Class information for:
Level 2: MOLECULAR BIOLOGY AND EVOLUTION//BIOINFORMATICS//MATHEMATICAL & COMPUTATIONAL BIOLOGY

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
126 23963 39.8 78%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
90 3       MATHEMATICAL & COMPUTATIONAL BIOLOGY//BIOINFORMATICS//BMC BIOINFORMATICS 77178
126 2             MOLECULAR BIOLOGY AND EVOLUTION//BIOINFORMATICS//MATHEMATICAL & COMPUTATIONAL BIOLOGY 23963
922 1                   SYSTEMATIC BIOLOGY//PHYLOGENETIC NETWORK//PHYLOGENETIC TREE 2957
2111 1                   MOTIF DISCOVERY//TRANSCRIPTION FACTOR BINDING SITE//MOTIF FINDING 2353
2338 1                   MULTIPLE SEQUENCE ALIGNMENT//SEQUENCE ALIGNMENT//COMPUTER APPLICATIONS IN THE BIOSCIENCES 2277
2829 1                   CODON USAGE//CODON USAGE BIAS//SYNONYMOUS CODON USAGE 2138
6844 1                   LATERAL GENE TRANSFER//TREE OF LIFE//HORIZONTAL GENE TRANSFER 1437
8300 1                   WHOLE GENOME DUPLICATION//GENOME DUPLICATION//GENE DUPLICATION 1269
9683 1                   EMBL OUTSTN//LECTURE NOTES IN BIOINFORMATICS//PROT INFORMAT OURCE 1131
10256 1                   CODON MODELS//POSITIVE SELECTION//MOLECULAR BIOLOGY AND EVOLUTION 1078
11342 1                   GENE PREDICTION//GENE FINDING//GENE RECOGNITION 990
13045 1                   ISOCHORES//EVOLUZ MOL//MALE MUTATION BIAS 864
14677 1                   GENOME REARRANGEMENT//SORTING BY REVERSALS//GENOME REARRANGEMENTS 756
15359 1                   STANDARDS IN GENOMIC SCIENCES//BIOL DATA MANAGEMENT TECHNOL//GEBA 717
16263 1                   INTRALOCUS SEXUAL CONFLICT//SEX BIASED GENE EXPRESSION//SEXUAL ANTAGONISM 664
17904 1                   INTRON GAIN//INTRON LOSS//INTRON EVOLUTION 576
18864 1                   DATABASE LIFE SCI//DDBJ//EMTRAIN 533
19074 1                   NATURAL ANTISENSE TRANSCRIPT//WRAP53//OVERLAPPING GENES 523
19282 1                   CONSERVED NON CODING ELEMENTS//IROQUOIS//ENERGY ENVIRONM BIOL COMP 513
19783 1                   EXPRESSION EVOLUTION//TRANS REGULATION//CIS REGULATORY DIVERGENCE 489
19900 1                   GENE INDEXED MUTANT//NAA PLANT SOIL NUTR UNIT//ORYZABASE 485
20039 1                   ORTHOLOGY//BIDIRECTIONAL BEST HIT//GENOME FUNCTIONAL PREDICTION 479
20234 1                   RECOMBINATION DETECTION//SPECIES CONCEPT//PERIODIC SELECTION 470
22783 1                   BIDIRECTIONAL PROMOTER//OPERON PREDICTION//INTERGENIC DISTANCE 369
24117 1                   EVOLUTIONARY BIOINFORMAT//FOLD SUPERFAMILY//EVOLUTION OF DOMAIN ARCHITECTURE 323
25327 1                   R391//R997//GENOMIC ISLAND 285
28425 1                   PROCESSED PSEUDOGENES//CYP4Z2P//DUPLICATED PSEUDOGENES 207
36483 1                   GENOMIC DATA VISUALIZATION//ALTERNATE ASSEMBLIES OF COW GENOMES//BAC FISH MAPPING 80

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with term
in class
1 MOLECULAR BIOLOGY AND EVOLUTION journal 300029 5% 21% 1148
2 BIOINFORMATICS journal 289584 7% 15% 1560
3 MATHEMATICAL & COMPUTATIONAL BIOLOGY WoSSC 256789 19% 5% 4585
4 STANDARDS IN GENOMIC SCIENCES journal 211504 1% 50% 334
5 EVOLUTIONARY BIOLOGY WoSSC 162653 17% 3% 4177
6 BMC BIOINFORMATICS journal 156804 4% 13% 965
7 GENETICS & HEREDITY WoSSC 156517 34% 2% 8134
8 BIOL DATA MANAGEMENT TECHNOL address 153974 1% 70% 174
9 SYSTEMATIC BIOLOGY journal 152688 2% 30% 401
10 JOURNAL OF COMPUTATIONAL BIOLOGY journal 139448 2% 27% 414

