[171cba]: / papers / qbib.bib

Download this file

1312 lines (1174 with data), 41.8 kB

   1
   2
   3
   4
   5
   6
   7
   8
   9
  10
  11
  12
  13
  14
  15
  16
  17
  18
  19
  20
  21
  22
  23
  24
  25
  26
  27
  28
  29
  30
  31
  32
  33
  34
  35
  36
  37
  38
  39
  40
  41
  42
  43
  44
  45
  46
  47
  48
  49
  50
  51
  52
  53
  54
  55
  56
  57
  58
  59
  60
  61
  62
  63
  64
  65
  66
  67
  68
  69
  70
  71
  72
  73
  74
  75
  76
  77
  78
  79
  80
  81
  82
  83
  84
  85
  86
  87
  88
  89
  90
  91
  92
  93
  94
  95
  96
  97
  98
  99
 100
 101
 102
 103
 104
 105
 106
 107
 108
 109
 110
 111
 112
 113
 114
 115
 116
 117
 118
 119
 120
 121
 122
 123
 124
 125
 126
 127
 128
 129
 130
 131
 132
 133
 134
 135
 136
 137
 138
 139
 140
 141
 142
 143
 144
 145
 146
 147
 148
 149
 150
 151
 152
 153
 154
 155
 156
 157
 158
 159
 160
 161
 162
 163
 164
 165
 166
 167
 168
 169
 170
 171
 172
 173
 174
 175
 176
 177
 178
 179
 180
 181
 182
 183
 184
 185
 186
 187
 188
 189
 190
 191
 192
 193
 194
 195
 196
 197
 198
 199
 200
 201
 202
 203
 204
 205
 206
 207
 208
 209
 210
 211
 212
 213
 214
 215
 216
 217
 218
 219
 220
 221
 222
 223
 224
 225
 226
 227
 228
 229
 230
 231
 232
 233
 234
 235
 236
 237
 238
 239
 240
 241
 242
 243
 244
 245
 246
 247
 248
 249
 250
 251
 252
 253
 254
 255
 256
 257
 258
 259
 260
 261
 262
 263
 264
 265
 266
 267
 268
 269
 270
 271
 272
 273
 274
 275
 276
 277
 278
 279
 280
 281
 282
 283
 284
 285
 286
 287
 288
 289
 290
 291
 292
 293
 294
 295
 296
 297
 298
 299
 300
 301
 302
 303
 304
 305
 306
 307
 308
 309
 310
 311
 312
 313
 314
 315
 316
 317
 318
 319
 320
 321
 322
 323
 324
 325
 326
 327
 328
 329
 330
 331
 332
 333
 334
 335
 336
 337
 338
 339
 340
 341
 342
 343
 344
 345
 346
 347
 348
 349
 350
 351
 352
 353
 354
 355
 356
 357
 358
 359
 360
 361
 362
 363
 364
 365
 366
 367
 368
 369
 370
 371
 372
 373
 374
 375
 376
 377
 378
 379
 380
 381
 382
 383
 384
 385
 386
 387
 388
 389
 390
 391
 392
 393
 394
 395
 396
 397
 398
 399
 400
 401
 402
 403
 404
 405
 406
 407
 408
 409
 410
 411
 412
 413
 414
 415
 416
 417
 418
 419
 420
 421
 422
 423
 424
 425
 426
 427
 428
 429
 430
 431
 432
 433
 434
 435
 436
 437
 438
 439
 440
 441
 442
 443
 444
 445
 446
 447
 448
 449
 450
 451
 452
 453
 454
 455
 456
 457
 458
 459
 460
 461
 462
 463
 464
 465
 466
 467
 468
 469
 470
 471
 472
 473
 474
 475
 476
 477
 478
 479
 480
 481
 482
 483
 484
 485
 486
 487
 488
 489
 490
 491
 492
 493
 494
 495
 496
 497
 498
 499
 500
 501
 502
 503
 504
 505
 506
 507
 508
 509
 510
 511
 512
 513
 514
 515
 516
 517
 518
 519
 520
 521
 522
 523
 524
 525
 526
 527
 528
 529
 530
 531
 532
 533
 534
 535
 536
 537
 538
 539
 540
 541
 542
 543
 544
 545
 546
 547
 548
 549
 550
 551
 552
 553
 554
 555
 556
 557
 558
 559
 560
 561
 562
 563
 564
 565
 566
 567
 568
 569
 570
 571
 572
 573
 574
 575
 576
 577
 578
 579
 580
 581
 582
 583
 584
 585
 586
 587
 588
 589
 590
 591
 592
 593
 594
 595
 596
 597
 598
 599
 600
 601
 602
 603
 604
 605
 606
 607
 608
 609
 610
 611
 612
 613
 614
 615
 616
 617
 618
 619
 620
 621
 622
 623
 624
 625
 626
 627
 628
 629
 630
 631
 632
 633
 634
 635
 636
 637
 638
 639
 640
 641
 642
 643
 644
 645
 646
 647
 648
 649
 650
 651
 652
 653
 654
 655
 656
 657
 658
 659
 660
 661
 662
 663
 664
 665
 666
 667
 668
 669
 670
 671
 672
 673
 674
 675
 676
 677
 678
 679
 680
 681
 682
 683
 684
 685
 686
 687
 688
 689
 690
 691
 692
 693
 694
 695
 696
 697
 698
 699
 700
 701
 702
 703
 704
 705
 706
 707
 708
 709
 710
 711
 712
 713
 714
 715
 716
 717
 718
 719
 720
 721
 722
 723
 724
 725
 726
 727
 728
 729
 730
 731
 732
 733
 734
 735
 736
 737
 738
 739
 740
 741
 742
 743
 744
 745
 746
 747
 748
 749
 750
 751
 752
 753
 754
 755
 756
 757
 758
 759
 760
 761
 762
 763
 764
 765
 766
 767
 768
 769
 770
 771
 772
 773
 774
 775
 776
 777
 778
 779
 780
 781
 782
 783
 784
 785
 786
 787
 788
 789
 790
 791
 792
 793
 794
 795
 796
 797
 798
 799
 800
 801
 802
 803
 804
 805
 806
 807
 808
 809
 810
 811
 812
 813
 814
 815
 816
 817
 818
 819
 820
 821
 822
 823
 824
 825
 826
 827
 828
 829
 830
 831
 832
 833
 834
 835
 836
 837
 838
 839
 840
 841
 842
 843
 844
 845
 846
 847
 848
 849
 850
 851
 852
 853
 854
 855
 856
 857
 858
 859
 860
 861
 862
 863
 864
 865
 866
 867
 868
 869
 870
 871
 872
 873
 874
 875
 876
 877
 878
 879
 880
 881
 882
 883
 884
 885
 886
 887
 888
 889
 890
 891
 892
 893
 894
 895
 896
 897
 898
 899
 900
 901
 902
 903
 904
 905
 906
 907
 908
 909
 910
 911
 912
 913
 914
 915
 916
 917
 918
 919
 920
 921
 922
 923
 924
 925
 926
 927
 928
 929
 930
 931
 932
 933
 934
 935
 936
 937
 938
 939
 940
 941
 942
 943
 944
 945
 946
 947
 948
 949
 950
 951
 952
 953
 954
 955
 956
 957
 958
 959
 960
 961
 962
 963
 964
 965
 966
 967
 968
 969
 970
 971
 972
 973
 974
 975
 976
 977
 978
 979
 980
 981
 982
 983
 984
 985
 986
 987
 988
 989
 990
 991
 992
 993
 994
 995
 996
 997
 998
 999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
%% Created using Papers on Tue, 02 Sep 2014.
