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Protein structure alignment using a genetic algorithm
2000
Proteins: Structure, Function, and Bioinformatics
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A web-based server and additional supporting information are available at http://engpub1.bu.edu/ϳjosephs. Proteins 2000;38:428 -440. ...
If they align well, we would expect d 12 A to be similar to d 12 B , d 13 A to be similar to d 13 B , and d 23 A to be similar to d B 23 . ...
th residue and the j B
th
residue in protein B; d* ij is the average of d ij
A and d ij
B
TABLE III . ...
doi:10.1002/(sici)1097-0134(20000301)38:4<428::aid-prot8>3.0.co;2-n
pmid:10707029
fatcat:wlgrshjcovdo3clu7rdtkm35ba
Computational Identification of Operons in Microbial Genomes
2001
Genome Research
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Nodes with the labels A,B,C,D in the pathway graph and the genome (line) are matched enzymes. ...
pneumoniae
24
1.2
75/190
0.39
3.1
4
0.007
B. burgdorferi
20
1.5
50/138
0.36
2.5
2
0.001
T. pallidum
15
1.2
44/152
0.29
2.9
5
0.03
Synechocystis
24
3.6
59/453
0.13
2.5
8
0.02
D. ...
doi:10.1101/gr.200602
pmid:12176930
pmcid:PMC186635
fatcat:pdxyu2uzofhexoubmxk4et4x24
Identification of novel pathway regulation during myogenic differentiation
2006
Genomics
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D ...
-7543/$ -see front matter D 2005 Elsevier Inc. ...
(D, E) Luciferase reporter gene assays showing the effects of differentiation on a MEF2-responsive promoter (D) and 2 kb of the PGC-1a gene promoter (E) in the absence or presence of the myogenic antagonist ...
doi:10.1016/j.ygeno.2005.08.009
pmid:16300922
fatcat:uatrjxctdvbz7cl4agntkfytni
Genome-Wide Association Analysis Identifies Genetic Correlates of Immune Infiltrates in Solid Tumors
[article]
2017
bioRxiv
pre-print
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C D 7 9 A , M S 4 A 1 B c e l l N K K I R 2 D L 1 , K I R 2 D L 3 , K I R 2 D L 4 , K I R 3 D L 1 , K I R 3 D L 2 , K I R 3 D L 3 , K I R 2 D S 4 N a t u r a l k i l l e r c e l l M o n o C D 8 6 , C S ...
d . ...
doi:10.1101/106039
fatcat:5nlr4vnpzneknde5veu3vo3swq
The use of haplotype-specific transcripts improves sample annotation consistency
2014
Biomarker Research
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Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research. Results: Candidate markers were explored through the application of Hartigans' dip test statistics to a publically available human whole genome microarray dataset. The marker performance was tested on 188 serial samples from 53 donors and of variable tissue origin from five public microarray datasets. A qualified transcript marker panel consisting of three probe sets for human
doi:10.1186/2050-7771-2-17
pmid:25285214
pmcid:PMC4184161
fatcat:ax7y5bcpmrd25hwfws5wgfqb2i
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... yte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in six of the 188 test samples. About 3% of the test samples require root-cause analysis due to unresolvable inaccuracies. Conclusions: The transcript marker panel consisting of HLA-DQA1 and HLA-DRB4 represents a robust, tissue-independent composite marker to assist control donor annotation concordance at the transcript level. Allele-selectivity of HLA genes renders them good candidates for "fingerprinting" with donor specific expression pattern.
Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors
2017
PLoS ONE
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(D) Relationship of TP53 mutation to CD8+ Tcell estimates in head and neck cancer. ...
D: Mutual rank-based co-regulatory network around macrophage marker VSIG4 in TCGA. VSIG4, CD163, and MS4A4A were selected to create a signature to estimate macrophage content in tumors. ...
doi:10.1371/journal.pone.0179726
pmid:28749946
pmcid:PMC5531551
fatcat:wh7qjiupyvfnvkrovjl6suybye
Identification of Novel Genes and Pathways Regulating SREBP Transcriptional Activity
2009
PLoS ONE
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(D) Effect of the 176 selected activators and suppressors (grey points) on mutant SRE promoter. ...
(B-D) Error bars indicate standard deviations (n = 3).
Figure 2 . 2 Primary and secondary screen results. ...
doi:10.1371/journal.pone.0005197
pmid:19381295
pmcid:PMC2668173
fatcat:43m76qioljf4vihtoc2436ytxe
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data
2013
Computer applications in the biosciences : CABIOS
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Pyruvate induces mitochondrial biogenesis by a PGC-1 α-independent mechanism
2007
American Journal of Physiology - Cell Physiology
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Szustakowski for the GeneChip data analysis, Daniel Kemp for the myogenic gene set, and Thomas Hughes for critical review of this manuscript. ...
wildtype myoblasts, Mark Montminy for the shRNA PGC-1␣ adenovirus, Deborah Ahern-Ridlon and Akos Szilvasi for technical assistance with the confocal microscopy and FACS analyses, Nanguneri Nirmala and Joseph ...
