions': [1845], 'S2C': [1848], 'D).': [1850], 'assembled': [1855], 'related': [1861, 3100, 3183], 'division': [1865], 'GO': [1867, 2605], 'annotations': [1868], 'mitotic': [1870], 'Daily': [1873], 'only': [1887, 2076, 2238, 3715], '10': [1888], 'statistically': [1893], '0.05;': [1901, 2029, 3397, 3472], 'S2E': [1904], 'F).': [1906], 'Together,': [1907, 2764], 'implied': [1909], 'does': [1914, 1942], 'way': [1920, 2758, 3104], 'profiles.': [1925], 'An': [1926], 'important': [1927, 3980], 'property': [1928], 'clocks': [1931, 4032], '"temperature': [1934], 'compensation",': [1935], 'whereby': [1936], 'speed': [1944], 'up': [1945], 'slow': [1947], 'down': [1948], 'significantly': [1949, 2900, 2957], 'when': [1950, 2902, 3110], 'maintained': [1951], 'high': [1954, 3108, 3421], 'temperatures,': [1957], 'respectively': [1958, 4390], '(Konopka': [1959], '1989).': [1962], 'exhibited': [1969, 3527], 'phenomenon,': [1971], 'low-coverage': [1975], '(that': [1982], 'is,': [1983], '3°C': [1985], 'higher': [1986, 1997, 2901], 'than': [1987, 1999, 3743], 'original': [1989], 'course).': [1991], 'did': [1994, 2227, 3352], 'tolerate': [1996], 'temperatures': [1998], 'this,': [2000, 2053, 2339, 2362, 2834, 2852, 3350], 'restricting': [2001], 'range': [2004, 2083], 'use': [2008], 'experimentally.': [2009], '144': [2012], '(7%)': [2013, 2391], '2,035': [2016], 'displayed': [2019, 2354, 2690, 3757], '21–27': [2024], '0.31;': [2032], 'S3A–C).': [2035], 'If': [2036, 3132], 'there': [2037, 2303, 2452, 2853, 3135, 3207], 'compensation,': [2041], 'increased': [2042, 2189, 2205, 2935], 'should': [2044, 3136], 'lead': [2045], 'shorter': [2047, 2081], 'test': [2052, 2338, 2833, 3349], 'number': [2057, 2427], 'periods': [2062], '12': [2064, 2136, 3172, 4188, 4295], 'contrast': [2069], 'analysis,': [2073, 3468], '71': [2077], 'importantly,': [2091], '0.99,': [2095], 'implying': [2096], 'all': [2098, 2588, 2689, 3692], 'positives': [2104], 'S3D).': [2107], 'indicates': [2109], 'dominant': [2114], '28°C.': [2116, 4210], 'observed': [2130], 'very': [2131], '(periods': [2134], '194': [2140], '1;': [2148], 'S3E).': [2151], 'sets': [2160, 2665, 2859], '1F': [2170], 'S3F).': [2174], 'Notably,': [2175, 2740], 'became': [2177], 'soon': [2180], 'threshold': [2183, 2210], 'JTK': [2186, 2213], 'above': [2190], '0.1': [2191], '(one-sided': [2192], 'S3G)': [2198], 'shared': [2203], 'S3H).': [2217], 'fashion': [2221], 'experiments,': [2225], 'observe': [2229], 'overt': [2230], 'periodicity': [2231], 'cycle-related': [2234], 'S3I': [2247], 'J).': [2249], 'Collectively,': [2250, 3861], 'uncharacterised': [2256], 'mechanism,': [2257], 'cycle,': [2266], 'involved': [2268, 2309], 'temperature-compensated': [2273, 3913], 'proteome': [2282, 2771, 2805], 'abundant': [2286, 2735, 2778], 'proteins': [2287, 2369, 2382, 2430, 2463, 2529, 2539, 2586, 2589, 2593, 2659, 2727, 2752, 2864, 3157, 3198, 3326, 3724, 3804, 3831], 'that,': [2297], 'addition': [2299], 'processes,': [2302], 'overrepresentation': [2306, 3704], 'translation': [2312, 2500], 'us': [2321], 'hypothesise': [2323], 'global': [2325, 2823], 'changes': [2326, 4199], 'levels': [2329, 3786], 'might': [2330, 2825, 2871, 3340], 'occurring': [2332, 4200, 4243], 'timescale.': [2336], 'quantified': [2342, 2380, 2737], 'total': [2343], 'content': [2345], 'S4A).': [2360], 'proceeded': [2364], 'specific': [2368, 2502], 'regulated': [2371, 2790], 'multiplexed': [2374], '2A).': [2378], '4,759': [2381, 