aboutsummaryrefslogtreecommitdiffstats
path: root/skate/testdata/release/cqkm3hyn3rgcng3d3alwtciwpq
blob: 44ff402749529b99bf8530098d0ab82d395b8f02 (plain)
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
{
  "abstracts": [],
  "container_id": "s3gm7274mfe6fcs7e3jterqlri",
  "contribs": [
    {
      "extra": {
        "seq": "first"
      },
      "index": 0,
      "raw_name": "Marc Harper",
      "role": "author"
    },
    {
      "index": 1,
      "raw_name": "Luisa Gronenberg",
      "role": "author"
    },
    {
      "index": 2,
      "raw_name": "James Liao",
      "role": "author"
    },
    {
      "index": 3,
      "raw_name": "Christopher Lee",
      "role": "author"
    },
    {
      "extra": {
        "seq": "first"
      },
      "raw_name": "Mickaël Desvaux",
      "role": "editor"
    }
  ],
  "ext_ids": {
    "core": "44314049",
    "doi": "10.1371/journal.pone.0088072",
    "pmcid": "PMC3935835",
    "pmid": "24586303",
    "wikidata_qid": "Q35106021"
  },
  "extra": {
    "crossref": {
      "license": [
        {
          "URL": "http://creativecommons.org/licenses/by/4.0/",
          "content-version": "unspecified",
          "delay-in-days": 0,
          "start": "2014-02-26T00:00:00Z"
        }
      ],
      "type": "journal-article"
    }
  },
  "ident": "cqkm3hyn3rgcng3d3alwtciwpq",
  "language": "en",
  "license_slug": "CC-BY",
  "pages": "e88072",
  "publisher": "Public Library of Science (PLoS)",
  "refs": [
    {
      "container_name": "Microb Cell Fact",
      "extra": {
        "authors": [
          "JJ Minty"
        ],
        "doi": "10.1186/1475-2859-10-18",
        "volume": "10"
      },
      "index": 0,
      "key": "ref1",
      "locator": "18",
      "title": "Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli",
      "year": 2011
    },
    {
      "extra": {
        "unstructured": "Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, <etal>et al</etal>.. (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Sys Bio 6."
      },
      "index": 1,
      "key": "ref2"
    },
    {
      "extra": {
        "unstructured": "Umland TC, Schultz LW, MacDonald U, Beanan JM, Olson R, <etal>et al</etal>.. (2012) In vivo-validated essential genes identified in Acinetobacter baumannii by using human ascites overlap poorly with essential genes detected on laboratory media. mBio 3."
      },
      "index": 2,
      "key": "ref3"
    },
    {
      "container_name": "Genetics",
      "extra": {
        "authors": [
          "S Sarin"
        ],
        "doi": "10.1534/genetics.110.116319",
        "volume": "185"
      },
      "index": 3,
      "key": "ref4",
      "locator": "417",
      "title": "Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing",
      "year": 2010
    },
    {
      "container_name": "Genetics",
      "extra": {
        "authors": [
          "Y Zhu"
        ],
        "doi": "10.1534/genetics.112.141986",
        "volume": "192"
      },
      "index": 4,
      "key": "ref5",
      "locator": "139",
      "title": "Gene discovery using mutagen-induced polymorphisms and deep sequencing: Application to plant disease resistance",
      "year": 2012
    },
    {
      "container_name": "PloS one",
      "extra": {
        "authors": [
          "MA Harper"
        ],
        "doi": "10.1371/journal.pone.0016517"
      },
      "index": 5,
      "key": "ref6",
      "locator": "e16517",
      "title": "Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants",
      "year": 2011
    },
    {
      "container_name": "PloS one",
      "extra": {
        "authors": [
          "LH Reyes"
        ],
        "doi": "10.1371/journal.pone.0017678"
      },
      "index": 6,
      "key": "ref7",
      "locator": "e17678",
      "title": "Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli",
      "year": 2011
    },
    {
      "container_name": "Genome res",
      "extra": {
        "authors": [
          "Y Erlich"
        ],
        "doi": "10.1101/gr.092957.109",
        "volume": "19"
      },
      "index": 7,
      "key": "ref8",
      "locator": "1243",
      "title": "Dna sudoku - harnessing high- throughput sequencing for multiplexed specimen analysis",
      "year": 2009
    },
    {
      "container_name": "BMC bioinformatics",
      "extra": {
        "authors": [
          "R Emanuele"
        ],
        "doi": "10.1186/1471-2105-13-239",
        "volume": "13"
      },
      "index": 8,