D: total cellular lysates were made from C2C12 myoblasts incubated in basal or SP test media at indicated time points. ...
doi:10.1152/ajpcell.00428.2006
pmid:17182725
fatcat:ayszzgx2jjbahggxzdxz2hchay
Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles
2008
BioData Mining
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Contrary to the traditional biology approach, where the expression patterns of a handful of genes are studied at a time, microarray experiments enable biologists to study the expression patterns of many genes simultaneously from gene expression profile data and decipher the underlying hidden biological mechanism from the observed gene expression changes. While the statistical significance of the gene expression data can be deduced by various methods, the biological interpretation of the data
doi:10.1186/1756-0381-1-4
pmid:18822150
pmcid:PMC2553773
fatcat:hcibsqu7lrdpxeyzdzmtraem54
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... sents a challenge. Results: A method, called CisTransMine, is proposed to help infer the underlying biological mechanisms for the observed gene expression changes in microarray experiments. Specifically, this method will predict potential cis-regulatory elements in promoter regions which could regulate gene expression changes. This approach builds on the MotifADE method published in 2004 and extends it with two modifications: up-regulated genes and down-regulated genes are tested separately and in addition, tests have been implemented to identify combinations of transcription factors that work synergistically. The method has been applied to a genome wide expression dataset intended to study myogenesis in a mouse C2C12 cell differentiation model. The results shown here both confirm the prior biological knowledge and facilitate the discovery of new biological insights. Conclusion: The results validate that the CisTransMine approach is a robust method to uncover the hidden transcriptional regulatory mechanisms that can facilitate the discovery of mechanisms of transcriptional regulation.
Dynamic resolution of functionally related gene sets in response to acute heat stress
2007
BMC Molecular Biology
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(A-D) Transcriptional activity of the indicated genes was measured using Affymetrix GeneChips and data was analyzed using GeneSpring bioinformatics software. ...
doi:10.1186/1471-2199-8-46
pmid:17550601
pmcid:PMC1904231
fatcat:ivqm26swszgwtb27za72sxhu5i
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks
2005
BMC Bioinformatics
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Let D i , i = 1,2, ... n. denote the protein sequences contained in Cluster D and let E j , j = 1,2, ..., m denote the protein sequence contained in Cluster E. ...
The geometric mean distance G between Cluster D and Cluster E is defined as Equation 4:
Equation 4: The hierarchical average linkage clustering works in an iterative process: it begins with each protein ...
doi:10.1186/1471-2105-6-242
pmid:16202129
pmcid:PMC1261163
fatcat:gz2cehmobredzbw3qcxkcnqllu
Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer
[article]
2019
bioRxiv
pre-print
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Fabrizio D, Lieber D, Malboeuf C, Silterra J, White E, Coyne M, et al. ...
Rizvi H, Sanchez-Vega F, La K, Chatila W, Jonsson P, Halpenny D, et al. ...
doi:10.1101/626143
fatcat:m77jhuidefcudge2kwl7fgkuve
Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples
2011
PLoS ONE
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Large-scale molecular profiling technologies have assisted the identification of disease biomarkers and facilitated the basic understanding of cellular processes. However, samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent
doi:10.1371/journal.pone.0027156
pmid:22110609
pmcid:PMC3217948
fatcat:i5h37rlrize7hlmfkvz2pxuliu
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... statistical studies. We describe an approach that builds upon a linear latent variable model, in which expression levels from mixed cell populations are modeled as the weighted average of expression from different cell types. We solve these equations using quadratic programming, which efficiently identifies the globally optimal solution while preserving non-negativity of the fraction of the cells. We applied our method to various existing platforms to estimate proportions of different pure cell or tissue types and gene expression profilings of distinct phenotypes, with a focus on complex samples collected in clinical trials. We tested our methods on several well controlled benchmark data sets with known mixing fractions of pure cell or tissue types and mRNA expression profiling data from samples collected in a clinical trial. Accurate agreement between predicted and actual mixing fractions was observed. In addition, our method was able to predict mixing fractions for more than ten species of circulating cells and to provide accurate estimates for relatively rare cell types (,10% total population). Furthermore, accurate changes in leukocyte trafficking associated with Fingolomid (FTY720) treatment were identified that were consistent with previous results generated by both cell counts and flow cytometry. These data suggest that our method can solve one of the open questions regarding the analysis of complex transcriptional data: namely, how to identify the optimal mixing fractions in a given experiment.
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
2007
Computer applications in the biosciences : CABIOS
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., 2006; Szustakowski et al., 2006; Tian et al., 2005; Tomfohr et al., 2005; Zahn et al., 2006) . ...
The LBF test first transforms the data according to Z ij ¼ X ij À median X i ð Þ , where X ij corresponds to the jth data point from the ith sample. ...
doi:10.1093/bioinformatics/btm116
pmid:17392327
fatcat:ehbl5245crhlpg3m25unu5ivsu
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