%% http://papersapp.com/papers/
@article{Dougherty:2001wr,
author = {Dougherty, G},
title = {{A comparison of the texture of computed tomography and projection radiography images of vertebral trabecular bone using fractal signature and lacunarity}},
journal = {Medical Engineering {\&} Physics},
year = {2001},
volume = {23},
number = {5},
pages = {313--321},
month = jun
}
@inproceedings{Silla:gz,
author = {Silla, Carlos N and Kaestner, Celso A A},
title = {{Hierarchical Classification of Bird Species Using Their Audio Recorded Songs}},
booktitle = {2013 IEEE International Conference on Systems, Man and Cybernetics (SMC 2013)},
pages = {1895--1900},
publisher = {IEEE}
}
@article{Williams:2013uz,
author = {Williams, S and Grenfell, Bryan T},
title = {{Host Species Barriers to Influenza Virus Infections}},
year = {2013},
volume = {312},
number = {5772},
pages = {394--397}
}
@article{Schenzle:1984uj,
author = {Schenzle, Dieter},
title = {{An Age-Structured Model of Pre- and Post-Vaccination Measles Transmission}},
journal = {IMA Journal of Mathematics Applied in Medicine and Biology},
year = {1984},
volume = {1},
pages = {169--191}
}
@article{Grenfell:1999td,
author = {Grenfell, B T and Courchamp, F and Clutton-Brock, T},
title = {{Inverse density dependence and the Allee effect.}},
journal = {Trends in ecology {\&} evolution},
year = {1999},
volume = {14},
number = {10},
pages = {405--410}
}
@article{Keeling:1998tg,
author = {Keeling, M J and Grenfell, B T},
title = {{Effect of variability in infection period on the persistence and spatial spread of infectious diseases.}},
journal = {Mathematical biosciences},
year = {1998},
volume = {147},
number = {2},
pages = {207--226},
month = jan
}
@article{Balakrishnan:2014jx,
author = {Balakrishnan, Rohini and Bahuleyan, Jimmy and Nandi, Diptarup and Jain, Manjari},
title = {{Modelling the effects of chorus species composition and caller density on acoustic masking interference in multispecies choruses of crickets and katydids}},
journal = {Ecological Informatics},
year = {2014},
volume = {21},
pages = {50--58},
month = may
}
@inproceedings{Lopes:hn,
author = {Lopes, Marcelo T and Gioppo, Lucas L and Higushi, Thiago T and Kaestner, Celso A A and Silla Jr, Carlos N and Koerich, Alessandro L},
title = {{Automatic Bird Species Identification for Large Number of Species}},
booktitle = {2011 IEEE International Symposium on Multimedia (ISM)},
pages = {117--122},
publisher = {IEEE}
}
@article{Restif:2006bq,
author = {Restif, O and Grenfell, B T and Grenfell, Bryan T},
title = {{Integrating life history and cross-immunity into the evolutionary dynamics of pathogens}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2006},
volume = {273},
number = {1585},
pages = {409--416},
month = feb
}
@article{Holmes:2009gy,
author = {Holmes, Edward C and Grenfell, Bryan T},
title = {{Discovering the Phylodynamics of RNA Viruses}},
journal = {PLoS Computational Biology},
year = {2009},
volume = {5},
number = {10},
pages = {e1000505},
month = oct
}
@article{Boyll:2001uq,
author = {Bo{\"y}ll, Pau and Zibulevsky, Michael},
title = {{Underdetermined blind source separation using sparse representations}},
year = {2001},
volume = {81},
pages = {2353--2362}
}
@article{Bansal:2007ct,
author = {Bansal, S and Grenfell, B T and Grenfell, Bryan T and Meyers, Lauren Ancel and Bansal, Shweta and Meyers, L A},
title = {{When individual behaviour matters: homogeneous and network models in epidemiology}},
journal = {Journal of The Royal Society Interface},
year = {2007},
volume = {4},
number = {16},
pages = {879--891},
month = oct
}
@article{Graham:2010ih,
author = {Graham, Andrea L and Hayward, Adam D and Watt, Kathryn A and Pilkington, Jill G and Pemberton, Josephine M and Nussey, Daniel H},
title = {{Fitness correlates of heritable variation in antibody responsiveness in a wild mammal.}},
journal = {Science},
year = {2010},
volume = {330},
number = {6004},
pages = {662--665},
month = oct
}
@article{Lee:2000ty,
author = {Lee, J Y and Bowden, D S},
title = {{Rubella virus replication and links to teratogenicity.}},
journal = {Clinical microbiology reviews},
year = {2000},
volume = {13},
number = {4},
pages = {571--587},
month = oct
}
@article{Cliff:1983wq,
author = {Cliff, Andrew D and Haggett, Peter and Graham, Rosemary},
title = {{Reconstruction of diffusion processes at local scales: the 1846, 1882, and 1904 measles epidemics in northwest Iceland}},
year = {1983},
volume = {9},
number = {4},
pages = {347--368}
}
@article{Black:1966wd,
author = {Black, F L},
title = {{Measles endemicity in insular populations: critical community size and its evolutionary implication.}},
year = {1966},
volume = {11},
number = {2},
pages = {207--211}
}
@article{Volz:2009eo,
author = {Volz, E M and Kosakovsky Pond, S L and Ward, M J and Leigh Brown, A J and Frost, S D W},
title = {{Phylodynamics of Infectious Disease Epidemics}},
journal = {Genetics},
year = {2009},
volume = {183},
number = {4},
pages = {1421--1430},
month = dec
}
@article{Nussey:2014ft,
author = {Nussey, Daniel H and Watt, Kathryn A and Clark, Abigail and Pilkington, Jill G and Pemberton, Josephine M and Graham, Andrea L and McNeilly, Tom N},
title = {{Multivariate immune defences and fitness in the wild: complex but ecologically important associations among plasma antibodies, health and survival.}},
journal = {Proceedings. Biological sciences / The Royal Society},
year = {2014},
volume = {281},
number = {1779},
pages = {20132931--20132931},
month = mar
}
@article{Roweis:2S-b5PMP,
author = {Roweis, Sam T},
title = {{One Microphone Source Separation}}
}
@article{Pedregosa:2011tv,
author = {Pedregosa, Fabian and Varoquaux, Gaeel and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Edouard},
