Elucidating Novel Hepatitis C Virus–Host Interactions Using Combined Mass Spectrometry and Functional Genomics Approaches

Name: Work Video:
Duration: 3 min 30 s
Marie-Anne Germain; Laurent Chatel‐Chaix; Bridget Gagné; Éric Bonneil; Pierre Thibault; Fabrine Pradezynski; Benoı̂t de Chassey; Laurène Meyniel‐Schicklin; Vincent Lotteau; Martin Baril; Daniel Lamarre
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'virus–host': [114, 182, 396, 464, 1860], 'interaction': [115, 160, 397, 442, 891, 968, 1402, 1676, 3415], 'studies': [116, 398, 2075, 2197, 2211], 'demonstrates': [117, 399], '24.5%': [118, 400], 'shared': [119, 401], 'interactors': [121, 189, 270, 403, 471, 552, 2521, 2712, 2727, 2945, 4159], 'overall': [122, 404], '(24/98),': [123, 405], 'illustrating': [124, 406], 'reliability': [126, 408], 'approach.': [129, 411], 'show': [134, 416], 'enriched': [135, 417, 2519, 2620, 4148], 'Gene': [136, 418], 'Ontology': [137, 419], 'terms': [138, 420], 'endoplasmic': [142, 424], 'reticulum,': [143, 425], 'transport': [144, 248, 426, 530, 2690], 'major': [148, 430], 'contribution': [149, 274, 431, 556, 2731], 'NS3/4A': [151, 239, 433, 521, 1903, 2683, 3043, 3091], 'interactors,': [152, 434], 'transmembrane': [154, 436], 'Core': [157, 439, 3219], 'interactors.': [158, 440], 'network': [161, 443], 'emphasizes': [162, 444, 1382], 'high': [164, 168, 172, 446, 450, 454, 2005, 2715], 'degree': [165, 447, 2716], 'distribution,': [166, 170, 448, 452], 'betweenness': [169, 451], 'interconnectivity': [173, 455], 'targeted': [175, 457, 1635, 1900], 'proteins,': [177, 459, 1380], 'in': [178, 210, 460, 492, 723, 736, 799, 819, 1017, 1479, 1691, 1727, 1783, 1840, 1885, 1986, 2357, 2396, 2506, 2533, 2545, 2552, 2629, 2760, 2797, 2847, 3127, 3278, 3328, 3353, 3374, 3446, 3520, 3525, 3616, 3630, 3650, 3667, 3724, 3854, 3934, 4097, 4143, 4191], 'agreement': [179, 461], 'interactome': [183, 465, 2052], 'studies.': [184, 466], 'also': [190, 472, 1680, 1857, 2198, 2610], 'shows': [191, 473], 'extensive': [192, 474], 'enrichment': [193, 209, 475, 491, 1667, 4112, 4141], 'known': [195, 477], 'targets': [196, 478], 'other': [198, 480, 4132], 'viruses.': [199, 481], 'combined': [201, 483, 1832, 2558], 'proteomic': [202, 484, 2559], 'gene': [204, 486, 2222, 2543, 2561, 3124, 3147], 'silencing': [205, 487, 2544, 2562, 2701], 'study': [206, 263, 488, 545, 2709], 'revealed': [207, 264, 489, 546], 'strong': [208, 490, 2577], 'modulators': [211, 493], 'replication,': [215, 497, 1283], '11': [220, 502, 2582], 'cofactors': [222, 504, 1432, 2244, 2306, 2614, 2655], 'among': [223, 505, 2618], 'our': [224, 506, 2619], 'specific': [227, 509, 1180, 2522, 4158], 'Finally,': [230, 512, 2676], 'immune': [235, 517, 1866, 1984, 2679, 3386], 'evasion': [236, 518, 1985, 2680], 'mechanism': [237, 519, 2681], 'based': [241, 523, 1858, 2160], 'on': [242, 524, 1040, 1365, 1389, 1409, 1859, 2206, 3556], 'its': [243, 525, 811, 1366, 1370, 1589, 2703], 'ability': [244, 526], 'affect': [246, 528], 'nucleocytoplasmic': [247, 529, 2689], 'type': [250, 532], 'I': [251, 533], 'interferon-mediated': [252, 534], 'signal': [253, 535, 897, 974], 'transducer': [254, 536, 616, 671, 898, 975], 'activator': [256, 538, 618, 673, 900, 977], 'transcription': [258, 540, 620, 675, 902, 979, 4193], '1': [259, 541, 625, 680, 860, 886, 903, 909, 911, 937, 963, 980, 986, 988, 2896, 3301, 3336, 4028], 'nuclear': [260, 542], 'translocation.': [261, 543], 'highly': [265, 547], 'association': [267, 549, 2723], 'between': [268, 550, 2217, 2724], 'their': [272, 554, 2729, 4043], 'replication': [278, 560, 1195, 1214, 1387, 1408, 1664, 1774, 2361, 2400, 2574, 2634, 2821, 2851], 'cycle': [279, 561, 2736], 'pathogenesis.': [281, 563, 2738], 'Infecting': [564], 'almost': [565], 'worldwide,': [569], '(HCV)': [573], '1The': [574, 629], 'abbreviations': [575, 630], 'are:HCVhepatitis': [577, 632], 'virusIFNinterferonILF2interleukin': [579, 634], 'enhancer-binding': [580, 635, 843, 920], 'factor': [581, 636, 844, 921, 1477, 1547, 1909], '2IPimmunoprecipitationIP-MS/MSimmunoprecipitation': [582, 637], 'tandem': [585, 640, 850, 881, 927, 958, 2484], 'identificationISREinterferon-stimulated': [588, 643], 'response': [589, 644, 855, 932, 1919, 3115], 'elementEGLN1egl': [590, 645], 'nine': [591, 646, 858, 935], 'homolog': [592, 647, 859, 936], '1EXOC7exocyst': [593, 648], 'complex': [594, 649, 862, 939, 1157, 1162], 'component': [595, 650, 863, 940], '7FKBPFK506-binding': [596, 651], 'proteinFlucfirefly': [597, 652], 'luciferaseHSPheat': [598, 653], 'shock': [599, 654, 870, 947], 'proteinRlucRenilla': [600, 655], 'luciferaseLC-MS/MSliquid': [601, 656], 'chromatography–tandem': [602, 657, 875, 952], 'spectrometryMOImultiplicity': [604, 659], 'infectionMS/MStandem': [606, 661], 'spectrometryMTHFD1methylenetetrahydrofolate': [608, 663], 'dehydrogenase': [609, 664, 885, 962], '1NSnonstructuralNTnontarget': [610, 665], 'sequencePPIprotein–protein': [611, 666], 'interactionRNAiRNA': [612, 667], 'interferenceshRNAshort': [613, 668], 'hairpin': [614, 669, 895, 972, 2548], 'RNASTAT1signal': [615, 670], '1TARDBPTAR': [621, 676], 'DNA': [622, 677, 905, 982, 4170], 'binding': [623, 678, 906, 983], 'proteinTNPO1transportin': [624, 