      "key": "ref9",
      "locator": "239",
      "title": "SNP calling by sequencing pooled samples",
      "year": 2012
    },
    {
      "container_name": "Genome res",
      "extra": {
        "authors": [
          "C Honisch"
        ],
        "doi": "10.1101/gr.2977704",
        "volume": "14"
      },
      "index": 9,
      "key": "ref10",
      "locator": "2495",
      "title": "High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12",
      "year": 2004
    },
    {
      "container_name": "PNAS",
      "extra": {
        "authors": [
          "GJ Velicer"
        ],
        "doi": "10.1073/pnas.0510740103",
        "volume": "103"
      },
      "index": 10,
      "key": "ref11",
      "locator": "8107",
      "title": "Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor",
      "year": 2006
    },
    {
      "container_name": "Genome res",
      "extra": {
        "authors": [
          "DR Smith"
        ],
        "doi": "10.1101/gr.077776.108",
        "volume": "18"
      },
      "index": 11,
      "key": "ref12",
      "locator": "1638",
      "title": "Rapid whole-genome mutational profiling using next-generation sequencing technologies",
      "year": 2008
    },
    {
      "container_name": "J bacteriology",
      "extra": {
        "authors": [
          "J Klockgether"
        ],
        "doi": "10.1128/jb.01515-09",
        "volume": "192"
      },
      "index": 12,
      "key": "ref13",
      "locator": "1113",
      "title": "Genome diversity of Pseudomonas aeruginosa pao1 laboratory strains",
      "year": 2010
    },
    {
      "container_name": "App Env microbiology",
      "extra": {
        "authors": [
          "DH Lee"
        ],
        "doi": "10.1128/aem.00373-10",
        "volume": "76"
      },
      "index": 13,
      "key": "ref14",
      "locator": "4158",
      "title": "Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, l-1, 2-propanediol",
      "year": 2010
    },
    {
      "container_name": "PloS one",
      "extra": {
        "authors": [
          "PE Chen"
        ],
        "doi": "10.1371/journal.pone.0012397"
      },
      "index": 14,
      "key": "ref15",
      "locator": "e12397",
      "title": "Rapid identification of ge- netic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing",
      "year": 2010
    },
    {
      "container_name": "Nature genetics",
      "extra": {
        "authors": [
          "CD Herring"
        ],
        "doi": "10.1038/ng1906",
        "volume": "38"
      },
      "index": 15,
      "key": "ref16",
      "locator": "1406",
      "title": "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale",
      "year": 2006
    },
    {
      "container_name": "Genome Biol",
      "extra": {
        "authors": [
          "TM Conrad"
        ],
        "doi": "10.1186/gb-2009-10-10-r118",
        "volume": "10"
      },
      "index": 16,
      "key": "ref17",
      "locator": "R118",
      "title": "Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals exible selection of adaptive mutations",
      "year": 2009
    },
    {
      "container_name": "PLoS genetics",
      "extra": {
        "authors": [
          "A Srivatsan"
        ],
        "doi": "10.1371/journal.pgen.1000139"
      },
      "index": 17,
      "key": "ref18",
      "locator": "e1000139",
      "title": "High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies",
      "year": 2008
    },
    {
      "container_name": "Mutation Res",
      "extra": {
        "authors": [
          "J Ohnishi"
        ],
        "doi": "10.1016/j.mrgentox.2007.10.003",
        "volume": "649"
      },
      "index": 18,
      "key": "ref19",
      "locator": "239",
      "title": "Characterization of mutations induced by N-methyl-N'-nitro-N-nitrosoguanidine in an industrial Corynebacterium glutamicum strain",
      "year": 2008
    },
    {
      "container_name": "PNAS",
      "extra": {
        "authors": [
          "S Le Crom"
        ],
        "doi": "10.1073/pnas.0905848106",
        "volume": "106"
      },
      "index": 19,
      "key": "ref20",
      "locator": "16151",
      "title": "Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel dna sequencing",
      "year": 2009
    },
    {
      "container_name": "App Env microbiology",
      "extra": {
        "authors": [
          "YP Chao"
        ],
        "volume": "59"
      },
      "index": 20,
      "key": "ref21",