title = {{Scikit-learn: Machine Learning in Python}},
journal = {Journal of Machine Learning Research},
year = {2011},
volume = {12},
pages = {2825--2830},
month = oct
}
@article{Hensley:2009fq,
author = {Hensley, S E and Das, S R and Bailey, A L and Schmidt, L M and Hickman, H D and Jayaraman, A and Viswanathan, K and Raman, R and Sasisekharan, R and Bennink, J R and Yewdell, J W},
title = {{Hemagglutinin Receptor Binding Avidity Drives Influenza A Virus Antigenic Drift}},
journal = {Science},
year = {2009},
volume = {326},
number = {5953},
pages = {734--736},
month = oct
}
@article{VanBoeckel:2014bl,
author = {Van Boeckel, Thomas P and Gandra, Sumanth and Ashok, Ashvin and Caudron, Quentin and Grenfell, Bryan T and Levin, Simon A and Laxminarayan, Ramanan},
title = {{Global antibiotic consumption 2000 to 2010: an analysis of national pharmaceutical sales data.}},
journal = {The Lancet. Infectious diseases},
year = {2014},
volume = {14},
number = {8},
pages = {742--750},
month = aug
}
@article{Cooper:2006il,
author = {Cooper, Ben S and Pitman, Richard J and Edmunds, W John and Gay, Nigel J},
title = {{Delaying the International Spread of Pandemic Influenza}},
journal = {PLoS Medicine},
year = {2006},
volume = {3},
number = {6},
pages = {e212}
}
@article{Xia:2004bo,
author = {Xia, Yingcun and Bj{\o}rnstad, Ottar N and Grenfell, Bryan T},
title = {{Measles metapopulation dynamics: a gravity model for epidemiological coupling and dynamics.}},
journal = {The American naturalist},
year = {2004},
volume = {164},
number = {2},
pages = {267--281},
month = aug
}
@article{Ionides:2011hs,
author = {Ionides, Edward L and Bhadra, Anindya and Atchade, Yves and King, Aaron},
title = {{Iterated Filtering}},
journal = {Annals of Statistics},
year = {2011},
volume = {39},
number = {3},
pages = {1776--1802},
month = jun
}
@article{Finkenstadt:2000kr,
author = {Finkenst{\"a}dt, B F and Grenfell, B T},
title = {{Time series modelling of childhood diseases: a dynamical systems approach}},
journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
year = {2000},
volume = {49},
number = {2},
pages = {187--205}
}
@article{Schaffer:2007ji,
author = {Schaffer, W M and Bronnikova, T V},
title = {{Parametric dependence in model epidemics. I: Contact-related parameters}},
journal = {Journal of Biological Dynamics},
year = {2007},
volume = {1},
number = {2},
pages = {183--195},
month = apr
}
@article{DeAssisZampirolli:nmz4dbRg,
author = {De Assis Zampirolli, Francisco and Stransky, Beatriz and Lorena, Ana Carolina},
title = {{Segmentation and classification of histological images - application of graph analysis and machine learning methods}}
}
@article{Schaffer:2007cz,
author = {Bronnikova, T V and Schaffer, W M},
title = {{Parametric dependence in model epidemics. II: Non-contact rate-related parameters}},
journal = {Journal of Biological Dynamics},
year = {2007},
volume = {1},
number = {3},
pages = {231--248},
month = jul
}
@article{Grenfell:2004ho,
author = {Grenfell, B T and Wood, James L N and Grenfell, Bryan T and Gog, Julia R and Daly, Janet M and Pybus, Oliver G and Holmes, Edward C},
title = {{Unifying the Epidemiological and Evolutionary Dynamics of Pathogens}},
journal = {Science},
year = {2004},
volume = {303},
number = {5656},
pages = {327--332},
month = jan
}
@article{Gouy:2010jv,
author = {Gouy, Manolo and Guindon, St{\'e}phane and Gascuel, Olivier},
title = {{SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.}},
journal = {Molecular Biology and Evolution},
year = {2010},
volume = {27},
number = {2},
pages = {221--224},
month = feb
}
@article{Grenfell:2002wb,
author = {Grenfell, B T and Bjornstad, O N and Finkenst{\"a}dt, B F},
title = {{Dynamics of measles epidemics: scaling noise, determinism, and predictability with the TSIR model}},
journal = {Ecological Monographs},
year = {2002},
volume = {72},
number = {2},
pages = {185--202}
}
@article{Cheng:2012cy,
author = {Cheng, Jinkui and Xie, Bengui and Lin, Congtian and Ji, Liqiang},
title = {{A comparative study in birds: call-type-independent species and individual recognition using four machine-learning methods and two acoustic features}},
journal = {Bioacoustics},
year = {2012},
volume = {21},
number = {2},
pages = {157--171},
month = jun
}
@article{Cliff:2004cj,
author = {Cliff, A and Haggett, Peter},
title = {{Time, travel and infection}},
journal = {British Medical Bulletin},
year = {2004},
volume = {69},
number = {1},
pages = {87--99},
month = dec
}
@article{Gurcan:2009io,
author = {Gurcan, M N and Boucheron, L and Can, A and Madabhushi, A and Rajpoor, N and Yener, B},
title = {{Histopathological Image Analysis: A Review}},
journal = {IEEE Rev Biomed Eng},
year = {2009},
volume = {2},
pages = {147--171}
}
@article{Dougherty:2002vd,
author = {Dougherty, G and Henebry, G M},
title = {{Lacunarity analysis of spatial pattern in CT images of vertebral trabecular bone for assessing osteoporosis}},
journal = {Medical Engineering {\&} Physics},
year = {2002},
volume = {24},
number = {2},
pages = {129--138},
month = mar
}
@article{Ruifrok:2001vb,
author = {Ruifrok, A C and Johnston, D A},
title = {{Quantification of Histochemical Staining by Color Deconvolution}},
journal = {Analytical and Quantitative Cytology and Histology},
year = {2001},
volume = {23},
number = {4},
pages = {291--299}
}
@article{Caudron:2012vn,
author = {Caudron, Q},
title = {{Neuronal computation on complex dendritic morphologies}},
year = {2012}
}
@article{Rhodes:1996vi,
author = {Rhodes, C J and Anderson, R M},
title = {{A scaling analysis of measles epidemics in a small population}},
journal = {Philosophical Transactions: Biological Sciences},
year = {1996},
volume = {351},
number = {1348},
pages = {1679--1688}
}
@article{Fagerlund:2007fx,
author = {Fagerlund, Seppo},