679], 'isoform': [626, 681, 910, 987], '1vRNAviral': [627, 682], 'RNAXPOexportin.': [628, 683], 'is': [684, 834, 993, 1061, 1142, 1198, 1301, 1324, 1403, 1586, 1634, 1660, 1679, 1711, 1997, 2053, 2183, 2684, 3878], 'leading': [686], 'cause': [687], 'chronic': [689, 804, 1990], 'hepatitis,': [690], 'liver': [691], 'fibrosis,': [692], 'cirrhosis,': [693], 'hepatocellular': [695], 'carcinoma': [696], '(1Poynard': [697], 'T.': [698, 1028, 1524, 1530, 2103, 2302, 2331, 2345], 'Yuen': [699], 'M.F.': [700], 'Ratziu': [701], 'V.': [702, 1500, 1510, 1603, 1816, 2087, 2128], 'Lai': [703], 'C.L.': [704], 'Viral': [705], 'C.Lancet.': [707], '2003;': [708], '362:': [709], '2095-2100Abstract': [710], 'Full': [711, 713, 1443, 1445, 1960, 1962, 2255, 2257, 2412, 2414, 2666, 2668, 3940, 3942], 'Text': [712, 714, 1444, 1446, 1961, 1963, 2256, 2258, 2413, 2415, 2667, 2669, 3941, 3943], 'PDF': [715, 1447, 1964, 2259, 2416, 2670, 3944], 'PubMed': [716, 772, 1047, 1101, 1260, 1353, 1448, 1488, 1558, 1595, 1647, 1733, 1792, 1848, 1965, 2140, 2175, 2260, 2321, 2370, 2417, 2456, 2671, 3945, 3988], 'Scopus': [717, 773, 1048, 1261, 1354, 1449, 1489, 1559, 1596, 1648, 1734, 1793, 1849, 1966, 2141, 2176, 2261, 2322, 2371, 2418, 2457, 2672, 3946, 3989], '(746)': [718], 'Google': [719, 775, 1050, 1102, 1263, 1356, 1451, 1491, 1561, 1598, 1650, 1736, 1795, 1851, 1968, 2143, 2178, 2263, 2324, 2373, 2420, 2459, 2674, 3948, 3991], 'Scholar).': [720, 776, 1051, 1103, 1264, 1357, 1651, 1852, 1969, 2179, 2460, 2675, 3992], 'Major': [721], 'improvements': [722], 'patient': [724], 'treatment': [725, 761, 1696], 'were': [726, 2076, 2527, 2539, 2626, 2758, 2809, 2836, 2864, 2880, 2927, 2953, 2989, 3002, 3046, 3065, 3161, 3177, 3195, 3209, 3271, 3298, 3341, 3370, 3388, 3444, 3469, 3492, 3517, 3539, 3554, 3611, 3648, 3722, 3738, 3761, 3837, 3894, 3997, 4058, 4070, 4103, 4155], 'achieved': [727], 'approval': [730], 'first': [733], 'direct-acting': [734, 756, 2013, 2045], '2011,': [737], 'namely,': [738], 'Incivek': [739], '(Vertex': [740], 'Pharmaceuticals)': [741], 'Victrelis': [743], '(Merck': [744], '&': [745], 'Co)': [746], '(2Welsch': [747], 'C.': [748, 1032, 1238, 1504, 1611, 1745, 1814, 2126, 2148, 2298, 3265, 3959, 4176], 'Jesudian': [749], 'A.': [750, 1087, 1218, 1220, 1230, 1601, 1704, 1804, 2093, 2114, 2351, 2388, 2427], 'Zeuzem': [751], 'S.': [752, 1024, 1232, 1234, 1502, 1607, 1617, 2095, 2150, 2276, 2282, 2382, 3924, 3965], 'Jacobson': [753], 'I.': [754, 1216, 1512, 1753], 'New': [755], 'antiviral': [757, 1641, 1918, 2014, 2035, 2046, 2057], 'agents': [758, 2015], 'infection': [766, 880, 957, 1719, 1991, 2132, 2311], 'perspectives.Gut.': [768], '2012;': [769, 1257, 1644, 3985], '61:': [770], 'i36-i46Crossref': [771], '(159)': [774], 'However,': [777, 2180], 'these': [778, 2210, 3063], 'drugs': [779, 1683], 'co-administered': [780], 'pegylated': [782], 'interferon': [783, 841, 918, 1907], '(IFN)-α': [784], 'ribavirin': [786], 'inflict': [787], 'heavy': [789], 'burden': [790], 'side': [792], 'effects': [793], 'have': [795, 2199], 'relatively': [796], 'low': [797], 'effectiveness': [798], 'IFN-experienced': [800], 'nonresponder': [801], 'patients.': [802], 'Unlike': [803], 'HIV': [805], 'infection,': [806], 'does': [808], 'not': [809, 1267, 2184, 2213, 2825], 'integrate': [810], 'genome': [812, 1060], 'into': [813, 1063, 1068, 2905, 2933, 2975, 2991, 3055, 3763], 'host': [815, 1007, 1314, 1367, 1391, 1476, 1546, 1658, 2029, 2221, 2354, 2441, 2503, 2569, 2943, 4108, 4149], 'chromosomes': [816], 'replicate': [818, 2000], 'cytoplasm': [821, 1065], 'cell.': [824], 'This': [825, 2913], 'suggests': [826], 'that': [827, 1201, 1585, 1862, 2625, 2686, 4039], 'eradicating': [828], 'from': [830, 1284, 2786, 2961, 3006, 3018, 3073, 3086, 3163, 3179, 3197, 3211, 3222, 3232, 3243, 3252, 3264, 3391, 3576, 3678, 3976, 4010, 4116, 4167, 4175], 'all': [831, 4076], 'individuals': [833], 'achievable': [836], 'goal.': [837], 'interleukin': [842, 919], '2': [845, 922, 2782, 3338, 3733], 'interferon-stimulated': [854, 931, 3114], 'element': [856, 933, 3116], 'egl': [857, 934], 'exocyst': [861, 938], '7': [864, 941], 'FK506-binding': [865, 942], 'firefly': [867, 944, 3121], 'luciferase': [868, 873, 945, 950, 3122, 3145], 'heat': [869, 946], 'Renilla': [872, 949, 3144], 'liquid': [874, 951], 'multiplicity': [878, 955], 'methylenetetrahydrofolate': [884, 961], 'nonstructural': [887, 964, 1130], 'nontarget': [888, 965], 'sequence': [889, 966], 'protein–protein': [890, 967, 1972], 'short': [894, 971, 2547], 'TAR': [904, 981], 'transportin': [908, 985], 'exportin.': [914, 991], 'Hepacivirus': [995], 'member': [996], 'Flaviviridae': [999], 'family.': [1000], 'Following': [1001, 4178], 'attachment': [1002], 'factors': [1008, 2442], 'at': [1009, 1150, 1670, 2003, 2794, 2838, 2866, 3397, 3431, 3435, 3461, 3471, 3474, 3484, 3494, 3497, 3512, 3589, 3653], 'surface': [1011], 'hepatocytes,': [1013], 'virions': [1014], 'internalized': [1016], 'clathrin-dependent': [1019], 'manner': [1020], '(3Blanchard': [1021], 'E.': [1022], 'Belouzard': [1023], 'Goueslain': [1025], 'L.': [1026, 1456, 1605, 1739, 2089, 2376, 3922], 'Wakita': [1027], 'Dubuisson': [1029], 'J.': [1030, 1240, 