24:
167:
Once tools are developed and validated, the Center disseminates data and software throughout the
University and the broader biomedical research community. Various mechanisms such as training videos, tutorials, and demonstrations and presentations at prominent scientific conferences are used to share
143:
The Center develops computational methods to effectively access and integrate biological data. Driving
Biological Projects (DBPs) provide a starting point from which tool development is informed, launched, and tested. Current DBPs include
140:. NCIBI's mission is to create targeted knowledge environments for molecular biomedical research to help guide experiments and enable new insights from the analysis of complex diseases. It was established in October 2005.
137:
222:
data. It uses the data from
Edinburgh Human Metabolic Network reconstruction. MetScape facilitates visualization of complex networks and displays related information about
202:
gene set enrichment testing and concept mapping tool. This web-based tool can be used both to identify biological gene sets (called concepts) enriched with differentially
873:
858:
88:
60:
67:
176:
In addition to the tools listed below, the enriched data contained in many NCIBI databases is available from the
Databases tab on the Try Our Tools page.
74:
45:
38:
56:
324:
206:(or any other user-identified gene list), and to explore networks of relationships among biological concepts from diverse biological sources
523:
Gao, J.; Tarcea, V. G.; Karnovsky, A.; Mirel, B. R.; Weymouth, T. E.; Beecher, C. W.; Cavalcoli, J. D.; Athey, B. D.; Omenn, G. S. (2010).
343:
A literature exploration tool that provides new ways to explore relationships among anatomical structures, pathophysiological processes,
474:
Sartor, M. A.; Mahavisno, V.; Keshamouni, V. G.; Cavalcoli, J.; Wright, Z.; Karnovsky, A.; Kuick, R.; Jagadish, H.V.; Mirel, B. (2009).
125:
81:
853:
311:
A tool that uses a statistical approach to reliably and automatically annotate metabolites with the concepts defined in MeSH, the
868:
863:
621:
Tarcea, V. G.; Weymouth, T.; Ade, A.; Bookvich, A.; Gao, J.; Mahavisno, V.; Wright, Z.; Chapman, A.; Jayapandian, M. (2009).
525:"Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks"
107:
348:
247:
774:
Shannon, P.; Markiel, A; Ozier, O; Baliga, NS; Wang, JT; Ramage, D; Amin, N; Schwikowski, B; Ideker, T (2003).
129:
719:
Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Song, Jean; Athey, Brian; Watson, Stanley J; Meng, Fan (2009).
312:
296:
572:
Gao, J.; Ade, A. S.; Tarcea, V. G.; Weymouth, T. E.; Mirel, B. R.; Jagadish, H.V.; States, D. J. (2008).
368:
295:
An automated annotation tool that associates
Medical Subject Heading (MeSH) terms with genes using the
287:
A tool that renders the contents of large biomedical document collections into a single, dynamic map
34:
388:
133:
776:"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks"
8:
848:
440:
747:
720:
696:
671:
647:
622:
598:
573:
549:
524:
500:
475:
800:
775:
160:. In addition to testing tools for function, a separate team is dedicated to testing
843:
805:
752:
701:
652:
603:
554:
505:
451:
223:
687:
589:
540:
491:
795:
787:
742:
732:
691:
683:
642:
634:
593:
585:
544:
536:
495:
487:
462:
259:
157:
344:
203:
670:
States, D. J.; Ade, A. S.; Wright, Z. C.; Bookvich, A. V.; Athey, B. D. (2009).
574:"Integrating and annotating the interactome using the MiMI plugin for cytoscape"
737:
383:
837:
407:
809:
756:
705:
656:
623:"Michigan molecular interactions r2: from interacting proteins to pathways"
607:
558:
509:
638:
243:
219:
199:
145:
791:
364:
476:"ConceptGen: a gene set enrichment and gene set relation mapping tool"
429:
335:
citations and display them ranked by relevancy to research interests
239:
215:
161:
418:
23:
371:
to help researchers explore literature from different perspectives
149:
473:
132:'s (NIH) Roadmap for Medical Research. The center is based at the
352:
227:
153:
824:
National Center for
Integrative Biomedical Informatics homepage
332:
328:
300:
408:
773:
620:
828:
823:
168:
NCIBI data and software nationally and internationally.