title = {{Bird Species Recognition Using Support Vector Machines}},
journal = {EURASIP Journal on Advances in Signal Processing},
year = {2007},
volume = {2007},
number = {1},
pages = {038637}
}
@article{Lee:cv,
author = {Lee, Chang-Hsing and Hsu, Sheng-Bin and Shih, Jau-Ling and Chou, Chih-Hsun},
title = {{Continuous Birdsong Recognition Using Gaussian Mixture Modeling of Image Shape Features}},
journal = {IEEE Transactions on Multimedia},
volume = {15},
number = {2},
pages = {454--464}
}
@article{Wang:2000tj,
author = {Wang, Avery Li-chun and Street, Kensington High},
title = {{An Industrial-Strength Audio Search Algorithm}},
year = {2000}
}
@article{KEELING:2000bq,
author = {KEELING, MATT J and Grenfell, Bryan T and Grenfell, B T},
title = {{Individual-based Perspectives on R0}},
journal = {Journal of Theoretical Biology},
year = {2000},
volume = {203},
number = {1},
pages = {51--61},
month = mar
}
@article{Chatfield:SQo1tvTP,
author = {Chatfield, C},
title = {{The Analysis of Time Series}}
}
@article{Compeau:2011gl,
author = {Compeau, Phillip E C and Pevzner, Pavel A and Tesler, Glenn},
title = {{How to apply de Bruijn graphs to genome assembly}},
journal = {Nature Biotechnology},
year = {2011},
volume = {29},
number = {11},
pages = {987--991},
month = nov
}
@article{Gray:2009fo,
author = {Gray, R R and Tatem, A J and Lamers, S and Hou, W and Laeyendecker, O and Serwadda, D and Sewankambo, N and Gray, R H and Wawer, M and Quinn, T C and Goodenow, M M and Salemi, M},
title = {{Spatial phylodynamics of HIV-1 epidemic emergence in east Africa}},
journal = {AIDS},
year = {2009},
volume = {23},
number = {14},
pages = {1--14}
}
@article{BARTELS:1988tk,
author = {BARTELS, P H and WEBER, J E and DUCKSTEIN, L},
title = {{Machine Learning in Quantitative Histopathology}},
journal = {Analytical and Quantitative Cytology and Histology},
year = {1988},
volume = {10},
number = {4},
pages = {299--306},
month = aug
}
@article{XinQi:cq,
author = {Xin Qi and Fuyong Xing and Foran, D J and Lin Yang},
title = {{Robust Segmentation of Overlapping Cells in Histopathology Specimens Using Parallel Seed Detection and Repulsive Level Set}},
journal = {IEEE Transactions on Biomedical Engineering},
volume = {59},
number = {3},
pages = {754--765}
}
@article{Schaffer:1985tx,
author = {Schaffer, W M and Kot, M},
title = {{Nearly one dimensional dynamics in an epidemic.}},
year = {1985},
volume = {112},
number = {2},
pages = {403--427}
}
@article{Gupta:1998ui,
author = {Gupta, S and Ferguson, N and Anderson, R},
title = {{Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents.}},
journal = {Science (New York, N.Y.)},
year = {1998},
volume = {280},
number = {5365},
pages = {912--915}
}
@article{GarciaRojo:2009bw,
author = {Garcia Rojo, Marcial and Bueno, Gloria and Slodkowska, Janina},
title = {{Review of imaging solutions for integrated quantitative immunohistochemistry in the Pathology daily practice}},
journal = {Folia Histochemica Et Cytobiologica},
year = {2009},
volume = {47},
number = {3},
pages = {349--354}
}
@article{Taelman:2010wg,
author = {Taelman, Joachim and Van Huffel, Sabine},
title = {{Source Separation From Single-Channel Recordings by Combining Empirical-Mode Decomposition and}},
year = {2010},
volume = {57},
number = {9},
pages = {2188--2196}
}
@article{Holmes:2005ci,
author = {Holmes, Edward C and Taubenberger, Jeffery K and Lipman, David J and Ghedin, Elodie and Grenfell, Bryan T and Taylor, Jill and George, Kirsten St and Miller, Naomi and Bao, Yiming and St George, Kirsten and Salzberg, Steven L and Fraser, Claire M},
title = {{Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses}},
journal = {PLoS Biology},
year = {2005},
volume = {3},
number = {9},
pages = {e300}
}
@article{Taylor:XwXcgtQM,
author = {Taylor, Kantapon Kaewtip Lee Ngee Tan Abeer Alwan Charles E},
title = {{A ROBUST AUTOMATIC BIRD PHRASE CLASSIFIER USING DYNAMIC TIME-WARPING WITH PROMINENT REGION IDENTIFICATION}}
}
@inproceedings{Chen:kd,
author = {Chen, Sha-Sha and Li, Ying},
title = {{Automatic Recognition of Bird Songs Using Time-Frequency Texture}},
booktitle = {2013 5th International Conference on Computational Intelligence and Communication Networks (CICN)},
pages = {262--266},
publisher = {IEEE}
}
@article{Goyette:2011jc,
author = {Goyette, Jennifer L and Howe, Robert W and Wolf, Amy T and Robinson, W Douglas},
title = {{Detecting tropical nocturnal birds using automated audio recordings}},
journal = {Journal of Field Ornithology},
year = {2011},
volume = {82},
number = {3},
pages = {279--287}
}
@article{Tidd:1993ka,
author = {Tidd, C W and Olsen, L F and Schaffer, W M},
title = {{The Case for Chaos in Childhood Epidemics. II. Predicting Historical Epidemics from Mathematical Models}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {1993},
volume = {254},
number = {1341},
pages = {257--273},
month = dec
}
@article{Mossong:2008kk,
author = {Mossong, Jo{\"e}l and Hens, Niel and Edmunds, W John and Jit, Mark and Beutels, Philippe and Auranen, Kari and Mikolajczyk, Rafael and Massari, Marco and Salmaso, Stefania and Tomba, Gianpaolo Scalia and Wallinga, Jacco and Heijne, Janneke and Sadkowska-Todys, Malgorzata and Rosinska, Magdalena},
title = {{Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases}},
journal = {PLoS Medicine},
year = {2008},
volume = {5},
number = {3},
pages = {e74}
}
@article{Bansal:2010iq,
author = {Bansal, Shweta and Pourbohloul, Babak and Grenfell, Bryan and Hupert, Nathaniel and Meyers, Lauren Ancel},
title = {{The Shifting Demographic Landscape of Pandemic Influenza}},
journal = {PLoS ONE},
year = {2010},
volume = {5},
number = {2},
pages = {e9360},
month = feb
}
@article{Breto:2009dc,
author = {Breto, Carles and He, Daihai and Ionides, Edward L and King, Aaron A},