1460, 1494, 1506, 1514, 1516, 1747, 1755, 1767, 2108, 2292, 2347, 2380, 3961], 'Wychowski': [1031], 'Rouille': [1033], 'Y.': [1034, 1415, 1921, 2118, 2154, 2156, 2227, 2333, 2638, 3087], 'Hepatitis': [1035, 1573, 2129], 'entry': [1038, 1078, 1090], 'depends': [1039], 'clathrin-mediated': [1041], 'endocytosis.J.': [1042], 'Virol.': [1043, 1097, 1554, 1591, 1729], '2006;': [1044], '80:': [1045], '6964-6972Crossref': [1046], '(438)': [1049], 'Subsequent': [1052], 'membrane': [1054, 1181, 1248], 'fusion,': [1055, 3083], '9.6-kb': [1057], 'released': [1062], 'translated': [1067], 'single': [1070, 3765], '3,000-amino-acid': [1071], 'polyprotein': [1072, 1110, 1148], 'precursor': [1073, 1111, 3693, 3703, 3736], 'via': [1074, 2542, 3004, 3095], 'internal': [1076, 3153], 'ribosome': [1077, 1089], 'site': [1079, 1091], '(4Tsukiyama-Kohara': [1080], 'K.': [1081, 1528, 1931, 1939, 2152, 2158], 'Iizuka': [1082], 'N.': [1083, 1421, 1935, 2110, 2233, 2384, 2644, 3963], 'Kohara': [1084], 'M.': [1085, 1458, 1462, 1520, 1522, 1532, 1615, 1749, 1802, 1808, 1937, 2106, 2122, 2268, 2278, 2286, 2300, 2349, 3920, 3926, 3928, 3951, 3953], 'Nomoto': [1086], 'Internal': [1088], 'within': [1092, 1190, 3689], 'RNA.J.': [1096], '1992;': [1098], '66:': [1099], '1476-1483Crossref': [1100], 'Host': [1104, 1438, 2250, 2661, 4135], 'peptidases': [1107], 'cleave': [1108], 'form': [1113], '10': [1114, 1378, 3279, 3809], 'mature': [1115, 1322, 1379], 'proteins:': [1117], 'E1,': [1119, 1334], 'E2,': [1120], 'P7,': [1121], 'NS3,': [1123, 1309], 'NS4A,': [1124, 1159], 'NS5B.': [1128], '(NS)': [1131], 'important': [1134, 1302, 2722], 'intracellular': [1137, 1361], 'life': [1138, 1372, 2469, 2735], 'cycle.': [1139, 1373], 'Briefly,': [1140, 3993], 'NS2': [1141], 'serine': [1144, 1171], 'protease': [1145, 1904, 1952, 3291], 'required': [1146, 2443], 'cleavage': [1149], 'NS2–NS3': [1152], 'junction.': [1153], 'NS3': [1154, 3194], 'forms': [1155, 1292], 'this': [1161, 2181], 'possesses': [1163], 'two': [1164, 2613, 3888, 4089, 4100], 'main': [1165], 'enzymes,': [1166], 'ATPase/helicase': [1168], 'protease.': [1172], 'NS4B': [1173, 2168], 'induces': [1174], 'formation': [1176], 'structure,': [1182], 'membranous': [1184, 1205, 1672], 'web,': [1185], 'creates': [1187], 'microdomain': [1189], 'cell': [1192, 2555, 2756, 3296, 3983], 'where': [1193], 'occurs.': [1196], 'NS5A': [1197, 1678], 'phosphoprotein': [1200], 'contributes': [1202], 'web': [1206], 'by': [1207, 1631, 1636, 1775, 1901, 1949, 2362, 2401, 2929, 2955, 3032, 3061, 3067, 3315, 3343, 3366, 3624, 4088], 'inducing': [1208], 'double-membrane': [1209], 'vesicles': [1210], 'controls': [1212], '(5Romero-Brey': [1215], 'Merz': [1217], 'Chiramel': [1219], 'Lee': [1221, 2379], 'J.Y.': [1222], 'Chlanda': [1223], 'P.': [1224, 1236, 1496, 1619, 1751, 1763, 1818, 1822, 2124, 2280, 2337, 3930, 3957, 3969], 'Haselman': [1225], 'U.': [1226, 1743], 'Santarella-Mellwig': [1227], 'R.': [1228, 1242, 1609, 1622, 1706, 1761, 1798, 1826, 2296, 2339, 2341], 'Habermann': [1229], 'Hoppe': [1231], 'Kallis': [1233], 'Walther': [1235], 'Antony': [1237], 'Krijnse-Locker': [1239], 'Bartenschlager': [1241, 1760], 'Three-dimensional': [1243], 'architecture': [1244], 'biogenesis': [1246], 'structures': [1249], 'replication.PLoS': [1255], 'Pathog.': [1256, 1643], '8:': [1258, 1645], 'e1003056Crossref': [1259], '(378)': [1262], 'Last': [1265], 'but': [1266, 2209, 2824], 'least,': [1268], 'RNA-dependent': [1270], 'polymerase': [1272, 1954, 3035], 'generates': [1274], 'negative': [1276], 'strand-template': [1278], '(vRNA)': [1282], 'it': [1286], 'produces': [1287], 'genomic': [1289, 1428, 2240, 2630, 2651], 'strands.': [1290], 'P7': [1291], 'ion': [1294, 3633, 3670, 3694, 3806, 3813, 4000], 'channel': [1295], 'viporin': [1298], 'family': [1299], 'virion': [1304, 1323], 'assembly,': [1305], 'together': [1306], 'NS5A.': [1311, 2922], 'Together': [1312], 'acquired': [1316, 3649, 3702, 3723], 'during': [1317, 2822, 2826], 'release': [1319], 'process,': [1320], 'composed': [1325], 'vRNA': [1328, 1407], 'structural': [1331], 'E2': [1336], '(6Moradpour': [1337], 'D.': [1338], 'Penin': [1339, 2115], 'F.': [1340, 1613, 1698, 2099, 2116, 2378], 'Rice': [1341, 2303], 'C.M.': [1342, 2304], 'Replication': [1343], 'virus.Nat.': [1347], 'Rev.': [1348], 'Microbiol.': [1349], '2007;': [1350, 2318, 2367], '5:': [1351, 1441, 1790, 2253, 2664], '453-463Crossref': [1352], '(1105)': [1355], 'As': [1358, 1869], 'obligatory': [1360], 'parasite,': [1362], 'relies': [1364], 'complete': [1369], 'Furthermore,': [1374], 'encodes': [1376], 'only': [1377, 3880], 'dependence': [1384, 1405], 'steps': [1388], 'co-opted': [1390], 'factors.': [1392], 'Probably': [1393], 'most': [1395, 3637], 'characterized': [1396, 2532], 'example': [1397], 'such': [1399], 'indispensable': [1401], 'phosphatidylinositol-4-kinase': [1410, 1656], 'α': [1411, 1657], '(7Tai': [1412, 2224, 2635], 'A.W.': [1413, 2225, 2636], 'Benita': [1414, 2226, 2637], 'Peng': [1416, 2228, 2639], 'L.F.': [1417, 2229, 2640], 'Kim': [1418, 2230, 2641], 'S.S.': [1419, 2231, 2642], 'Sakamoto': [1420, 2232, 2643], 'Xavier': [1422, 2234, 2430, 2645], 'R.J.': [1423, 2235, 2431, 2646], 'Chung': [1424, 2236, 2647], 