2592], 'points': [2386, 4347], '342': [2390, 2527, 2559], '2B': [2398], 'S4B;': [2402], 'JTK-Cycle,': [2403, 3393], '0.28).': [2410], 'As': [2411, 2445], 'before,': [2412, 3106], 'employed': [2414], 'further': [2416, 2951], 'rhythm': [2417, 3905], 'S4C;': [2433], 'case': [2448, 3149], 'biphasic': [2455], '2C).': [2460, 3203], 'However,': [2461, 3120], 'peaked': [2464], '2C),': [2468], 'while': [2469, 3196], 'CT12': [2476, 3193], 'C).': [2480], 'Together': [2481], 'tandem': [2494, 2519, 3436], 'proteins.': [2503, 2561, 2610, 2989, 3065, 3077, 3347], '2.': [2505], 'Proteome': [2506], 'Sample': [2512], 'collection': [2513, 4242, 4310], 'procedure': [2514], 'labelling': [2516, 2626], 'scheme': [2517], 'mass': [2520], 'tag': [2521], '(TMT)': [2522], 'proteomics.': [2523], 'Validation': [2543], 'TMT': [2545], 'quantitation': [2546], 'label': [2552], 'samples.': [2553], 'Distribution': [2554, 3040, 3066, 3578], 'amplitudes': [2556], 'Amplitudes': [2562, 3098], 'calculated': [2564], 'taking': [2566], 'ratio': [2568], 'maximum': [2571], 'minimum': [2574], 'profile.': [2578], 'Cumulative': [2579, 2990], 'abundances': [2583], 'vs.': [2587, 2884], 'quantified;': [2594], 'Wilcoxon': [2595], 'rank-sum': [2596, 3024], '10−4).': [2600, 2680], 'quantification': [2619, 2662, 2696], 'strategy': [2623], 'multiplex': [2625], 'S4D).': [2629], 'then': [2631, 3360], 'correlated': [2632, 2837, 2874, 3686, 3707, 3759, 3844], 'generated': [2635], 'initial': [2638], 'labellings,': [2641], 'demonstrated': [2643, 3815], 'both': [2645, 2914, 2947, 3007, 3111], 'protocols': [2646], 'yield': [2647], 'reproducible': [2648], 'S4E': [2652], 'F),': [2654], 'validation': [2664], 'S4G;': [2671], '5': [2678], '×': [2679], 'For': [2681, 3748, 3829, 4173, 4252], 'example,': [2682, 3749, 3830], 'ImpL3,': [2683], 'pyruvate': [2684], 'carboxylase': [2685], '(PCB)': [2686], 'fat-spondin,': [2688], 'almost': [2691], '2D).': [2699], 'Similarly': [2700], '(Mauvoisin': [2706], '2014;': [2709, 3308], 'Robles': [2710, 3309], '2014),': [2713], '2E).': [2723], 'Interestingly,': [2724, 3224], 'however,': [2725], 'ones': [2736], '2F).': [2739], 'again': [2742], 'functionally': [2748, 3328], 'overrepresented': [2749], 'among': [2750, 3381, 3490, 4058], '2G),': [2754, 3334], 'enzymes': [2780], 'cyclical': [2793], 'manner.': [2794], 'Different': [2795], 'contributions': [2796], 'post-transcriptional': [2800, 3281], 'mechanisms': [2801, 3282], 'must': [2809, 3283], 'translated': [2811], 'into': [2812, 3412, 4226, 4279], 'proteins,': [2813, 2843], 'expected': [2827], 'coupled.': [2831], 'abundance': [2839], 'tight': [2847], 'correlation': [2848, 2894, 2937, 2960, 2994, 3109, 3652, 3658, 3740, 3764, 3792, 3802], '3A).': [2850], 'Despite': [2851], 'little': [2855], '3B).': [2866], 'understand': [2868], 'why': [2869], 'be,': [2872], 'categories': [2877], 'RNA-protein': [2879, 2939, 3001, 3035, 3045, 3061, 3071, 3096], 'pairs': [2880, 2944, 3036, 3046, 3062, 3072, 3645, 3736, 3819], '(e.g.': [2881], 'so': [2888], 'on).': [2889], 'if': [2912], '3C),': [2917], 'independently': [2921], 'cross-correlation': [2924], 'S5A).': [2927], 'Detrending': [2928], 'pairs,': [2940], 'highlighting': [2952], 'structure': [2961], 'S5B).': [2964], '3.': [2966], 'Integration': [2967], 'Scatter': [2973], 'plot': [2974], 'expression.': [2979], 'Venn': [2980], 'diagram': [2981], 'distributions': [2991], "Pearson's": [2993, 3651, 3657, 3763], 'coefficients': [2995], 