title = {{Time Series Analysis via Mechanistic Models}},
journal = {Annals of Applied Statistics},
year = {2009},
volume = {3},
number = {1},
pages = {319--348},
month = mar
}
@article{Acevedo:2009cj,
author = {Acevedo, Miguel A and Corrada-Bravo, Carlos J and Corrada-Bravo, H{\'e}ctor and Villanueva-Rivera, Luis J and Aide, T Mitchell},
title = {{Automated classification of bird and amphibian calls using machine learning: A comparison of methods}},
journal = {Ecological Informatics},
year = {2009},
volume = {4},
number = {4},
pages = {206--214},
month = sep
}
@article{Greenbaum:2008ki,
author = {Greenbaum, Benjamin D and Levine, Arnold J and Bhanot, Gyan and Rabadan, Raul},
title = {{Patterns of evolution and host gene mimicry in influenza and other RNA viruses}},
journal = {PLoS Pathogens},
year = {2008},
volume = {4},
number = {6},
month = jun
}
@article{Plotnick:1993vi,
author = {Plotnick, R E and Gardner, R H and O'Neill, R V},
title = {{Lacunarity indices as measures of landscape texture}},
journal = {Landscape ecology},
year = {1993}
}
@article{Goto:2013jo,
author = {Goto, Kensuke and Kumarendran, Balachandran and Mettananda, Sachith and Gunasekara, Deepa and Fujii, Yoshito and Kaneko, Satoshi},
title = {{Analysis of Effects of Meteorological Factors on Dengue Incidence in Sri Lanka Using Time Series Data}},
journal = {PLoS ONE},
year = {2013},
volume = {8},
number = {5},
pages = {e63717},
month = may
}
@article{Plotnick:1996wf,
author = {Plotnick, R E and Gardner, R H and Hargrove, W W},
title = {{Lacunarity analysis: a general technique for the analysis of spatial patterns}},
journal = {Physical review E},
year = {1996}
}
@article{Voss:2013iz,
author = {Voss, Andreas and Nagler, Markus and Lerche, Veronika},
title = {{Diffusion Models in Experimental Psychology}},
journal = {Experimental Psychology (formerly Zeitschrift f{\"u}r Experimentelle Psychologie)},
year = {2013},
volume = {60},
number = {6},
pages = {385--402},
month = jul
}
@article{Nelson:2006bx,
author = {Nelson, Martha I and Simonsen, Lone and Miller, Mark a and Taubenberger, Jeffery K and Viboud, C{\'e}cile and Grenfell, Bryan T and Holmes, Edward C and Taylor, Jill and George, Kirsten St and Griesemer, Sara B and Ghedin, Elodie and Sengamalay, Naomi a and Spiro, David J and Volkov, Igor and Lipman, David J},
title = {{Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus}},
journal = {PLoS Pathogens},
year = {2006},
volume = {2},
number = {12},
pages = {e125}
}
@article{Cazelles:2007ic,
author = {Cazelles, Bernard and Chavez, Mario and Constantin de Magny, Guillaume and Gu{\'e}gan, Jean-Francois and Hales, Simon},
title = {{Time-dependent spectral analysis of epidemiological time-series with wavelets}},
journal = {Journal of The Royal Society Interface},
year = {2007},
volume = {4},
number = {15},
pages = {625--636},
month = feb
}
@article{Ross:2014iu,
author = {Ross, Jesse C and Allen, Paul E},
title = {{Random Forest for improved analysis efficiency in passive acoustic monitoring}},
journal = {Ecological Informatics},
year = {2014},
volume = {21},
pages = {34--39},
month = may
}
@article{NELDER:1965tk,
author = {NELDER, J A and MEAD, R},
title = {{A Simplex-Method for Function Minimization}},
journal = {Computer Journal},
year = {1965},
volume = {7},
number = {4},
pages = {308--313}
}
@article{Smith:2004vg,
author = {Smith, Derek J and Lapedes, Alan S and De Jong, Jan C},
title = {{Mapping the Antigenic and Genetic Evolution of Influenza Virus}},
year = {2004},
volume = {305},
number = {July},
pages = {371--376}
}
@article{Untitled:EoBSZ3zo,
title = {{Danmarks Statistik}}
}
@article{Camacho:2011ig,
author = {Camacho, A and Ballesteros, S and Graham, A L and Carrat, F and Ratmann, O and Cazelles, B},
title = {{Explaining rapid reinfections in multiple-wave influenza outbreaks: Tristan da Cunha 1971 epidemic as a case study}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {2011},
volume = {278},
number = {1725},
pages = {3635--3643},
month = nov
}
@article{Ionides:2006fu,
author = {Ionides, E L and Bret{\'o}, C and King, A A},
title = {{Inference for nonlinear dynamical systems.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2006},
volume = {103},
number = {49},
pages = {18438--18443},
month = dec
}
@article{Belsare:2012kx,
author = {Belsare, A D},
title = {{Histopathological Image Analysis Using Image Processing Techniques: An Overview}},
journal = {Signal {\&} Image Processing : An International Journal},
year = {2012},
volume = {3},
number = {4},
pages = {23--36},
month = aug
}
@article{Dureau:2012vb,
author = {Dureau, Joseph and Kalogeropoulos, Konstantinos},
title = {{Capturing the time-varying drivers of an epidemic using stochastic dynamical systems}},
journal = {arXiv},
year = {2012}
}
@article{Untitled:JsFzT1NI,
title = {{Statistics Iceland}}
}
@article{Caudron:2012hi,
author = {Caudron, Quentin and Donnelly, Simon R and Brand, Samuel Pc and Timofeeva, Yulia},
title = {{Computational convergence of the path integral for real dendritic morphologies.}},
journal = {Journal of mathematical neuroscience},
year = {2012},
volume = {2},
number = {1},
pages = {11}
}
@article{Haggett:1981ub,
author = {Haggett, P and Cliff, A D and Ord, J K and Versey, G R},
title = {{Spatial Diffusion: An Historical Geography of Epidemics in an Island Community}},
journal = {Cambridge University Press},
year = {1981},
volume = {16},
number = {02}
}
@article{Fraser:2009ek,
author = {Fraser, C and Donnelly, C A and Fraser, Christophe and Ferguson, Neil M and Cauchemez, S and Hanage, W P and Van Kerkhove, M D and Hollingsworth, T D and Griffin, J and Baggaley, R F and Jenkins, H E and Lyons, E J and Jombart, T and Hinsley, W R and Grassly, N C and Balloux, F and Ghani, A C and Ferguson, N M and Rambaut, A and Pybus, O G and Lopez-Gatell, H and Alpuche-Aranda, C M and Chapela, I B and Zavala, E P and Guevara, D Ma E and Checchi, F and Garcia, E and Hugonnet, S and Roth, C and {The WHO Rapid Pandemic Assessment Collaboration}},