'R.T.': [1425, 2237, 2648], 'A': [1426, 1675, 1686, 1710, 1779, 2238, 2436, 2649, 2900, 3573], 'screen': [1429, 2241, 2439, 2652], 'identifies': [1430, 2242, 2653], 'cellular': [1431, 1917, 2067, 2243, 2654], 'replication.Cell': [1437, 2249, 2660], 'Microbe.': [1439, 2251, 2662], '2009;': [1440, 1485, 1555, 1845, 2252, 2453, 2663, 3937], '298-307Abstract': [1442, 2254, 2665], '(370)': [1450, 2262, 2673], 'Scholar,': [1452, 1492, 1562, 1599, 1737, 1796, 2144, 2264, 2325, 2374, 2421, 3949], '8Vaillancourt': [1453], 'F.H.': [1454], 'Pilote': [1455], 'Cartier': [1457], 'Lippens': [1459, 1764], 'Liuzzi': [1461], 'Bethell': [1463], 'R.C.': [1464], 'Cordingley': [1465], 'M.G.': [1466], 'Kukolj': [1467], 'G.': [1468, 1518, 1572, 1757, 1765, 1812, 2097, 2266, 2335, 3967], 'Identification': [1469, 2352, 2391], 'lipid': [1472], 'kinase': [1473], 'as': [1474, 2585, 3151, 3307, 3364, 3839, 3848, 3916, 4072, 4157], 'involved': [1478, 1884, 2356, 2395], 'replication.Virology.': [1484], '387:': [1486], '5-10Crossref': [1487], '(139)': [1490], '9Borawski': [1493], 'Troke': [1495], 'Puyang': [1497], 'X.': [1498, 1741], 'Gibaja': [1499], 'Zhao': [1501], 'Mickanin': [1503], 'Leighton-Davies': [1505], 'Wilson': [1507], 'C.J.': [1508], 'Myer': [1509], 'Cornellataracido': [1511], 'Baryza': [1513], 'Tallarico': [1515], 'Joberty': [1517], 'Bantscheff': [1519], 'Schirle': [1521], 'Bouwmeester': [1523], 'Mathy': [1525], 'J.E.': [1526, 1810], 'Lin': [1527, 1926], 'Compton': [1529], 'Labow': [1531], 'Wiedmann': [1533], 'B.': [1534, 2085], 'Gaither': [1535], 'L.A.': [1536], 'Class': [1537], 'III': [1538, 1580], 'phosphatidylinositol': [1539, 1578, 1582, 1625], '4-kinase': [1540, 1579, 1626], 'alpha': [1541], 'beta': [1543], 'regulators': [1548], 'replication.J.': [1553, 1590], '83:': [1556], '10058-10074Crossref': [1557], '(169)': [1560], '10Berger': [1563], 'K.L.': [1564], 'Kelly': [1565], 'S.M.': [1566, 1941], 'Jordan': [1567], 'T.X.': [1568], 'Tartell': [1569], 'M.A.': [1570], 'Randall': [1571], 'stimulates': [1576], 'alpha-dependent': [1581], '4-phosphate': [1583], 'production': [1584, 2879], 'essential': [1587, 1661, 1713, 1976, 2054], '2011;': [1592], '85:': [1593], '8870-8883Crossref': [1594], '(150)': [1597], '11Bianco': [1600], 'Reghellin': [1602], 'Donnici': [1604], 'Fenu': [1606], 'Alvarez': [1608], 'Baruffa': [1610], 'Peri': [1612], 'Pagani': [1614], 'Abrignani': [1616], 'Neddermann': [1618], 'De': [1620], 'Francesco': [1621], 'Metabolism': [1623], 'IIIalpha-dependent': [1627], 'PI4P': [1628], 'Is': [1629], 'subverted': [1630], '4-anilino': [1638], 'quinazoline': [1639], 'activity.PLoS': [1642], 'e1002576Crossref': [1646], '(103)': [1649], 'enzymatic': [1653], 'activity': [1654], 'cofactor': [1659, 1714], 'through': [1665], 'phosphatidylinositol-4-phosphate': [1669], 'web.': [1673], 'Cyclophilin': [1674, 1709], 'necessary,': [1681], 'targeting': [1684, 2009, 2027], 'cyclophilin': [1685, 1778, 1828], 'currently': [1688], 'being': [1689], 'tested': [1690], 'clinical': [1692], 'trials': [1693], '(12Yang': [1697], 'Robotham': [1699], 'J.M.': [1700], 'Nelson': [1701], 'H.B.': [1702], 'Irsigler': [1703], 'Kenworthy': [1705], 'Tang': [1707], 'H.': [1708, 1824, 1923, 2329], 'principal': [1722], 'mediator': [1723], 'cyclosporine': [1725], 'resistance': [1726, 2023, 2043], 'vitro.J.': [1728], '2008;': [1730, 1956, 2137, 2409], '82:': [1731], '5269-5278Crossref': [1732], '(201)': [1735], '13Coelmont': [1738], 'Hanoulle': [1740], 'Chatterji': [1742], 'Berger': [1744], 'Snoeck': [1746], 'Bobardt': [1748], 'Lim': [1750], 'Vliegen': [1752], 'Paeshuyse': [1754], 'Vuagniaux': [1756], 'Vandamme': [1758], 'A.M.': [1759], 'Gallay': [1762], 'Neyts': [1766], 'DEB025': [1768], '(Alisporivir)': [1769], 'inhibits': [1770], 'preventing': [1776], 'induced': [1780], 'cis-trans': [1781], 'isomerisation': [1782], 'domain': [1784], 'II': [1785], 'NS5A.PLoS': [1787], 'One.': [1788], '2010;': [1789, 2172], 'e13687Crossref': [1791], '(144)': [1794], '14Flisiak': [1797], 'Feinman': [1799], 'S.V.': [1800], 'Jablkowski': [1801], 'Horban': [1803], 'Kryczka': [1805], 'W.': [1806, 2343], 'Pawlowska': [1807], 'Heathcote': [1809], 'Mazzella': [1811], 'Vandelli': [1813], 'Nicolas-Metral': [1815], 'Grosgurin': [1817], 'Liz': [1819], 'J.S.': [1820], 'Scalfaro': [1821], 'Porchet': [1823], 'Crabbe': [1825], 'inhibitor': [1829, 3292], 'Debio': [1830], '025': [1831], 'PEG': [1834], 'IFNalpha2a': [1835], 'significantly': [1836], 'reduces': [1837], 'load': [1839, 2202], 'treatment-naive': [1841], 'patients.Hepatology.': [1844], '49:': [1846], '1460-1468Crossref': [1847], '(217)': [1850], 'Virus': [1853], 'virulence': [1854], 'determinants': [1855], 'interactions': [1861, 1973], 'inhibit': [1863], "host's": [1865], 'system': [1867, 2082, 2182, 3052, 3598], 'defenses.': [1868], 'example,': [1871], 'adaptor': [1873], 'molecules': [1874], 'TIR-domain-containing': [1875], 'adapter-inducing': [1876], 'interferon-β': [1877], '(TRIF)': [1878], 'mitochondrial': [1880], 'antiviral-signaling': [1881], '(MAVS),': [1883], 'Toll-like': [1887], 'receptor': [1888, 1893], '3': [1889, 1910], '(TLR3)': [1890], 'RIG-I-like': [1892], 'pathogen': [1894], 'recognition': [1895], 'signaling': [1896, 1948], 