57:"National Center for Integrative Biomedical Informatics"
669:
522:
122:
363:
A literature exploration tool that provides multiple
721:"Open Biomedical Ontology-based Medline exploration"
571:
138:
874:Medical and health organizations based in Michigan
419:National Centers for Biomedical Computing, Summary
268:
148:in cancers, major organ-specific complications of
315:'s controlled vocabulary for biomedical concepts
859:Medical research institutes in the United States
835:
718:
325:National Center for Biotechnology Information
323:A literature search tool that works with the
246:interactive visualization tool for analyzing
799:
746:
736:
695:
646:
597:
548:
499:
126:National Centers for Biomedical Computing
108:Learn how and when to remove this message
156:, and co-morbid disease associations of
255:Michigan Molecular Interactions (MiMI)
179:
836:
672:"MiSearch adaptive pubMed search tool"
44:Please improve this article by adding
218:plugin used to visualize and analyze
17:
13:
171:
14:
885:
817:
355:literature and experimental data
258:A web based protein, pathway and
22:
854:Research institutes in Michigan
712:
663:
614:
269:Conceptual literature searching
565:
516:
467:
456:
445:
434:
423:
412:
401:
1:
869:National Institutes of Health
767:
688:10.1093/bioinformatics/btn033
590:10.1093/bioinformatics/btn501
541:10.1093/bioinformatics/btq048
492:10.1093/bioinformatics/btp683
250:and their biological effects
130:National Institutes of Health
46:secondary or tertiary sources
864:Bioinformatics organizations
349:protein–protein interactions
313:National Library of Medicine
297:National Library of Medicine
7:
377:
10:
890:
738:10.1186/1471-2105-10-S5-S6
633:(Database issue): D642–6.
369:Open Biomedical Ontologies
463:NCIBI Try Our Tools page
394:
124:(NCIBI) is one of seven
441:NCIBI Virtual Workshops
627:Nucleic Acids Research
389:Biomedical Informatics
164:and user interaction.
134:University of Michigan
33:relies excessively on
430:NCIBI YouTube Channel
303:literature database
248:protein interactions
180:Exploratory analysis
452:NCIBI Presentations
136:and is part of the
792:10.1101/gr.1239303
725:BMC Bioinformatics
639:10.1093/nar/gkn722
351:in the context of
331:to rapidly search
242:plugin that is an
375:
374:
266:
265:
118:
117:
110:
92:
881:
813:
803:
786:(11): 2498–504.
761:
760:
750:
740:
716:
710:
709:
699:
667:
661:
660:
650:
618:
612:
611:
601:
569:
563:
562:
552:
520:
514:
513:
503:
471:
465:
460:
454:
449:
443:
438:
432:
427:
421:
416:
410:
405:
273:
272:
260:gene interaction
184:
183:
158:bipolar disorder
152:, nutrition and
113:
106:
102:
99:
93:
91:
50:
26:
18:
889:
888:
884:
883:
882:
880:
879:
878:
834:
833:
820:
780:Genome Research
770:
765:
764:
731:(Suppl 5): S6.
717:
713:
668:
664:
619:
615:
570:
566:
521:
517:
472:
468:
461:
457:
450:
446:
439:
435:
428:
424:
417:
413:
406:
402:
397:
380:
345:gene expression
271:
230:, and pathways
204:expressed genes
182:
174:
172:Available tools
114:
103:
97:
94:
51:
49:
43:
39:primary sources
27:
12:
11:
5:
887:
877:
876:
871:
866:
861:
856:
851:
846:
832:
831:
826:
819:
818:External links
816:
815:
814:
769:
766:
763:
762:
711:
676:Bioinformatics
662:
613:
578:Bioinformatics
564:
529:Bioinformatics
515:
480:Bioinformatics
466:
455:
444:
433:
422:
411:
399:
398:
396:
393:
392:
391:
386:
384:Bioinformatics
379:
376:
373:
372:
361:
357:
356:
341:
337:
336:
321:
317:
316:
309:
305:
304:
293:
289:
288:
285:
281:
280:
277:
270:
267:
264:
263:
256:
252:
251:
236:
232:
231:
212:
208:
207:
196:
192:
191:
188:
181:
178:
173:
170:
128:funded by the
116:
115:
30:
28:
21:
9:
6:
4:
3:
2:
886:
875:
872:
870:
867:
865:
862:
860:
857:
855:
852:
850:
847:
845:
842:
841:
839:
830:
827:
825:
822:
821:
811:
807:
802:
797:
793:
789:
785:
781:
777:
772:
771:
758:
754:
749:
744:
739:
734:
730:
726:
722:
715:
707:
703:
698:
693:
689:
685:
681:
677:
673:
666:
658:
654:
649:
644:
640:
636:
632:
628:
624:
617:
609:
605:
600:
595:
591:
587:
583:
579:
575:
568:
560:
556:
551:
546:
542:
538:
534:
530:
526:
519:
511:
507:
502:
497:
493:
489:
486:(4): 456–63.