      "locator": "4261",
      "title": "Alteration of growth yield by overexpression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase in Escherichia coli",
      "year": 1993
    },
    {
      "container_name": "App Env microbiology",
      "extra": {
        "authors": [
          "P Kim"
        ],
        "doi": "10.1128/aem.70.2.1238-1241.2004",
        "volume": "70"
      },
      "index": 21,
      "key": "ref22",
      "locator": "1238",
      "title": "Effect of overexpression of Actinobacillus suc- cinogenes phosphoenolpyruvate carboxykinase on succinate production in Escherichia coli",
      "year": 2004
    },
    {
      "container_name": "Annals of the NYAS",
      "extra": {
        "authors": [
          "JC Liao"
        ],
        "volume": "745"
      },
      "index": 22,
      "key": "ref23",
      "locator": "21",
      "title": "Alteration of the biochemical valves in the central metabolism of Escherichia colia",
      "year": 1994
    },
    {
      "container_name": "J Bio Chem",
      "extra": {
        "authors": [
          "S Fong"
        ],
        "doi": "10.1074/jbc.m510016200",
        "volume": "281"
      },
      "index": 23,
      "key": "ref24",
      "locator": "8024",
      "title": "Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes",
      "year": 2006
    },
    {
      "container_name": "FEMS microbiology reviews",
      "extra": {
        "authors": [
          "U Sauer"
        ],
        "volume": "29"
      },
      "index": 24,
      "key": "ref25",
      "locator": "765",
      "title": "The pep-pyruvate-oxaloacetate node as the switch point for carbon ux distribution in bacteria",
      "year": 2005
    },
    {
      "container_name": "Biotechnology and bioengineering",
      "extra": {
        "authors": [
          "Y Dharmadi"
        ],
        "doi": "10.1002/bit.21025",
        "volume": "94"
      },
      "index": 25,
      "key": "ref26",
      "locator": "821",
      "title": "Anaerobic fermentation of glycerol by Escherichia coli : a new platform for metabolic engineering",
      "year": 2006
    },
    {
      "container_name": "PNAS",
      "extra": {
        "authors": [
          "X Zhang"
        ],
        "doi": "10.1073/pnas.0905396106",
        "volume": "106"
      },
      "index": 26,
      "key": "ref27",
      "locator": "20180",
      "title": "Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli",
      "year": 2009
    },
    {
      "container_name": "Appl microbiology and biotechnology",
      "extra": {
        "authors": [
          "R Liu"
        ],
        "doi": "10.1007/s00253-012-3896-4",
        "volume": "94"
      },
      "index": 27,
      "key": "ref28",
      "locator": "959",
      "title": "Fermentation of xylose to succinate by enhancement of ATP supply in metabolically engineered Escherichia coli",
      "year": 2012
    },
    {
      "container_name": "Bioprocess and biosystems engineering",
      "extra": {
        "authors": [
          "S Park"
        ],
        "doi": "10.1007/s00449-012-0759-4",
        "volume": "36"
      },
      "index": 28,
      "key": "ref29",
      "locator": "127",
      "title": "Oxaloacetate and malate production in engineered Escherichia coli by expression of codon-optimized phosphoenolpyruvate carboxylase2 gene from Dunaliella salina",
      "year": 2013
    },
    {
      "extra": {
        "doi": "10.1016/j.ymben.2012.07.001",
        "unstructured": "Zhang B, Skory C, Yang S (2012) Metabolic engineering of Rhizopus oryzae: Effects of overex- pressing pyc and pepc genes on fumaric acid biosynthesis from glucose. Metab eng."
      },
      "index": 29,
      "key": "ref30"
    },
    {
      "container_name": "App microbiology and biotechnology",
      "extra": {
        "authors": [
          "HJ Kim"
        ],
        "doi": "10.1007/s00253-011-3779-0",
        "volume": "94"
      },
      "index": 30,
      "key": "ref31",
      "locator": "1079",
      "title": "An engineered Escherichia coli having a high in- tracellular level of ATP and enhanced recombinant protein production",
      "year": 2012
    },
    {
      "extra": {
        "doi": "10.1007/s00253-004-1567-9",
        "unstructured": "Peng L, Shimizu K (2004) Effect of ppc gene knockout on the metabolism of Escherichia coli in view of gene expressions, enzyme activities and intracellular metabolite concentrations. Appl microbiology and biotechnology."