'pathways,': [1897], 'respectively,': [1898], 'block': [1906], 'regulatory': [1908], '(IRF3)–dependent': [1911], 'expression': [1912, 2875, 2908, 2977, 2993, 3079], 'IFNB1': [1914], 'IFN-mediated': [1916], '(15Liang': [1920], 'Ishida': [1922], 'Lenz': [1924], 'O.': [1925, 1929, 3955], 'T.I.': [1927, 2327], 'Nyanguile': [1928], 'Simmen': [1930], 'Pyles': [1932], 'R.B.': [1933], 'Bourne': [1934], 'Yi': [1936], 'Li': [1938], 'Lemon': [1940], 'Antiviral': [1942], 'suppression': [1943], 'vs': [1944], 'restoration': [1945], 'RIG-I': [1947], 'inhibitors.Gastroenterology.': [1955], '135:': [1957], '1710-1718,': [1958], 'e1712Abstract': [1959], '(48)': [1967], 'Thus': [1970], '(PPI)': [1974], 'propagation': [1979], 'strategies': [1982], 'order': [1987], 'be': [1993], 'established.': [1994], 'Because': [1995], 'thought': [1998], 'mutate': [2002], 'rate,': [2006], 'directly': [2008], 'subject': [2017], 'fast': [2020], 'appearance': [2021], 'mutation.': [2024], 'Consequently,': [2025], 'alternative.': [2033], 'Host-targeting': [2034], 'possess': [2037], 'greater': [2039, 4138], 'genetic': [2040, 2438], 'barrier': [2041], 'therapies.': [2047], 'Thus,': [2048], 'unraveling': [2049], 'host–virus': [2051], 'target': [2058, 3745, 3860, 4124], 'better': [2063, 2465], 'understanding': [2064], 'biology.': [2070], 'majority': [2072], 'done': [2077, 3314], 'using': [2078, 2910, 2972, 2995, 3033, 3048, 3098, 3400, 3411, 3421, 3568, 3613, 3728, 3896, 4187, 4217], 'yeast': [2080], 'two-hybrid': [2081], '(16de': [2083], 'Chassey': [2084], 'Navratil': [2086], 'Tafforeau': [2088], 'Hiet': [2090], 'M.S.': [2091], 'Aublin-Gex': [2092], 'Agaugue': [2094], 'Meiffren': [2096], 'Pradezynski': [2098], 'Faria': [2100], 'B.F.': [2101], 'Chantier': [2102], 'Le': [2104], 'Breton': [2105], 'Pellet': [2107], 'Davoust': [2109], 'Mangeot': [2111], 'P.E.': [2112], 'Chaboud': [2113], 'Jacob': [2117], 'Vidalain': [2119], 'P.O.': [2120], 'Vidal': [2121], 'Andre': [2123], 'Rabourdin-Combe': [2125], 'Lotteau': [2127], 'network.Mol.': [2134], 'Syst.': [2135], 'Biol.': [2136, 2407], '4:': [2138], '230Crossref': [2139], '(315)': [2142], '17Tripathi': [2145], 'L.P.': [2146], 'Kataoka': [2147], 'Taguwa': [2149], 'Moriishi': [2151], 'Mori': [2153], 'Matsuura': [2155], 'Mizuguchi': [2157], 'Network': [2159], 'analysis': [2161], 'core': [2166], 'interactions.Mol.': [2170], 'Biosyst.': [2171], '6:': [2173], '2539-2553Crossref': [2174], '(45)': [2177], 'optimal': [2185], 'membrane-bound': [2187], 'those': [2190, 3882], 'HCV.': [2192], 'Genome-wide': [2193], '(RNAi)': [2196], 'yielded': [2200], 'valuable': [2204], 'information': [2205], 'biology,': [2208], 'did': [2212], 'provide': [2214], 'link': [2216], 'products': [2223], '18Randall': [2265], 'Panis': [2267], 'Cooper': [2269], 'J.D.': [2270], 'Tellinghuisen': [2271], 'T.L.': [2272], 'Sukhodolets': [2273], 'K.E.': [2274], 'Pfeffer': [2275], 'Landthaler': [2277], 'Landgraf': [2279], 'Kan': [2281], 'Lindenbach': [2283], 'B.D.': [2284], 'Chien': [2285], 'Weir': [2287], 'D.B.': [2288], 'Russo': [2289], 'J.J.': [2290], 'Ju': [2291], 'Brownstein': [2293], 'M.J.': [2294], 'Sheridan': [2295], 'Sander': [2297], 'Zavolan': [2299], 'Tuschl': [2301], 'Cellular': [2305], 'affecting': [2307], 'replication.Proc.': [2313], 'Natl.': [2314, 2449], 'Acad.': [2315, 2450], 'Sci.': [2316, 2451], 'U.S.A.': [2317, 2452], '104:': [2319], '12884-12889Crossref': [2320], '(476)': [2323], '19Ng': [2326], 'Mo': [2328], 'Pilot-Matias': [2330], 'He': [2332, 2342], 'Koev': [2334], 'Krishnan': [2336], 'Mondal': [2338], 'Pithawalla': [2340], 'Dekhtyar': [2344], 'Packer': [2346], 'Schurdak': [2348], 'Molla': [2350], 'genes': [2355], 'small': [2363, 2402], 'interfering': [2364], 'technology.Hepatology.': [2366], '45:': [2368], '1413-1421Crossref': [2369], '(117)': [2372], '20Supekova': [2375], 'Supek': [2377], 'Chen': [2381], 'Gray': [2383], 'Pezacki': [2385], 'J.P.': [2386], 'Schlapbach': [2387], 'Schultz': [2389], 'P.G.': [2390], 'kinases': [2394], 'library': [2405, 3012], 'screening.J.': [2406], 'Chem.': [2408], '283:': [2410], '29-36Abstract': [2411], '(95)': [2419], '21Li': [2422], 'Q.': [2423], 'Brass': [2424], 'A.L.': [2425], 'Ng': [2426], 'Hu': [2428], 'Z.': [2429], 'Liang': [2432], 'T.J.': [2433], 'Elledge': [2434], 'S.J.': [2435], 'genome-wide': [2437], 'propagation.Proc.': [2448], '106:': [2454], '16410-16415Crossref': [2455], '(309)': [2458], 'In': [2461], 'effort': [2463], 'understand': [2466], 'cycle,': [2470], 'systems': [2474], 'biology': [2475], '(IP)': [2481], 'RNAi': [2491], 'elucidate': [2494], 'interactions.': [2500, 2535], 'From': [2501], '426': [2502], 'detected': [2505], 'IP-MS/MS': [2508], 'NS5B,': [2516], 'statistically': [2518], 'identified,': [2528], 'including': [2529], '24': [2530], 'previously': [2531, 2586, 2627, 3701, 3918], 'further': [2540], 'assessed': [2541], 'lentiviral-based': [2546], '(shRNA)': [2550], 'relevant': [2553], 'models.': [2556], 'approaches': [2563], 'total': [2566], '37': [2568, 2795, 3472, 3495, 3513], 'modulating': [2571], 'provided': [2576, 3686], 'evidence': [2578], 'following': [2581], 'partners': [2584, 2624], 'uncharacterized': [2587], 'cofactors:': [2589], 'HSD17B12': [2590, 3240], '(Core);': [2591], 