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*  PathogenSeq: TBDR
Tue Mar 14 08:54:22 2017: Finding mutations. Tue Mar 14 08:54:42 2017: Finalising results. Tue Mar 14 08:54:43 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58c7af8980064&name=58c7af8980064
*  PathogenSeq: TBDR
Thu Mar 2 03:55:45 2017: Finding mutations. Thu Mar 2 03:55:49 2017: Finalising results. Thu Mar 2 03:55:50 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58b797b838c5b&name=58b797b838c5b
*  PLOS Genetics: U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
... indels), and translocations. We found 2,384,470 SNVs, 191,743 small indels, and 1,314 large structural variations. Known gene ... models were used to predict the effect of these mutations on protein-coding sequence. Mutational analysis revealed 512 genes ... The major mutational mechanisms in this brain cancer cell line are small indels and large structural variations. The genomic ... homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and up to 35 by interchromosomal ...
  http://journals.plos.org/plosgenetics/article/comments?id=10.1371/journal.pgen.1000832
*  PathogenSeq: TBDR
Tue Feb 14 11:12:40 2017: Finding mutations. Tue Feb 14 11:13:33 2017: Finalising results. Tue Feb 14 11:13:34 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58a2e5f7c78da&name=58a2e5f7c78da
*  PLOS Genetics: U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
... indels), and translocations. We found 2,384,470 SNVs, 191,743 small indels, and 1,314 large structural variations. Known gene ... and accurate mutational analysis of the U87MG genome comprehensively identifies different classes of genetic mutations ... The major mutational mechanisms in this brain cancer cell line are small indels and large structural variations. The genomic ... Mutational analysis revealed 512 genes homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large ...
  http://journals.plos.org/plosgenetics/article/figure?id=10.1371/journal.pgen.1000832.g006
*  Genomic distance under gene substitutions | BMC Bioinformatics | Full Text
... consider indels and the double cut and join (DCJ) operation [7], that is able to represent most large scale mutation events in ... Since substitutions include indels, is upper bounded by the DCJ-indel distance, the minimum number of DCJ and indel operations ... Insertions and deletions can be shortly called indels. In [4], the operations allowed are inversions and indels, while the ... i) An optimal sorting scenario with DCJ operations and indels. (ii) An optimal sorting scenario with DCJ operations and indels ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-S9-S8
*  PathogenSeq: TBDR
Mon Feb 13 10:06:10 2017: Finding mutations. Mon Feb 13 10:06:44 2017: Finalising results. Mon Feb 13 10:06:45 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58a18497b261d&name=58a18497b261d
*  PathogenSeq: TBDR
Fri Feb 3 10:46:25 2017: Finding mutations. Fri Feb 3 10:46:25 2017: Finalising results. Fri Feb 3 10:46:26 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58945f814fc3c&name=58945f814fc3c
*  PathogenSeq: TBDR
Thu Mar 9 11:00:11 2017: Finding mutations. Thu Mar 9 11:01:10 2017: Finalising results. Thu Mar 9 11:01:11 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58c135594a4cc&name=58c135594a4cc
*  PathogenSeq: TBDR
Tue Mar 21 16:16:39 2017: Finding mutations. Tue Mar 21 16:16:49 2017: Finalising results. Tue Mar 21 16:16:50 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58d151d5068df&name=58d151d5068df
*  PathogenSeq: TBDR
Mon Feb 6 14:38:15 2017: Finding mutations. Mon Feb 6 14:38:29 2017: Finalising results. Mon Feb 6 14:38:30 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58988a38cbd5d&name=58988a38cbd5d
*  PathogenSeq: TBDR
Thu Mar 16 09:35:36 2017: Finding mutations. Thu Mar 16 09:35:51 2017: Finalising results. Thu Mar 16 09:35:53 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58ca5c48ace61&name=58ca5c48ace61
*  PathogenSeq: TBDR
Mon Feb 13 23:33:55 2017: Finding mutations. Mon Feb 13 23:34:03 2017: Finalising results. Mon Feb 13 23:34:04 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58a2425a22b65&name=58a2425a22b65
*  PathogenSeq: TBDR
Mon May 1 00:55:14 2017: Finding mutations. Mon May 1 00:56:01 2017: Finalising results. Mon May 1 00:56:02 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=590679587ef78&name=590679587ef78
*  PathogenSeq: TBDR
Wed Mar 22 11:12:32 2017: Finding mutations. Wed Mar 22 11:12:42 2017: Finalising results. Wed Mar 22 11:12:43 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58d25c0e7cc8a&name=58d25c0e7cc8a
*  PathogenSeq: TBDR
Mutations in candidate genes:. Gene. Chromosome Position. Mutation. Lineage. gyrB. 6533. Indel: GCC/GC. ... Mon May 1 00:07:12 2017: Finding mutations. Mon May 1 00:08:17 2017: Finalising results. Mon May 1 00:08:19 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=59066e0a6521b&name=59066e0a6521b
*  PathogenSeq: TBDR
Wed Feb 15 08:44:35 2017: Finding mutations. Wed Feb 15 08:44:44 2017: Finalising results. Wed Feb 15 08:44:45 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58a414e179ab8&name=58a414e179ab8
*  PathogenSeq: TBDR
Wed Feb 15 08:01:24 2017: Finding mutations. Wed Feb 15 08:01:38 2017: Finalising results. Wed Feb 15 08:01:39 2017: End. ... Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG ...