title = {{Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings}},
journal = {Science},
year = {2009},
volume = {324},
number = {5934},
pages = {1557--1561},
month = jun
}
@article{Aide:2013jg,
author = {Aide, T Mitchell and Corrada-bravo, Carlos and Campos-Cerqueira, Marconi and Milan, Carlos and Vega, Giovany and Alvarez, Rafael},
title = {{Real-time bioacoustics monitoring and automated species identification}},
journal = {PeerJ},
year = {2013},
volume = {1},
pages = {e103}
}
@article{Alizon:2010iv,
author = {Alizon, Samuel and von Wyl, Viktor and Stadler, Tanja and Kouyos, Roger D and Yerly, Sabine and Hirschel, Bernard and B{\"o}ni, J{\"u}rg and Shah, Cyril and Klimkait, Thomas and Furrer, Hansjakob and Rauch, Andri and Pietro L Vernazza and Bernasconi, Enos and Battegay, Manuel and B{\"u}rgisser, Philippe and Telenti, Amalio and G{\"u}nthard, Huldrych F and Bonhoeffer, Sebastian and Study, the Swiss HIV Cohort},
title = {{Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load}},
journal = {PLoS Pathogens},
year = {2010},
volume = {6},
number = {9},
pages = {e1001123},
month = sep
}
@article{Grenfell:2004iv,
author = {Grenfell, B T and Hallett, T B and Coulson, T and Pilkington, J G and Pemberton, J M},
title = {{Why large-scale climate indices seem to predict ecological processes better than local weather}},
journal = {Nature Letters},
year = {2004},
volume = {430},
pages = {71--75}
}
@article{Cregger:2006db,
author = {Cregger, M and Berger, A J and Rimm, D L},
title = {{Immunohistochemistry and quantitative analysis of protein expression}},
journal = {Archives of pathology {\&} {\ldots}},
year = {2006}
}
@article{Jenkins:2003hy,
author = {Jenkins, G M and Holmes, E C},
title = {{The extent of codon usage bias in human RNA viruses and its evolutionary origin}},
journal = {Virus Research},
year = {2003},
volume = {92},
number = {1},
pages = {1--7},
month = mar
}
@article{Sanjuan:2012cb,
author = {Sanju{\'a}n, Rafael},
title = {{From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses}},
journal = {PLoS Pathogens},
year = {2012},
volume = {8},
number = {5},
pages = {e1002685},
month = may
}
@article{Alwan:QaMbv9GZ,
author = {Alwan, Wei Chu Abeer},
title = {{A Correlation-Maximization Denoising Filter Used as An Enhancement Frontend for Noise Robust Bird Call Classification}}
}
@article{Grenfell:2001co,
author = {Grenfell, B T and Bjornstad, O N and Kappey, J},
title = {{Travelling waves and spatial hierarchies in measles epidemics}},
journal = {Nature},
year = {2001},
volume = {414},
number = {6865},
pages = {716--723},
month = dec
}
@article{Klein:2003vt,
author = {Klein, David J and K{\"o}nig, Peter and K{\"o}rding, Konrad P},
title = {{Sparse Spectrotemporal Coding of Sounds}},
year = {2003},
volume = {2003},
number = {7},
pages = {659--667}
}
@inproceedings{Kiapuchinski:en,
author = {Kiapuchinski, Davi Miara and Lima, Carlos Raimundo Erig and Kaestner, Celso Antonio Alves},
title = {{Spectral Noise Gate Technique Applied to Birdsong Preprocessing on Embedded Unit}},
booktitle = {2012 IEEE International Symposium on Multimedia (ISM)},
pages = {24--27},
publisher = {IEEE}
}
@article{Diamond:2004ea,
author = {Diamond, J and Anderson, N H and BARTELS, P H and Montironi, R},
title = {{The use of morphological characteristics and texture analysis in the identification of tissue composition in prostatic neoplasia}},
journal = {Human Pathology},
year = {2004}
}
@article{ManikkaBaduge:2009cp,
author = {Manikka-Baduge, Dantha C and Dougherty, Geoff},
title = {{Texture analysis using lacunarity and average local variance}},
journal = {SPIE Medical Imaging},
year = {2009},
volume = {7259},
pages = {725953--725953--12},
month = feb
}
@article{Sankar:2014eo,
author = {Sankar, Martial and Nieminen, Kaisa and Ragni, Laura and Xenarios, Ioannis and Hardtke, Christian S},
title = {{Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth}},
journal = {Elife},
year = {2014},
volume = {3}
}
@article{Finkelman:2007kg,
author = {Finkelman, Brian S and Grenfell, Bryan T and Viboud, C{\'e}cile and Koelle, Katia and Ferrari, Matthew J and Bharti, Nita},
title = {{Global Patterns in Seasonal Activity of Influenza A/H3N2, A/H1N1, and B from 1997 to 2005: Viral Coexistence and Latitudinal Gradients}},
journal = {PLoS ONE},
year = {2007},
volume = {2},
number = {12},
pages = {e1296},
month = dec
}
@article{Ruifrok:2001vba,
author = {Ruifrok, A C and Johnston, D A},
title = {{Quantification of histochemical staining by color deconvolution}},
journal = {Analytical and Quantitative Cytology and Histology},
year = {2001},
volume = {23},
number = {4},
pages = {291--299},
month = aug
}
@article{Science:1995tr,
author = {Science, Analytical},
title = {{Definition and Application of a Fourier Domain Texture Measure: Applications to Histological Image Segmentation}},
journal = {Comput. Biol. Med.},
year = {1995},
volume = {25},
number = {6},
pages = {551--557}
}
@article{Mitchell:1978eu,
author = {Mitchell, O R and Carlton, S G},
title = {{Image segmentation using a local extrema texture measure}},
journal = {Pattern Recognition},
year = {1978},
volume = {10},
number = {3},
pages = {205--210},
month = jan
}
@article{Koelle:2013wq,
author = {Koelle, Katia and Grenfell, Bryan and Cobey, Sarah and Pascual, Mercedes},
title = {{Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans}},
year = {2013},
volume = {314},
number = {5807},
pages = {1898--1903}
}
@article{Qin:2012wt,
author = {Qin, Yujie},