'EXOC7,': [2592, 3172], 'KPNB1,': [2593, 3192], 'TARDBP,': [2594], 'TNPO1,': [2595], 'MTHFD1': [2597, 3160], '(NS3/4A);': [2598], 'WNK1': [2599], '(NS4B);': [2600], 'BIN1,': [2601], 'EGLN1,': [2602, 3191], 'SMYD3': [2604], '(NS5A);': [2605], 'FKBP5': [2607], '(NS5B).': [2608], 'confirmed': [2611], 'COPB1': [2615], 'RAN': [2617], 'screens': [2631], 'described': [2685, 3365], 'blocks': [2687], 'STAT1,': [2692, 3040, 3174], 'phenotype': [2694], 'reminiscent': [2695], 'obtained': [2699], 'partner': [2704], 'KPNB1.': [2706], 'Overall,': [2707], 'stringency': [2718], 'provides': [2720], 'some': [2725], 'HEK': [2739], '293T': [2740], '(human': [2741, 2745, 2749], 'embryonic': [2742], 'kidney),': [2743], 'Huh7.5': [2744, 2832], 'hepatoma-derived),': [2746], 'Con1b': [2748, 2807], 'hepatoma': [2750], 'containing': [2751, 2936, 3112, 3795], 'subgenomic': [2754], 'replicon)': [2755], 'lines': [2757], 'cultured': [2759], "Dulbecco's": [2761], 'modified': [2762], "Eagle's": [2763], 'medium': [2764], '(DMEM)': [2765], '(Wisent,': [2766], 'St-Bruno,': [2767], 'Québec,': [2768], 'Canada)': [2769, 4200, 4216], 'supplemented': [2770], '10%': [2772, 3577], 'fetal': [2773, 3009], 'bovine': [2774], 'serum,': [2775], '100': [2776, 2779, 3282, 3401, 3566, 3755], 'units/ml': [2777], 'penicillin,': [2778], 'μg/ml': [2780, 2814], 'streptomycin,': [2781], 'mm': [2783, 3280, 3283, 3357, 3360, 3451, 3486, 3546], 'glutamine': [2784], '(all': [2785], 'Wisent),': [2787], '1%': [2789, 3868], 'nonessential': [2790], 'amino': [2791], 'acids': [2792], '(Invitrogen)': [2793], '°C': [2796, 3399, 3433, 3473, 3496], 'atmosphere': [2799], '5%': [2801, 3530, 4146], 'CO2.': [2802], 'Huh7': [2803], 'cells': [2804, 2835, 2843, 2863, 2868, 3270], 'harboring': [2805], 'replicon': [2808], 'submitted': [2810], '500': [2813], 'G418': [2815], 'selection': [2816], 'pressure': [2817], 'maintain': [2819], 'culturing': [2823], 'screening.': [2827], 'screening,': [2829], 'Con1b/Huh7': [2830], '(for': [2833], 'infection)': [2834], 'seeded': [2837, 2865], 'concentration': [2840, 3437, 3464], '5,000': [2842], 'per': [2844, 2869, 3890], '96-well': [2845, 2854], 'plate': [2846], 'white': [2848], 'plates': [2849, 2856], 'assays': [2852], 'black': [2855], 'AlamarBlue': [2858], 'assays.': [2859], 'lentivirus': [2861, 2878], 'production,': [2862], '3,000,000': [2867], '100-mm': [2870], 'dish.': [2871], 'Transfections': [2872], 'or': [2876, 3022, 3057, 3075, 3424, 4090], 'performed': [2881, 3420, 3510, 3612], 'linear': [2883, 3632, 3669], '25-kDa': [2884], 'polyethylenimine': [2885], '(PEI)': [2886], '(Polysciences,': [2887], 'Inc.,': [2888], 'Warrington,': [2889], 'PA)': [2890], '(3': [2891], 'μg': [2892, 2897, 3506], 'PEI': [2894], 'DNA).': [2899], '3xFLAG': [2901, 2931, 3425], 'cassette': [2902, 2932], 'was': [2903, 2915, 3093, 3125, 3149, 3220, 3230, 3241, 3250, 3260, 3313, 3419, 3455, 3487, 3509, 3584, 3599, 3622, 3705, 3801, 3846, 3869, 3907, 4045, 4114, 4165, 4185], 'inserted': [2904], 'pcDNA3.1': [2907, 2934], 'vector': [2909, 2914, 2935, 2994, 3080], 'AflII/AgeI': [2911], 'enzymes.': [2912, 2997], 'clone': [2918], 'cloned': [2928, 2990, 3047], 'inserting': [2930, 2956], 'protein.': [2939, 3891], 'FLAG-tagged': [2940], 'versions': [2941, 2980], '(FLAG-eYFP,': [2946], 'FLAG-HSD17B12,': [2947], 'FLAG-MTHFD1,': [2948], 'FLAG-XPO1,': [2949], 'FLAG-HBxIP,': [2950], 'FLAG-FKBP5)': [2952], 'produced': [2954, 4166], 'PCR': [2958, 3005], 'product': [2959], 'amplified': [2960, 3003], 'commercial': [2963], 'fully': [2964], 'sequenced': [2965], 'cDNA': [2966, 3011], '(Thermo': [2967, 3607], 'Scientific,': [2968], 'Lafayette,': [2969], 'CO,': [2970, 3226], 'USA)': [2971], 'Pfl23II/NotI': [2973], 'enzymes': [2974], 'pcDNA3.1_FLAG-MCS(MB)': [2976], 'vector.': [2978], 'MYC-tagged': [2979], '(MYC-Core,': [2984], 'MYC-NS3/4A,': [2985], 'MYC-NS2,': [2986], 'MYC-NS5B)': [2988], 'pcDNA3.1_MYC-MCS': [2992], 'EcoRV/HindIII': [2996], 'STAT1': [2998], 'ORFs': [3001, 3064], 'brain': [3010], '(OriGene,': [3013], 'Lake': [3014], 'Forest,': [3015], 'CA)': [3016], 'JFH-1': [3019], '(Core,': [3020], 'NS2)': [3021], '1b': [3024], 'genotype': [3025], '(Con1': [3026], 'isolate,': [3027], 'GenBankTM': [3028], 'accession': [3029], 'number': [3030], 'AJ238799)': [3031], 'KOD': [3034], '(EMD': [3036], 'Millipore,': [3037], 'Billerica,': [3038], 'MA).': [3039], 'S139A': [3044, 3092], 'constructs': [3045], 'recombinational': [3050, 3071], 'cloning': [3051, 3072], '(Gateway,': [3053], 'Invitrogen)': [3054], 'pDONR207': [3056, 3074], 'pDONR223.': [3058], 'After': [3059], 'validation': [3060, 3416], 'sequencing,': [3062], 'transferred': [3066], 'means': [3068], 'Gateway': [3070], 'pDONR223': [3076], 'pCI-neo-3xFLAG': [3081], '(3xFLAG': [3082], 'gift': [3085, 3263, 4174], 'Jacob).': [3088], 'mutant': [3090], 'generated': [3094, 4186], 'site-directed': [3096], 'mutagenesis': [3097], 'Quickchange': [3100], 'kit': [3101, 4194], '(Stratagene,': [3102], 'La': [3103], 'Jolla,': [3104], 'CA,': [3105], 'USA).': [3106], 'pISRE-Fluc': [3108], 'cis-reporter': [3109], 'plasmid': [3110, 3132], '(Stratagene)': [3111], '(ISRE)': [3117], 'upstream': [3118, 3141], '(Fluc)': [3123], 'pRL-SV40': [3131, 3136], '(Promega,': [3133], 