485:
481:
477:
470:
464:
459:
453:
448:
442:
437:
431:
426:
420:
415:
409:
404:
400:
390:
387:
385:
382:
381:
370:
366:
362:
359:
358:
354:
350:
346:
342:
339:
338:
334:
330:
326:
322:
319:
318:
314:
310:
307:
306:
302:
298:
294:
291:
290:
286:
284:BioSearch-2D
283:
282:
278:
275:
274:
261:
257:
254:
253:
249:
245:
241:
237:
234:
233:
229:
225:
221:
217:
213:
210:
209:
205:
201:
197:
194:
193:
189:
186:
185:
177:
169:
165:
163:
159:
155:
151:
147:
141:
139:
135:
131:
127:
123:
112:
109:
101:
98:November 2010
90:
87:
83:
80:
76:
73:
69:
66:
62:
59: –
58:
54:
53:Find sources:
47:
41:
40:
36:
31:This article
29:
25:
20:
19:
16:
783:
779:
728:
724:
714:
682:(7): 974–6.
679:
675:
665:
630:
626:
616:
584:(1): 137–8.
581:
577:
567:
535:(7): 971–3.
532:
528:
518:
483:
479:
469:
458:
447:
436:
425:
414:
403:
279:Description
235:MiMI Plugin
190:Description
175:
166:
142:
121:
119:
104:
95:
85:
78:
71:
64:
52:
32:
15:
347:levels and
340:PubAnatomy
308:Metab2MeSH
244:open source
220:metabolomic
200:open source
195:ConceptGen
146:gene fusion
849:Proteomics
838:Categories
768:References
365:ontologies
327:'s (NCBI)
292:Gene2Mesh
68:newspapers
35:references
829:Cytoscape
367:from the
320:MiSearch
240:Cytoscape
224:reactions
216:Cytoscape
211:MetScape
162:usability
844:Genomics
810:14597658
757:19426463
706:18326507
657:18978014
608:18812364
559:20139469
510:20007254
378:See also
360:PubOnto
150:diabetes
748:2679406
697:2660869
648:2686565
599:2638934
550:2844990
501:2852214
353:Medline
228:enzymes
154:obesity
82:scholar
808:
801:403769
798:
755:
745:
704:
694:
655:
645:
606:
596:
557:
547:
508:
498:
333:PubMed
329:Entrez
301:PubMed
84:
77:
70:
63:
55:
395:Notes
276:Name
262:tool
187:Name
89:JSTOR
75:books
806:PMID
753:PMID
702:PMID
653:PMID
604:PMID
555:PMID
506:PMID
120:The
61:news
796:PMC
788:doi
743:PMC
733:doi
692:PMC
684:doi
643:PMC
635:doi
594:PMC
586:doi
545:PMC
537:doi
496:PMC
488:doi
299:'s
198:An
37:to
840::
804:.
794:.
784:13
782:.
778:.
751:.
741:.
729:10
727:.
723:.
700:.
690:.
680:25
678:.
674:.
651:.
641:.
631:37
629:.
625:.
602:.
592:.
582:25
580:.
576:.
553:.
543:.
533:26
531:.
527:.
504:.
494:.
484:26
482:.
478:.
238:A
226:,
214:A
48:.
812:.
790::
759:.
735::
708:.
686::
659:.
637::
610:.
588::
561:.
539::
512:.
490::
111:)
105:(
100:)
96:(
86:·
79:·
72:·
65:·
42:.
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