      },
      "index": 31,
      "key": "ref32"
    },
    {
      "container_name": "Angewandte Chemie International Edition in English",
      "extra": {
        "authors": [
          "F Hucho"
        ],
        "doi": "10.1002/anie.197505911",
        "volume": "14"
      },
      "index": 32,
      "key": "ref33",
      "locator": "591",
      "title": "The pyruvate dehydrogenase multienzyme complex",
      "year": 1975
    },
    {
      "container_name": "Nucleic acids res",
      "extra": {
        "authors": [
          "IM Keseler"
        ],
        "doi": "10.1093/nar/gkn751",
        "volume": "37"
      },
      "index": 33,
      "key": "ref34",
      "locator": "D464",
      "title": "Ecocyc: a comprehensive view of Escherichia coli biology",
      "year": 2009
    },
    {
      "container_name": "Nucleic acids res",
      "extra": {
        "authors": [
          "D Nam"
        ],
        "doi": "10.1093/nar/gkq428",
        "volume": "38"
      },
      "index": 34,
      "key": "ref35",
      "locator": "W749",
      "title": "GSA-SNP: a general approach for gene set analysis of polymorphisms",
      "year": 2010
    },
    {
      "container_name": "BMC Sys Bio",
      "extra": {
        "authors": [
          "J Lee"
        ],
        "doi": "10.1186/1752-0509-5-s2-s11"
      },
      "index": 35,
      "key": "ref36",
      "locator": "S11",
      "title": "SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment",
      "year": 2011
    },
    {
      "container_name": "Nature",
      "extra": {
        "authors": [
          "JH McDonald"
        ],
        "doi": "10.1038/351652a0",
        "volume": "351"
      },
      "index": 36,
      "key": "ref37",
      "locator": "652",
      "title": "Adaptive protein evolution at the Adh locus in Drosophila",
      "year": 1991
    },
    {
      "container_name": "Mutation Res",
      "extra": {
        "authors": [
          "M Harper"
        ],
        "doi": "10.1016/j.mrfmmm.2011.10.011",
        "volume": "731"
      },
      "index": 37,
      "key": "ref38",
      "locator": "64",
      "title": "Genome-wide analysis of mutagenesis bias and context sensitivity of n-methyl-n'-nitro-n-nitrosoguanidine (ntg)",
      "year": 2012
    },
    {
      "container_name": "FEMS microbiology letters",
      "extra": {
        "authors": [
          "L Peng"
        ],
        "volume": "235"
      },
      "index": 38,
      "key": "ref39",
      "locator": "17",
      "title": "Metabolic ux analysis for a ppc mutant Escherichia coli based on 13c-labelling experiments together with enzyme activity assays and intracellular metabolite measurements",
      "year": 2004
    },
    {
      "extra": {
        "doi": "10.1111/1574-6968.12109",
        "unstructured": "Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P (2013) Reconciling a salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS microbiology letters."
      },
      "index": 39,
      "key": "ref40"
    },
    {
      "container_name": "J mol microbiology and biotechnology",
      "extra": {
        "authors": [
          "AJ Cozzone"
        ],
        "doi": "10.1159/000089642"
      },
      "index": 40,
      "key": "ref41",
      "locator": "132",
      "title": "Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli",
      "year": 2006
    },
    {
      "container_name": "J bacteriology",
      "extra": {
        "authors": [
          "SR Maloy"
        ],
        "volume": "149"
      },
      "index": 41,
      "key": "ref42",
      "locator": "173",
      "title": "Genetic regulation of the glyoxylate shunt in Escherichia coli K-12",
      "year": 1982
    },
    {
      "container_name": "BMC microbiology",
      "extra": {
        "authors": [
          "H Waegeman"
        ],
        "doi": "10.1186/1471-2180-11-70",
        "volume": "11"
      },
      "index": 42,
      "key": "ref43",
      "locator": "70",
      "title": "Effect of iclr and arca knockouts on biomass formation and metabolic uxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3)",
      "year": 2011
    },
    {
      "container_name": "PNAS",
      "extra": {
        "authors": [
          "R Teufel"
        ],
        "doi": "10.1073/pnas.1005399107",
        "volume": "107"
      },
      "index": 43,
      "key": "ref44",
      "locator": "14390",
      "title": "Bacterial phenylalanine and phenylacetate catabolic pathway revealed",
      "year": 2010
    },
    {
      "container_name": "Microbiology and Mol Bio Rev",
      "extra": {
        "authors": [
          "W Boos"
        ],
        "volume": "62"
      },
      "index": 44,
      "key": "ref45",
      "locator": "204",
      "title": "Maltose/maltodextrin system of Escherichia coli : transport, metabolism, and regulation",
      "year": 1998
    },
    {
      "container_name": "Biotechnology and bioengineering",
      "extra": {
        "authors": [
          "K Jantama"
        ],
        "doi": "10.1002/bit.21694",
        "volume": "99"
      },
      "index": 45,
      "key": "ref46",
      "locator": "1140",
      "title": "Combining metabolic en- gineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate",
      "year": 2008
    },
    {
      "container_name": "Appl Env microbiology",
      "extra": {
        "authors": [
          "R Chatterjee"
        ],
        "doi": "10.1128/aem.67.1.148-154.2001",
        "volume": "67"
      },
      "index": 46,
      "key": "ref47",
      "locator": "148",
      "title": "Mutation of the ptsG gene results in increased production of succinate in fermentation of glucose by Escherichia coli",
      "year": 2001
    },
    {
      "container_name": "Appl Env Microbiology",
      "extra": {
        "authors": [
          "X Zhang"
        ],
        "doi": "10.1128/aem.01758-09",
        "volume": "75"
      },
      "index": 47,
      "key": "ref48",
      "locator": "7807",
      "title": "Reengineering Escherichia coli for succinate production in mineral salts medium",
      "year": 2009
    },
    {
      "extra": {
        "doi": "10.1109/iembs.2006.260828",
        "unstructured": "Fury W, Batliwalla F, Gregersen PK, Li W (2006) Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion. In: Engineering in Medicine and Biology Society, 2006. EMBS'06. 28th Annual International Conference of the IEEE. IEEE, pp. 5531–5534."