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with term
in class
1 Mathematical & Computational Biology 256789 19% 5% 4585
2 Evolutionary Biology 162653 17% 3% 4177
3 Genetics & Heredity 156517 34% 2% 8134
4 Biotechnology & Applied Microbiology 70375 24% 1% 5685
5 Biochemical Research Methods 61129 17% 1% 4176
6 Biochemistry & Molecular Biology 35407 34% 0% 8161
7 Computer Science, Interdisciplinary Applications 6568 5% 1% 1217
8 Biology 6462 5% 1% 1273
9 Statistics & Probability 3653 4% 0% 848
10 Microbiology 3109 6% 0% 1486

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with term
in class
1 BIOL DATA MANAGEMENT TECHNOL 153974 1% 70% 174
2 BIOTECHNOL INFORMAT 94876 2% 19% 403
3 BIOINFORMAT 60510 3% 6% 820
4 EVOLUZ MOL 47999 0% 88% 43
5 LIB MED 39738 1% 16% 193
6 COMP SCI 28834 8% 1% 1945
7 ORG EVOLUC GENOMA 28261 0% 65% 34
8 EMBL OUTSTN 27787 0% 31% 71
9 EVOLUTIONARY BIOINFORMAT 21484 0% 65% 26
10 JOINT GENOME 20341 0% 18% 90

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with term
in class
1 MOLECULAR BIOLOGY AND EVOLUTION 300029 5% 21% 1148
2 BIOINFORMATICS 289584 7% 15% 1560
3 STANDARDS IN GENOMIC SCIENCES 211504 1% 50% 334
4 BMC BIOINFORMATICS 156804 4% 13% 965
5 SYSTEMATIC BIOLOGY 152688 2% 30% 401
6 JOURNAL OF COMPUTATIONAL BIOLOGY 139448 2% 27% 414
7 JOURNAL OF MOLECULAR EVOLUTION 118726 2% 16% 598
8 BIOTECHFORUM ( BTF ) 100818 2% 18% 454
9 NUCLEIC ACIDS RESEARCH 98325 7% 5% 1763
10 COMPUTER APPLICATIONS IN THE BIOSCIENCES 86419 1% 27% 249

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 CODON USAGE 132707 1% 41% 255 Search CODON+USAGE Search CODON+USAGE
2 ISOCHORES 115850 1% 68% 135 Search ISOCHORES Search ISOCHORES
3 CODON USAGE BIAS 110027 1% 71% 122 Search CODON+USAGE+BIAS Search CODON+USAGE+BIAS
4 PHYLOGENETIC NETWORK 100597 0% 68% 117 Search PHYLOGENETIC+NETWORK Search PHYLOGENETIC+NETWORK
5 GEBA 89174 0% 75% 94 Search GEBA Search GEBA
6 GC CONTENT 74949 1% 42% 140 Search GC+CONTENT Search GC+CONTENT
7 MULTIPLE SEQUENCE ALIGNMENT 71294 1% 40% 139 Search MULTIPLE+SEQUENCE+ALIGNMENT Search MULTIPLE+SEQUENCE+ALIGNMENT
8 SYNONYMOUS CODON USAGE 62722 0% 82% 60 Search SYNONYMOUS+CODON+USAGE Search SYNONYMOUS+CODON+USAGE
9 SEQUENCE ALIGNMENT 60505 1% 27% 174 Search SEQUENCE+ALIGNMENT Search SEQUENCE+ALIGNMENT
10 TRANSLATIONAL SELECTION 60347 0% 91% 52 Search TRANSLATIONAL+SELECTION Search TRANSLATIONAL+SELECTION