'Madison,': [3134], 'WI).': [3135], 'contains': [3137], 'SV40': [3139], 'enhancer': [3140], '(Rluc)': [3146], 'control': [3154], 'reporter.': [3155], 'Antibodies': [3156], 'FLAG': [3158, 3423], 'purchased': [3162, 3178, 3196, 3210, 3221, 3231, 3242, 3251], 'Sigma': [3164], '(St-Louis,': [3165], 'MO,': [3166], 'USA,': [3167, 3227], 'F3165': [3168], 'HPA001290);': [3170], 'FKBP5,': [3171], 'MYC,': [3173], 'XPO1': [3176], 'Santa': [3180], 'Cruz': [3181], 'Biotechnology': [3182], '(Dallas,': [3183], 'TX': [3184, 3215], 'sc-13983,': [3185], 'sc-365825,': [3186], 'sc-789,': [3187], 'sc-346,': [3188], 'sc-74454);': [3190], 'Abcam': [3198], '(Toronto,': [3199], 'Ontario,': [3200], 'Canada,': [3201], 'ab4561,': [3202], 'ab7811,': [3203], 'ab13830);': [3205], 'DDX3X': [3206], 'ILF2': [3208], 'Bethyl': [3212], 'Laboratories': [3213], '(Montgomery,': [3214], 'A-300–474A': [3216], 'A303–147A);': [3218], 'ABR-Affinity': [3223], 'Bioreagents': [3224], '(Golden,': [3225], 'MA1–080);': [3228], 'HSP90': [3229], 'Cell': [3233], 'Signaling': [3234], 'Technology,': [3235], 'Inc,': [3236], '(Danvers,': [3237], 'MA': [3238, 3256], '4874);': [3239], 'NovusBiologicals': [3244], '(Littleton,': [3245], 'CO': [3246], 'NBPI-81567);': [3247], 'ACTIN': [3249], 'Chemicon': [3253], 'International': [3254], '(Billerica,': [3255], 'MAB1501R).': [3257], 'TARDBP': [3258], 'antibody': [3259], 'kind': [3262, 4173], 'Vande': [3266], 'Velde.': [3267], 'protein-expressing': [3269], 'washed': [3272, 3371], 'twice': [3273, 3390], 'PBS': [3275], 'lysed': [3277], 'Tris-HCl,': [3281, 3358], 'NaCl,': [3284, 3361], '0.5%': [3285], 'Triton': [3286], 'X-100,': [3287], 'pH': [3288, 3362], '7.6,': [3289], 'mix': [3293], '(Roche).': [3294], 'Resulting': [3295], 'extracts': [3297], 'adjusted': [3299], 'mg/ml': [3302], 'subjected': [3304], 'IP': [3306], 'follows:': [3308], 'preclearing': [3309], 'lysates': [3312, 3317], 'incubating': [3316], '50:50': [3320], 'slurry': [3321], 'immunoglobulin': [3323], 'G-Sepharose': [3324], '(GE': [3325], 'Healthcare)': [3326], 'prepared': [3327, 3352], 'lysis': [3330, 3375], 'buffer': [3331, 3355, 3376], 'IgG': [3333], 'beads': [3334], 'h.': [3339], 'Supernatants': [3340], 'immunoprecipitated': [3342], 'adding': [3344], '40': [3345], 'μl': [3346, 3402, 3448, 3481, 3527, 3537], 'anti-Flag': [3348], 'affinity': [3349], 'gel': [3350], '(Sigma-Aldrich)': [3351, 3434], 'TBS': [3354], '(50': [3356], '150': [3359], '7.4)': [3363], 'manufacturer.': [3368], 'Immunoprecipitates': [3369], 'three': [3372, 3378], 'times': [3373, 3379], 'TBS.': [3381], 'MS/MS': [3383, 3628, 3720, 3759], 'sample': [3384, 3914], 'preparation,': [3385], 'eluted': [3389], 'resin': [3393], '15': [3395, 3690, 3713, 3718, 4022], 'min': [3396, 3430], '4': [3398, 3432], 'NH4OH': [3404], '0.5': [3405, 3817], 'm': [3406], '(pH': [3407], '11.7)': [3408], 'dried': [3410, 3518], 'SpeedVac.': [3413], 'analysis,': [3417], 'elution': [3418], 'purified': [3426, 4207], 'peptide': [3427, 3995, 4036, 4077, 4092], '45': [3429], '250': [3439], 'ng/μl.': [3440], 'Affinity-purified': [3441], 'resuspended': [3445], '50': [3447, 3450, 3526], 'ammonium': [3452], 'bicarbonate.': [3453], 'Tris(2-carboxyethyl)phosphine': [3454], 'added': [3456, 3488], 'samples': [3460, 3491, 3516], 'final': [3463], '5': [3466, 3550], 'mm.': [3467], 'Samples': [3468, 3535], 'incubated': [3470, 3493], '650': [3475, 3498], 'rpm': [3476, 3499], '30': [3478, 3480, 3501], 'min.': [3479, 3502], 'chloroacetamide': [3483], '55': [3485], 'Tryptic': [3503], 'digestion': [3504], '(1': [3505], 'each;': [3507], 'Promega)': [3508], 'overnight': [3511], '°C,': [3514], 'down': [3519], 'SpeedVac': [3522], 'resolubilized': [3524], 'aqueous': [3529], 'acetonitrile': [3531, 3580], '(formic': [3532], 'acid,': [3533], '0.2%).': [3534], '(20': [3536], 'each)': [3538], 'injected': [3540], 'onto': [3541], 'C18': [3543, 3558], 'precolumn': [3544], '(0.3': [3545], 'inner': [3547, 3563], 'diameter': [3548, 3564], '×': [3549, 3565], 'mm),': [3551], 'peptides': [3553, 3588, 3889, 4063], 'separated': [3555], 'analytical': [3559], 'column': [3560], '(150': [3561], 'μm': [3562], 'mm)': [3567], 'Eksigent': [3570], 'nanoLC-2D': [3571], 'system.': [3572], '56-min': [3574], 'gradient': [3575], '60%': [3579], '(0.2%': [3581], 'formic': [3582], 'acid)': [3583], 'elute': [3587], 'flow': [3591], 'rate': [3592, 3845, 3866], '600': [3594], 'nl/min.': [3595], 'LC': [3597], 'LTQ-Orbitrap': [3603], 'Velos': [3604], 'spectrometer': [3606], 'Fisher).': [3608], 'MS': [3609, 3620, 3644, 4013], 'data-dependent': [3614], 'acquisition': [3615], 'each': [3618, 4031, 4106], 'full': [3619], 'spectrum': [3621], 'followed': [3623], 'six': [3625], 'collision-induced': [3626, 3725], 'dissociation': [3627, 3726], 'spectra': [3629, 3645, 3721], 'trap': [3634], 'abundant': [3638], 'multiply': [3639], 'charged': [3640], 'ions.': [3641], 'conventional': [3643], '(survey': [3646], 'scan)': [3647], 'Orbitrap': [3652], 'resolution': [3655], '60,000': [3657], 'm/z': [3659, 3683, 4020], '400': [3660], 'after': [3661], 'accumulation': [3663], '106': [3665], 'ions': [3666, 3704, 3737], 'trap.': [3671], 'Mass': [3672], 'calibration': [3673], 'lock': [3676], 'ambient': [3679], 