title = {{Texture-based Tissue Segmentation in histological Images Texture-based Tissue Segmentation in histological Images Supervisors :}},
year = {2012}
}
@inproceedings{Souza:gs,
author = {Souza, Vinicius M A de and Silva, Diego F and Batista, Gustavo E A P A},
title = {{Classification of Data Streams Applied to Insect Recognition: Initial Results}},
booktitle = {2013 Brazilian Conference on Intelligent Systems (BRACIS)},
pages = {76--81},
publisher = {IEEE}
}
@article{Dougherty:2001vn,
author = {Dougherty, G and Henebry, G M},
title = {{Fractal signature and lacunarity in the measurement of the texture of trabecular bone in clinical CT images}},
journal = {Medical Engineering {\&} Physics},
year = {2001},
volume = {23},
number = {6},
pages = {369--380},
month = jul
}
@article{Cliff:1983tc,
author = {Cliff, A D and Haggett, P and Graham, R},
title = {{Reconstruction of diffusion processes at different geographical scales: the 1904 measles epidemic in northwest Iceland}},
journal = {Journal of Historical Geography},
year = {1983},
volume = {9},
number = {1},
pages = {29--46}
}
@article{Sievers:2011fn,
author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S{\"o}ding, Johannes and Thompson, Julie D and Higgins, Desmond G},
title = {{Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.}},
journal = {Molecular systems biology},
year = {2011},
volume = {7},
number = {1},
pages = {539--539}
}
@article{Simonsen:2007hb,
author = {Simonsen, L and Viboud, C{\'e}cile and Viboud, C and Grenfell, Bryan T and Miller, Mark a and Simonsen, Lone and Holmes, Edward C and Grenfell, B T and Dushoff, J and Jennings, L and Smit, M and Macken, C and Hata, M and Gog, J and Miller, M A and Holmes, E C},
title = {{The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {8},
pages = {1811--1820},
month = apr
}
@article{Murcia:2010hn,
author = {Murcia, P R and McCauley, John W and Grenfell, Bryan T and Wood, James L N and Holmes, Edward C and Baillie, G J and Daly, J and Elton, D and Jervis, C and Mumford, J A and Newton, R and Parrish, C R and Hoelzer, K and Dougan, G and Parkhill, J and Lennard, N and Ormond, D and Moule, S and Whitwham, A and McCauley, J W and McKinley, T J and Holmes, E C and Grenfell, B T and Wood, J L N},
title = {{Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus}},
journal = {Journal of Virology},
year = {2010},
volume = {84},
number = {14},
pages = {6943--6954},
month = jun
}
@article{Recker:2007jl,
author = {Recker, M and Pybus, Oliver G and Pybus, O G and Nee, S and Gupta, S},
title = {{The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types}},
journal = {Proceedings of the National Academy of Sciences},
year = {2007},
volume = {104},
number = {18},
pages = {7711--7716},
month = may
}
@article{Anonymous:2008bm,
title = {{Velvet: algorithms for de novo short read assembly using de Bruijn graphs.}},
journal = {Genome research},
year = {2008},
volume = {18},
number = {5},
pages = {821--829},
month = may
}
@article{Park:2009jp,
author = {Park, A W and Daly, J M and Grenfell, Bryan T and Daly, Janet M and Wood, James L N and Smith, Derek J and Lewis, N S and Smith, D J and Wood, J L N and Grenfell, B T},
title = {{Quantifying the Impact of Immune Escape on Transmission Dynamics of Influenza}},
journal = {Science},
year = {2009},
volume = {326},
number = {5953},
pages = {726--728},
month = oct
}
@article{CAUDRON:2013wl,
author = {CAUDRON, Quentin and Lyn-Adams, Ceri and Aston, John A D and Frenguelli, Bruno G and Moffat, Kevin G},
title = {{Quantitative assessment of ommatidial distortion in Drosophila melanogaster.}},
journal = {Drosophila Information Service},
year = {2013},
volume = {96},
pages = {136--143},
month = dec
}
@article{HOLTE:1993gs,
author = {HOLTE, R C},
title = {{Very Simple Classification Rules Perform Well on Most Commonly Used Datasets}},
journal = {Machine Learning},
year = {1993},
volume = {11},
number = {1},
pages = {63--91},
month = apr
}
@article{Taubenberger:2010fn,
author = {Taubenberger, Jeffery K and Kash, John C},
title = {{Influenza Virus Evolution, Host Adaptation, and Pandemic Formation}},
journal = {Cell Host {\&} Microbe},
year = {2010},
volume = {7},
number = {6},
pages = {440--451},
month = jun
}
@article{Cai:2010fb,
author = {Cai, Zhipeng and Zhang, Tong and Wan, Xiu-Feng},
title = {{A Computational Framework for Influenza Antigenic Cartography}},
journal = {PLoS Computational Biology},
year = {2010},
volume = {6},
number = {10},
pages = {e1000949},
month = oct
}
@article{Glass:2003kr,
author = {Glass, K and Grenfell, B T and Xia, Y},
title = {{Interpreting time-series analyses for continuous-time biological models{\textemdash}measles as a case study}},
journal = {Journal of Theoretical Biology},
year = {2003},
volume = {223},
number = {1},
pages = {19--25},
month = jul
}
@article{Bjornstad:2002ua,
author = {Bjornstad, O N and Grenfell, B T and Finkenst{\"a}dt, B F},
title = {{Dynamics of measles epidemics: estimating scaling of transmission rates using a time series SIR model}},
journal = {Ecological Monographs},
year = {2002},
volume = {72},
number = {2},
pages = {169--184}
}
@article{Arinaminpathy:2012ez,
author = {Arinaminpathy, N and Ratmann, Oliver and Viboud, C{\'e}cile and Koelle, Katia and Arinaminpathy, Nimalan and Ratmann, O and Grenfell, Bryan T and Koelle, K and Epstein, S L and Price, G E and Viboud, C and Miller, M A and Grenfell, B T},
title = {{Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza}},
journal = {Proceedings of the National Academy of Sciences},
year = {2012},
volume = {109},
number = {8},
pages = {3173--3177},
month = feb
}
@article{Saenz:2010go,
author = {Saenz, R A and Grenfell, Bryan T and Quinlivan, M and Elton, D and MacRae, S and Blunden, A S and Mumford, J A and Daly, J M and Digard, P and Cullinane, A and Grenfell, B T and McCauley, J W and Wood, J L N and Gog, J R},