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref. in
cl.		 Shr. of ref. in
cl.		 Citations
1 ALTSCHUL, SF , MADDEN, TL , SCHAFFER, AA , ZHANG, JH , ZHANG, Z , MILLER, W , LIPMAN, DJ , (1997) GAPPED BLAST AND PSI-BLAST: A NEW GENERATION OF PROTEIN DATABASE SEARCH PROGRAMS.NUCLEIC ACIDS RESEARCH. VOL. 25. ISSUE 17. P. 3389-3402 43 70% 41839
2 MORRISON, DA , (2006) PHYLOGENETIC ANALYSES OF PARASITES IN THE NEW MILLENNIUM.ADVANCES IN PARASITOLOGY, VOL 63. VOL. 63. ISSUE . P. 1 -124 246 73% 7
3 KUMAR, S , FILIPSKI, AJ , BATTISTUZZI, FU , POND, SLK , TAMURA, K , (2012) STATISTICS AND TRUTH IN PHYLOGENOMICS.MOLECULAR BIOLOGY AND EVOLUTION. VOL. 29. ISSUE 2. P. 457 -472 127 73% 54
4 ROGOZIN, IB , CARMEL, L , CSUROS, M , KOONIN, EV , (2012) ORIGIN AND EVOLUTION OF SPLICEOSOMAL INTRONS.BIOLOGY DIRECT. VOL. 7. ISSUE . P. - 153 56% 69
5 GUINDON, S , GASCUEL, O , (2003) A SIMPLE, FAST, AND ACCURATE ALGORITHM TO ESTIMATE LARGE PHYLOGENIES BY MAXIMUM LIKELIHOOD.SYSTEMATIC BIOLOGY. VOL. 52. ISSUE 5. P. 696-704 29 83% 9889
6 PLOTKIN, JB , KUDLA, G , (2011) SYNONYMOUS BUT NOT THE SAME: THE CAUSES AND CONSEQUENCES OF CODON BIAS.NATURE REVIEWS GENETICS. VOL. 12. ISSUE 1. P. 32-42 85 65% 365
7 GUINDON, S , DUFAYARD, JF , LEFORT, V , ANISIMOVA, M , HORDIJK, W , GASCUEL, O , (2010) NEW ALGORITHMS AND METHODS TO ESTIMATE MAXIMUM-LIKELIHOOD PHYLOGENIES: ASSESSING THE PERFORMANCE OF PHYML 3.0.SYSTEMATIC BIOLOGY. VOL. 59. ISSUE 3. P. 307 -321 25 86% 3880
8 SZOLLOSI, GJ , TANNIER, E , DAUBIN, V , BOUSSAU, B , (2015) THE INFERENCE OF GENE TREES WITH SPECIES TREES.SYSTEMATIC BIOLOGY. VOL. 64. ISSUE 1. P. E42 -E62 92 77% 23
9 MORRISON, DA , (2006) MULTIPLE SEQUENCE ALIGNMENT FOR PHYLOGENETIC PURPOSES.AUSTRALIAN SYSTEMATIC BOTANY. VOL. 19. ISSUE 6. P. 479 -539 184 57% 73
10 EDWARDS, SV , XI, ZX , JANKE, A , FAIRCLOTH, BC , MCCORMACK, JE , GLENN, TC , ZHONG, BJ , WU, SY , LEMMON, EM , LEMMON, AR , ET AL (2016) IMPLEMENTING AND TESTING THE MULTISPECIES COALESCENT MODEL: A VALUABLE PARADIGM FOR PHYLOGENOMICS.MOLECULAR PHYLOGENETICS AND EVOLUTION. VOL. 94. ISSUE . P. 447 -462 71 73% 12

Classes with closest relation at Level 2


Rank Class id link
1 3201 GRAPHICAL REPRESENTATION//AUTHORSHIP ATTRIBUTION//CODE CLONE
2 365 PROTEIN STRUCTURE PREDICTION//PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS//PSEUDO AMINO ACID COMPOSITION
3 868 BMC BIOINFORMATICS//MATHEMATICAL & COMPUTATIONAL BIOLOGY//BIOINFORMATICS
4 2924 SAGE//SERIAL ANALYSIS OF GENE EXPRESSION//DIFFERENTIAL DISPLAY
5 1101 BIOINFORMATICS//COPY NUMBER VARIATION//NEXT GENERATION SEQUENCING
6 826 CONSERVATION GENETICS RESOURCES//MICROSATELLITES//PHYLOGEOGRAPHY
7 3958 COMPUTER APPLICATIONS IN THE BIOSCIENCES//ADAPTIVE WEIGHTED LEAST SQUARES//AMBIGRAM
8 1046 INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY//POLYPHASIC TAXONOMY//YUNNAN MICROBIOL
9 2094 TRANSPOSABLE ELEMENTS//RETROTRANSPOSON//LTR RETROTRANSPOSON
10 1227 TRANSPOSABLE ELEMENTS//RETROTRANSPOSON//CHROMOSOMA

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