'air': [3680], '(protonated': [3681], '(Si(CH3)2O)6;': [3682], '445.120029)': [3684], 'accuracy': [3688], 'ppm': [3691, 4023], 'measurements.': [3696], 'dynamic': [3698], 'exclusion': [3699, 3715], 'enabled': [3706], '(repeat': [3707], 'count': [3708], '1,': [3709], 'repeat': [3710], 'duration': [3711, 3716], 's,': [3714], 's).': [3719], 'mode': [3727], 'isolation': [3730], 'window': [3731], 'Da,': [3734, 3818], 'sequentially': [3739], 'isolated': [3740], 'accumulated': [3742], 'value': [3746], '10,000': [3748, 4007], 'maximum': [3751], 'injection': [3752], 'time': [3753, 4026], 'ms.': [3756], 'centroided': [3758], 'data': [3760, 3893, 4015], 'merged': [3762], 'peak-list': [3766], 'file': [3767], '(Distiller,': [3768], 'V2.4.2.0)': [3769], 'searched': [3771, 3802], 'Mascot': [3774, 3800, 3898, 3994], 'search': [3775, 3902], 'engine': [3776], '(version': [3777], '2.2,': [3778], 'Matrix': [3779], 'Science,': [3780], 'London,': [3781], 'UK)': [3782], 'against': [3783], 'concatenated': [3785], 'forward': [3786, 3797], 'reversed': [3788], 'IPI': [3790], 'database': [3791, 3857], '(IPI': [3792], 'v3.54)': [3794], '150,858': [3796], 'sequences.': [3799], 'parent': [3805], 'tolerance': [3807, 3815], 'ppm,': [3810], 'fragment': [3812], 'miscleavage.': [3821], 'Carbamidomethylation': [3822], 'cysteine;': [3824], 'oxidation': [3825], 'methionine;': [3827], 'deamidation;': [3828], 'amd': [3829], 'phosphorylation': [3830], 'serine,': [3832], 'threonine,': [3833], 'tyrosine': [3835], 'residues': [3836], 'specified': [3838], 'variable': [3840], 'modifications.': [3841], 'false': [3843, 3864], 'discovery': [3844, 3865], 'calculated': [3847, 4071], 'percentage': [3850], 'positive': [3852], 'hits': [3853], 'decoy': [3856], 'versus': [3858], 'database,': [3861], 'considered': [3870, 4156], 'both': [3872], 'peptides.': [3875], 'Protein': [3876], 'reported': [3879, 3917], 'assigned': [3883], 'minimum': [3886, 4005], 'processed': [3895], '2.2': [3899], '(Matrix': [3900], 'Science)': [3901], 'engine.': [3903], 'Label-free': [3904], 'quantitative': [3905], 'profile': [3910], 'abundance': [3912], 'across': [3913, 4053, 4060], 'sets,': [3915], '(22Trost': [3919], 'English': [3921], 'Lemieux': [3923], 'Courcelles': [3925], 'Desjardins': [3927], 'Thibault': [3929, 3968], 'phagosomal': [3932], 'proteome': [3933, 3977], 'interferon-gamma-activated': [3935], 'macrophages.Immunity.': [3936], '30:': [3938], '143-154Abstract': [3939], '(180)': [3947], '23Trost': [3950], 'Sauvageau': [3952, 3966], 'Herault': [3954], 'Deleris': [3956], 'Pomies': [3958], 'Chagraoui': [3960], 'Mayotte': [3962], 'Meloche': [3964], 'Posttranslational': [3970], 'regulation': [3971], 'self-renewal': [3973], 'capacity:': [3974], 'insights': [3975], 'phosphoproteome': [3979], 'stem': [3982], 'leukemia.Blood.': [3984], '120:': [3986], 'e17-e27Crossref': [3987], '(19)': [3990], 'identifications': [3996], 'matched': [3998], 'intensity': [4001], '(MS': [4002], 'peak': [4003], 'intensity,': [4004], 'threshold:': [4006], 'counts)': [4008], 'extracted': [4009], 'aligned': [4012], 'raw': [4014], 'files': [4016], '(tolerances': [4017], '=': [4021, 4027], 'retention': [4025], 'min).': [4029], 'LC-MS': [4032], 'run,': [4033], 'normalized': [4035], 'ratios': [4037, 4069], 'so': [4038], 'median': [4041, 4074], 'logarithms': [4044], 'zero,': [4046], 'account': [4048], 'unequal': [4050], 'amounts': [4052], 'conditions': [4054], 'replicates.': [4056], 'Intensities': [4057], 'summed': [4059], 'fractions': [4061], 'identical': [4065], 'sequences,': [4066], 'ratios,': [4078], 'while': [4079], 'minimizing': [4080], 'effect': [4082], 'outliers.': [4084], 'Only': [4085], 'defined': [4087], 'more': [4091, 4098], 'quantification': [4093], 'events': [4094], 'independent': [4101], 'experiments': [4102], 'considered.': [4104], 'protein,': [4109], 'fold': [4111], 'change': [4113], 'determined': [4115], 'ratio': [4118], 'proportion': [4121, 4130], 'average': [4129], 'baits.': [4134], '3-fold': [4140], 'upper': [4145], 'J6/JFH(p7-Rluc2A)': [4163], 'lineated': [4168], 'Xba1': [4169], 'template': [4171], '(a': [4172], 'Rice).': [4177], 'phenol/chloroform': [4179], 'extraction': [4180], 'ethanol': [4182], 'precipitation,': [4183], 'MEGAscript': [4189], 'T7': [4190], 'vitro': [4192], '(Ambion,': [4195], 'Life': [4196], 'Technologies,': [4197], 'Burlington,': [4198], 'ON,': [4199, 4215], 'according': [4201], "manufacturer's": [4204], 'instructions': [4205], 'RNeasy': [4210], 'Mini': [4211], 'Kit': [4212], '(Qiagen,': [4213], 'Toronto,': [4214], 'cleanup': [4220], 'protocol.': [4221], 'electroporat': [4223]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2124927273', 'counts_by_year': [{'year': 2024, 'cited_by_count': 7}, {'year': 2023, 'cited_by_count': 11}, {'year': 2022, 'cited_by_count': 7}, {'year': 2021, 'cited_by_count': 4}, {'year': 2020, 'cited_by_count': 2}, {'year': 2019, 'cited_by_count': 5}, {'year': 2018, 'cited_by_count': 9}, {'year': 2017, 'cited_by_count': 8}, {'year': 2016, 'cited_by_count': 7}, {'year': 2015, 'cited_by_count': 10}, {'year': 2014, 'cited_by_count': 9}], 'updated_date': '2025-01-08T04:04:55.432777', 'created_date': '2016-06-24'}
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