title = {{Dynamics of Influenza Virus Infection and Pathology}},
journal = {Journal of Virology},
year = {2010},
volume = {84},
number = {8},
pages = {3974--3983},
month = mar
}
@article{Earn:2013vl,
author = {Earn, David J D and Rohani, Pejman and Bolker, Benjamin M and Grenfell, Bryan T},
title = {{A Simple Model for Complex Dynamical Transitions in Epidemics}},
journal = {Science},
year = {2013},
volume = {287},
number = {5453},
pages = {667--670}
}
@article{Kothari:2013ep,
author = {Kothari, Sonal and Phan, John H and Stokes, Todd H and Wang, May D},
title = {{Pathology imaging informatics for quantitative analysis of whole-slide images}},
journal = {Journal of the American Medical Informatics Association},
year = {2013},
volume = {20},
number = {6},
pages = {1099--1108},
month = nov
}
@article{Bardeli:2010ch,
author = {Bardeli, R and Wolff, D and Kurth, F and Koch, M and Tauchert, K H and Frommolt, K H},
title = {{Detecting bird sounds in a complex acoustic environment and application to bioacoustic monitoring}},
journal = {Pattern Recognition Letters},
year = {2010},
volume = {31},
number = {12},
pages = {1524--1534},
month = sep
}
@article{Briggs:2013wv,
author = {Briggs, Forrest},
title = {{Multi-instance multi-label learning : algorithms and applications to bird bioacoustics}},
year = {2013}
}
@article{He:2010jp,
author = {He, Daihai and Ionides, Edward L and King, Aaron A},
title = {{Plug-and-play inference for disease dynamics: measles in large and small populations as a case study.}},
journal = {Journal of the Royal Society, Interface / the Royal Society},
year = {2010},
volume = {7},
number = {43},
pages = {271--283},
month = feb
}
@article{Gulland:1992uw,
author = {Gulland, F M},
title = {{The role of nematode parasites in Soay sheep (Ovis aries L.) mortality during a population crash.}},
journal = {Parasitology},
year = {1992},
volume = {105 ( Pt 3)},
pages = {493--503},
month = dec
}
@phdthesis{Fuchs:2011tw,
author = {Fuchs, Thomas J},
title = {{Computational Pathology}},
year = {2011},
address = {Zurich, Switzerland},
month = jun
}
@article{Bolker:1993gs,
author = {Bolker, B M and Grenfell, B T},
title = {{Chaos and Biological Complexity in Measles Dynamics}},
journal = {Proceedings of the Royal Society B: Biological Sciences},
year = {1993},
volume = {251},
number = {1330},
pages = {75--81},
month = jan
}
@article{Belalov:2013bf,
author = {Belalov, Ilya S and Lukashev, Alexander N},
title = {{Causes and Implications of Codon Usage Bias in RNA Viruses}},
journal = {PLoS ONE},
year = {2013},
volume = {8},
number = {2}
}
@article{Torrence:1995wk,
author = {Torrence, Christopher and Compo, Gilbert P},
title = {{A Practical Guide to Wavelet Analysis}},
year = {1995}
}
@article{Olsen:1990wu,
author = {Olsen, L F and Schaffer, W M},
title = {{Chaos Versus Noisy Periodicity: Alternative Hypotheses for Childhood Epidemics}},
year = {1990},
volume = {249},
pages = {499--504}
}
@article{Taylor:IRxWLWS8,
author = {Taylor, Tan Kossan Cody},
title = {{A SPARSE REPRESENTATION-BASED CLASSIFIER FOR IN-SET BIRD PHRASE VERIFICATION AND CLASSIFICATION WITH LIMITED TRAINING DATA}}
}
@article{Wallace:2007td,
author = {Wallace, Robert G and Hodac, Hoangminh and Lathrop, Richard H and Fitch, Walter M},
title = {{A statistical phylogeography of influenza A H5N1 The geographic diffusion of highly pathogenic influenza A H5N1 has largely been traced from the perspective of the virus {\textquoteright} s victims . Birds of a variety of avian orders have been sampled across localities }},
year = {2007},
volume = {104},
number = {11}
}
@article{Volz:2013ff,
author = {Volz, Erik M and Koelle, Katia and Bedford, Trevor},
title = {{Viral Phylodynamics}},
journal = {PLoS Computational Biology},
year = {2013},
volume = {9},
number = {3},
pages = {e1002947},
month = mar
}
@article{Olsen:1988uj,
author = {Olsen, L F and Truty, G L and Schaffer, W M},
title = {{Oscillations and chaos in epidemics: a nonlinear dynamic study of six childhood diseases in Copenhagen, Denmark.}},
journal = {Theoretical population biology},
year = {1988},
volume = {33},
number = {3},
pages = {344--370},
month = jun
}
@article{Arinaminpathy:2010fr,
author = {Arinaminpathy, Nimalan and Grenfell, Bryan},
title = {{Dynamics of Glycoprotein Charge in the Evolutionary History of Human Influenza}},
journal = {PLoS ONE},
year = {2010},
volume = {5},
number = {12},
pages = {e15674},
month = dec
}
@article{Dureau:2013cb,
author = {Dureau, Joseph and Kalogeropoulos, Konstantinos and Baguelin, Marc},
title = {{Capturing the time-varying drivers of an epidemic using stochastic dynamical systems}},
journal = {Biostatistics},
year = {2013},
volume = {14},
number = {3},
pages = {541--555},
month = jul
}
@article{Shaman:2010ey,
author = {Shaman, Jeffrey and Pitzer, Virginia E and Grenfell, Bryan T and Viboud, C{\'e}cile and Lipsitch, Marc},
title = {{Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States}},
journal = {PLoS Biology},
year = {2010},
volume = {8},
number = {2},
pages = {e1000316},
month = feb
}
@article{Viboud:2006jw,
author = {Viboud, C{\'e}cile and Bj{\o}rnstad, Ottar N and Smith, David L and Simonsen, Lone and Miller, Mark a and Grenfell, Bryan T},
title = {{Synchrony, waves, and spatial hierarchies in the spread of influenza.}},
journal = {Science},
year = {2006},
volume = {312},
number = {5772},
pages = {447--451},
month = apr
}
@article{Abernathy:2013hc,
author = {Abernathy, Emily and Chen, Min-hsin and Bera, Jayati and Shrivastava, Susmita and Kirkness, Ewen and Zheng, Qi and Bellini, William and Icenogle, Joseph},
title = {{Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961-2009}},
journal = {Virology Journal},
year = {2013},
volume = {10},
number = {1}
}