'indicated': [2998, 4348], 'pairs.': [3002, 3097], 'RNA−Prot−,': [3003], 'neither': [3004], 'circadian;': [3005, 3008, 3015], 'RNA+Prot+,': [3006], 'RNA−Prot+,': [3009], 'RNA+Prot−,': [3016], '(Wilcoxon': [3023], 'test).': [3025], 'representations': [3027, 3053], 'accumulations': [3032, 3058], 'difference': [3043, 3069], 'examined': [3084], 'relationship': [3086, 3266], 'properties,': [3091], 'phase,': [3094], 'S5C).': [3119], 'poor': [3127], 'predictor': [3128], 'phase.': [3131], 'related,': [3134], 'narrow': [3139], 'differences': [3143], '(lags),': [3144], '3D': [3151], 'E).': [3153], 'By': [3154], 'delay': [3169, 3180], '3F': [3175], 'G).': [3177], 'around': [3192, 3200], '1C),': [3195], 'complex': [3210, 3276], 'underlying': [3211], 'relationships,': [3213], 'component': [3217], '(PCA)': [3219], 'set.': [3223], 'ordered': [3225], 'transitions': [3227], 'different': [3230], 'states': [3232, 3262], 'mostly': [3234], 'captured': [3235], 'PCA': [3240], 'S5D).': [3244], 'When': [3245, 3714], 'considering': [3246], 'matching': [3247], 'profiles,': [3249, 3845], 'saw': [3251], 'clustering': [3253], 'points,': [3256], 'but': [3257, 4011, 4088], 'cyclic': [3265], 'S5E).': [3269], 'Taken': [3270], 'together,': [3271], 'underline': [3274], 'combination': [3277], 'regulate': [3284], 'processing': [3286], 'degradation': [3288], 'shape': [3290], 'proteome,': [3293], 'systems': [3300], '(Reddy': [3301], '2006;': [3304], 'Mauvoisin': [3305], 'Central': [3313], 'hypothesised': [3336], 'before': [3358, 4305], 'untargeted': [3362], 'liquid': [3363], 'chromatography–mass': [3364], 'spectrometry': [3365], '(LC-MS)': [3366], 'ensemble': [3370], 'oscillating': [3372], 'metabolites': [3373, 3442, 3518, 3597, 3633, 3807, 3833], '1,339': [3379], 'features,': [3380], '466': [3383, 3552], '(35%)': [3384], '4A': [3388], 'S6A–C;': [3392], '0.18).': [3400], 'keeping': [3402, 4003], 'data,': [3407], 'features': [3409, 3554, 3569], 'clustered': [3411], '4B': [3416], 'C),': [3418], 'degree': [3422], 'organisation.': [3425], 'definitively': [3427], 'metabolites,': [3432], 'MS': [3437], '(MS2),': [3438], 'yielded': [3440], '54': [3441, 3589], '(4%': [3443], 'detected)': [3446], 'perform': [3451], 'enrichment': [3453, 3467, 3585], '4D,': [3456], 'S6D': [3460], 'Table': [3463, 3538, 3623], 'S1;': [3464], 'metabolite': [3465, 3721, 3874, 4114], 'raw': [3469], 'Xia': [3473], 'Wishart,': [3475], '2010).': [3476], 'Significantly,': [3477], 'associated': [3483, 3639, 3723], 'performing': [3501], 'targeted': [3502, 3663, 3806], 'LC-MS': [3503, 3553, 3594], 'pentose': [3507, 3600, 3836], 'phosphate': [3508, 3601, 3837], 'citric': [3511, 3523], 'ATP,': [3520], 'glutathione': [3521], 'intermediates': [3526], '4E': [3533], 'F,': [3535], 'S2).': [3539], '4.': [3541], 'metabolome': [3544], '(JTK-Cycle;': [3558], '18%).': [3564], 'Individual': [3565], 'traces': [3566], 'cluster': [3571, 3574, 3842], '(A).': [3577, 3582], 'Metabolite': [3583], 'identified': [3590], 'Targeted': [3593], '(PPP)': [3603], 'tricarboxylic': [3605], '(TCA)': [3607], 'colour': [3610], 'node': [3613], '(JTK-Cycle).': [3620], 'See': [3621], 'list': [3626], 'abbreviations.': [3628], 'Selected': [3629], 'together': [3636], 'P-value.': [3640], 'Two': [3641], 'examples': [3642], 'protein–metabolite': [3644, 3694, 3735, 3818], 'respective': [3650], 'coefficients.': [3653], 'profile': [3661], 'metabolomics': [3664], '(carbon': [3665], 'metabolism)': [3666], 