  http://tbdr.lshtm.ac.uk/?page=results&id=58a40ac1eec12&name=58a40ac1eec12
*  Application # 2016/0300013. METHOD FOR SIMULTANEOUS DETECTION OF GENOME-WIDE COPY NUMBER CHANGES, cnLOH, INDELS, AND GENE...
Detection of Mutations and Indels [0135] The high read depth allowed for the detection of single point mutations and indels in ... Identification of mutations and indels in Agilent SureCall software showing a 26-bp indel (on the right) and a heterozygous SNP ... METHOD FOR SIMULTANEOUS DETECTION OF GENOME-WIDE COPY NUMBER CHANGES, cnLOH, INDELS, AND GENE MUTATIONS Abstract. Provided ... 0124] The SNP calling algorithm SNPPET was used to call point mutations and indels (see, e.g., US Patent Application ...
  http://patents.com/us-20160300013.html
*  A System for Dosage-Based Functional Genomics in Poplar | Plant Cell
... indel mutations). Using high-precision dosage analysis, we detected indel mutations in ∼55% of the progeny. These indels varied ... A) For each chromosome, indel mutations are tiled across their length. Indel mutations vary in length (up to a whole chromosome ... A) Determination of the parental origin of each indel mutation. For each indel mutation identified (Figure 1), the percentage ... B) Density of indel mutations across the poplar genome. All indel mutations were pooled together, except for whole-chromosome ...
  http://www.plantcell.org/content/27/9/2370.full?sid=94ff4db9-637d-41ed-acb6-4d2a6a3e9c10
*  Nilesh Banavali, Ph.D.
Dynamic mechanisms behind indel mutations and their sequence dependence in nucleic acid replication:. Base pairing, or its ... We have recently delineated the underlying 3D strand slippage mechanism by which a single base insertion or deletion (indel) ... the possibility of specific non-canonical interactions providing a direct mechanism for sequence dependence of indel mutations ... Banavali, JACS, 2013). This work is being applied to understand the introduction of such mutations during strand extension by ...
  https://www.wadsworth.org/print/senior-staff/nilesh-banavali
*  GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris | BMC...
Indel mutation screenings with CRISPR/Cas9-BB3's were done in a CBS7435(MutS) strain stably expressing eGFP under control of ... InDel mutations using CRISPR/Cas9. Targeting efficiency of the modular CRISPR/Cas9 system on native sequences was evaluated by ... 2018.) This allowed rapid optimization of a CRISPR/Cas9-BB3 for efficient InDel mutations in P. pastoris within a short time. ... After restreaking the clones two times on selective agar plates the targeted loci were checked for InDel mutations by colony ...
  https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0492-3
*  Polymorphism patterns and expression levels in yeas | Open-i
Bottom Line: We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions ... Bottom Line: We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions ... and that large indels segregate in disordered regions in the human population.Our survey of polymorphism confirms patterns of ... and that large indels segregate in disordered regions in the human population.Our survey of polymorphism confirms patterns of ...
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC4494057_evv105f2p&req=4
*  John A McGrath
Novel indel mutation of STS underlies a new phenotype of self-healing recessive X-linked ichthyosis.. Authors:. Takuya Takeichi ... Novel TGM5 mutations in acral peeling skin syndrome.. Authors:. Jaap J A J van der Velden Michel van Geel Ruud G L Nellen ... Mutations in KLHL24 Add to the Molecular Heterogeneity of Epidermolysis Bullosa Simplex.. Authors:. John Y W Lee Lu Liu Chao- ... ATR gene mutations in HPV negative oropharyngeal cancer.. Authors:. Jean-Pierre Jeannon Akio Tanaka Selvam Thavaraj Teresa ...
  https://www.pubfacts.com/author/John+A+McGrath