      },
      "index": 48,
      "key": "ref49"
    },
    {
      "extra": {
        "unstructured": "Silhavy TJ, Berman ML, Enquist LW (1984) Experiments with gene fusions. Cold Spring Harbor Laboratory Cold Spring Harbor, New York."
      },
      "index": 49,
      "key": "ref50"
    },
    {
      "container_name": "Metabolic engineering",
      "extra": {
        "authors": [
          "S Atsumi"
        ],
        "doi": "10.1016/j.ymben.2007.08.003",
        "volume": "10"
      },
      "index": 50,
      "key": "ref51",
      "locator": "305",
      "title": "Metabolic engineering of Escherichia coli for 1-butanol production",
      "year": 2008
    },
    {
      "extra": {
        "unstructured": "Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, <etal>et al</etal>.. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the keio collection. Mol Sys Bio 2."
      },
      "index": 51,
      "key": "ref52"
    },
    {
      "extra": {
        "unstructured": "Miller JH (1972) Experiments in molecular genetics, volume 60. Cold Spring Harbor Laboratory Cold Spring Harbor, New York."
      },
      "index": 52,
      "key": "ref53"
    },
    {
      "container_name": "Bioinformatics",
      "extra": {
        "authors": [
          "H Li"
        ],
        "doi": "10.1093/bioinformatics/btp352",
        "volume": "25"
      },
      "index": 53,
      "key": "ref54",
      "locator": "2078",
      "title": "The sequence alignment/map format and SAMtools",
      "year": 2009
    },
    {
      "container_name": "SciPy",
      "extra": {
        "authors": [
          "C Lee"
        ]
      },
      "index": 54,
      "key": "ref55",
      "locator": "62",
      "title": "Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase",
      "year": 2009
    },
    {
      "extra": {
        "unstructured": "Jones E, Oliphant T, Peterson P (2001) SciPy: Open source scientific tools for Python. Available: <ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://www.scipy.org/\" xlink:type=\"simple\">http://www.scipy.org/</ext-link>. Accessed 2014 Jan 1."
      },
      "index": 55,
      "key": "ref56"
    },
    {
      "extra": {
        "unstructured": "R Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available: <ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://www.R-project.org\" xlink:type=\"simple\">http://www.R-project.org</ext-link>. ISBN 3-900051-07-0."
      },
      "index": 56,
      "key": "ref57"
    },
    {
      "extra": {
        "doi": "10.1007/978-0-387-21822-9",
        "unstructured": "Ewens W (2004) Mathematical population genetics: I. Theoretical introduction, volume 27. Springer."
      },
      "index": 57,
      "key": "ref58"
    },
    {
      "extra": {
        "unstructured": "Cover TM, Thomas JA (2012) Elements of information theory. Wiley-interscience."
      },
      "index": 58,
      "key": "ref59"
    },
    {
      "container_name": "FEMS microbiology letters",
      "extra": {
        "authors": [
          "L Peng"
        ],
        "doi": "10.1111/j.1574-6968.2004.tb09562.x",
        "volume": "235"
      },
      "index": 59,
      "key": "ref60",
      "locator": "17",
      "title": "Metabolic ux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements",
      "year": 2006
    }
  ],
  "release_date": "2014-02-26",
  "release_stage": "published",
  "release_type": "article-journal",
  "release_year": 2014,
  "revision": "cb5ba2a2-f669-4669-be42-8109c0c835f3",
  "state": "active",
  "title": "Comprehensive Detection of Genes Causing a Phenotype Using Phenotype Sequencing and Pathway Analysis",
  "work_id": "a5fegh5iyrfwpc32y33envrime"
}