'data.': [3669], 'mechanistic': [3676], 'relationships': [3677], 'two.': [3688], 'considered': [3691], 'possible': [3693], 'associations,': [3695], 'resulted': [3697], 'non-uniform': [3700], 'anti-correlated': [3709, 3783], 'S6E).': [3713], 'best': [3717], 'match': [3718], 'kept,': [3726], 'effect': [3728], 'much': [3730], 'pronounced,': [3732], 'since': [3733, 4049], 'absolute': [3739], 'coefficient': [3741], 'greater': [3742], '0.5': [3744], 'S6F).': [3747], 'lactate': [3750], '(ImpL3)': [3752], 'NAD,': [3754], 'its': [3755, 3788, 3853], 'substrate,': [3756], 'strongly': [3758], '4G;': [3762], '0.97).': [3766], 'phosphoribosylamidotransferase': [3769], '(Prat),': [3770], 'essential': [3772], 'enzyme': [3773], 'de': [3778], 'novo': [3779], 'purine': [3780], 'synthesis,': [3781], 'product': [3789], 'glutamate': [3790], "(Pearson's": [3791], '−0.82).': [3794], 'strategy,': [3798], 'analysed': [3800], '4H).': [3813], 'correlated,': [3821], 'especially': [3822], 'subpathway.': [3828], 'formed': [3839], 'small': [3841], 'exemplified': [3847], 'sedoheptulose': [3849], '7-phosphate': [3850], '(SH7P)': [3851], 'cognate': [3854], 'enzyme,': [3855], 'transaldolase': [3856], '(Taldo;': [3857], 'S6G).': [3860], 'robust': [3866], 'link': [3867], 'downstream': [3872], 'fundamental': [3877, 4124], 'biochemical': [3878], 'pathways.': [3879], 'Discussion': [3880], 'even': [3885], 'though': [3886], 'required': [3903, 3935], 'fly,': [3909], 'nevertheless': [3911], 'Our': [3923, 4074], 'network': [3931], 'may': [3932, 4039, 4079], 'genome-wide': [3938], 'S7A).': [3951], 'CLK': [3955], 'CYC': [3957], 'PAS': [3963], 'domain,': [3964], 'allows': [3966], 'molecular': [3967], 'sensing': [3968], 'intracellular': [3971], 'environment,': [3972], 'role': [3977, 4109], 'connecting': [3981], 'cog': [3982], 'programmes.': [3988], 'interpretation,': [3991], 'novel': [3998], 'encompasses': [4005], 'network.': [4018], 'speculate': [4020], 'tissue': [4024], 'genes,': [4033], 'tim,': [4038], 'nonetheless': [4040], 'relevant': [4048], 'been': [4052], 'somewhat': [4056], 'unique': [4057], 'organisms,': [4060], 'single-celled': [4062], 'cyanobacteria': [4063], 'mammals,': [4065], 'having': [4068], 'cell.': [4073], 'cell,': [4087], 'necessarily': [4090], 'based': [4091], 'of,': [4095, 4098], 'tim.': [4105], 'Understanding': [4106], 'relative': [4108], 'gene,': [4111], 'will': [4119], 'enhance': [4120], 'understanding': [4122], 'properties': [4125], 'Methods': [4138], 'purchased': [4145], 'Thermo': [4147], 'Fisher': [4148, 4160], 'Scientific': [4149], 'grown': [4152, 4261], "Schneider's": [4156, 4265], 'Media': [4158], '(Thermo': [4159], 'Scientific),': [4161], 'supplemented': [4162, 4268], '10%': [4164, 4270], 'heat-inactivated': [4165, 4271], 'FBS,': [4166], '1%': [4167, 4274], 'Pen-Strep': [4168], '1/500': [4170], 'MycoZap': [4171], 'Plus-CL.': [4172], 'entrainment': [4175], 'protocol,': [4176], 'subjected': [4180], '(12': [4184, 4291], '23°C,': [4187], '28°C)': [4191], 'media': [4198], '3–4': [4202], 'days': [4203, 4287], 'transition': [4206], '23': [4208], 'last': [4212], 'medium': [4213], 'change': [4214, 4319], 't': [4218, 4312], '0': [4220], 'plated': [4225, 4278], 'six-well': [4227, 4280], 'plates.': [4228], 'Cells': [4229, 4276], 'kept': [4231], 'remaining': [4236], 'experiment,': [4239], 'sample': [4241, 4309], '81': [4250], '28°C,': [4257, 4294, 4304], 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