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LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins

Yaxuan Yu, Rhodri Ceredig, Cathal Seoighe
2015 Nucleic Acids Research  
Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available.  ...  In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs.  ...  Given that TCR/IG sequencing data sets are tractable on a personal computer for typical data sets or on computer clusters for large projects this trade off is unnecessary.  ... 
doi:10.1093/nar/gkv1016 pmid:26446988 pmcid:PMC4770197 fatcat:x7cj3x676nfo7au2bsyczxzwu4

Identifying mRNA Editing Deaminase Targets by RNA-Seq [chapter]

Brad R. Rosenberg, Scott Dewell, F. Nina Papavasiliou
2011 Msphere  
The efficacy and utility of this approach is demonstrated for APOBEC1, a cytidine deaminase with a known and well-characterized mRNA editing target in the mammalian small intestine.  ...  Recent advances in ultra highthroughput sequencing technologies have allowed for whole transcriptome sequencing and expression profiling (RNA-Seq).  ...  Beginning with a TopHat generated SAM file, we use the publicly available, open source SAMTools software package (11) from the Sanger Institute for mismatch calling.  ... 
doi:10.1007/978-1-61779-018-8_6 pmid:21370044 fatcat:joenjumt6rcwnaagf2eoezkpne

Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets

K. C. Bader, C. Grothoff, H. Meier
2011 Bioinformatics  
Results: We have developed CaSSiS, a fast and scalable method for computing comprehensive collections of sequence-and sequence group-specific oligonucleotide signatures from large sets of hierarchically  ...  An upper limit of tolerated mismatches within the target group, as well as the minimum number of mismatches with non-target sequences, can be predefined.  ...  ACKNOWLEDGEMENT We thank Tina Lei and Ralf Westram for implementation support, and Krista Grothoff and Tilo Eißler for critically reading the article.  ... 
doi:10.1093/bioinformatics/btr161 pmid:21471017 fatcat:mxitezagovbyze44xskblyacr4

A stepwise cluster analysis approach for downscaled climate projection – A Canadian case study

Xiuquan Wang, Guohe Huang, Qianguo Lin, Xianghui Nie, Guanhui Cheng, Yurui Fan, Zhong Li, Yao Yao, Meiqin Suo
2013 Environmental Modelling & Software  
This study presents a statistical downscaling tool, SCADS, based on stepwise cluster analysis method.  ...  The validated cluster trees are then applied for generating future climate projections.  ...  Acknowledgments This research was supported by the Major Project Program of the Natural Sciences Foundation (51190095), the Program for Innovative Research Team in University (IRT1127), Environment Canada  ... 
doi:10.1016/j.envsoft.2013.08.006 fatcat:eykl6rtnsfatfjtdz5pky3y7iq

Large-Scale Functional Networks Identified from Resting-State EEG Using Spatial ICA

Stéphane Sockeel, Denis Schwartz, Mélanie Pélégrini-Issac, Habib Benali, Dezhong Yao
2016 PLoS ONE  
A significant tuning parameter for sICA was the number of independent components extracted for each subject.  ...  However, there were mismatches in temporal areas resulting from a poor sensitivity of fMRI in these regions or low SNR in the EEG signals.  ... 
doi:10.1371/journal.pone.0146845 pmid:26785116 pmcid:PMC4718524 fatcat:qeot3xzl4bcqnhs5kb7arakoce

Application of Bioinformatics in Cancer Epigenetics

2004 Annals of the New York Academy of Sciences  
For each chip, we have intensities from two scans called scan A and scan B. Generally, we used the intensity values from scan A.  ...  We extracted the intensity values for each probe from the .CEL files generated by Affymetrix MAS 4.0. The .CEL files contain the fluorescent intensity values for each of the probes.  ... 
doi:10.1196/annals.1310.008 pmid:15208184 fatcat:piehisclurajzlmyjgyxtx74me

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Gehendra Bhattarai, Ainong Shi, Devi R. Kandel, Nora Solís-Gracia, Jorge Alberto da Silva, Carlos A. Avila
2021 Scientific Reports  
The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified.  ...  Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries.  ...  Acknowledgements The authors would like to acknowledge funding support in part from the USDA-AMS, USDA-SCRI, and Texas A&M AgriLife Research and Extension Center at Weslaco, TX, to use genotyping resources  ... 
doi:10.1038/s41598-021-89473-0 pmid:33976335 fatcat:ieuf2owfrnbjxohbbl2khmjbra

A simulation test of the effectiveness of several methods for error-checking non-invasive genetic data

David A. Roon, Lisette P. Waits, Katherine C. Kendall
2005 Animal Conservation  
Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation.  ...  Thus, researchers have attempted to correct PCR errors in NGS datasets using non-comprehensive error checking methods, but these approaches have not been evaluated for reliability.  ...  Joyce for advice and critical review of many of the aspects of this research.  ... 
doi:10.1017/s1367943005001976 fatcat:qewyw2epxjhzbaw4kps57dvuq4

SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing

Nicholas J Hathaway, Christian M Parobek, Jonathan J Juliano, Jeffrey A Bailey
2017 Nucleic Acids Research  
Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single  ...  SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic  ...  ACKNOWLEDGEMENTS Special thanks is given to Michael Purcaro for extensive technical C++ programming support that was extremely valuable to the software development team.  ... 
doi:10.1093/nar/gkx1201 pmid:29202193 pmcid:PMC5829576 fatcat:ay3uqium5rhazdi2vfsezaz4m4

A Combined Epithelial Mesenchymal Transformation and DNA Repair Gene Panel in Colorectal Cancer With Prognostic and Therapeutic Implication

Xiaoliang Huang, Jungang Liu, Haizhou Liu, Xianwei Mo, Yongsheng Meng, Lihua Zhang, Yuqing Deng, Yawei Zhang, Weizhong Tang
2021 Frontiers in Oncology  
Unsupervised clustering was used for classification.  ...  The least absolute shrinkage and selection operator regression method was used to develop the risk model.ResultsThree distinct CRC clusters were determined.  ...  A predicted value was calculated for every patient in the validation set on the basis of the risk model constructed in the training set.  ... 
doi:10.3389/fonc.2020.595182 pmid:33520707 pmcid:PMC7843609 fatcat:o4qlslf66nh5rf2faeffvptc7u

Three methods for optimization of cross-laboratory and cross-platform microarray expression data

P. Stafford, M. Brun
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS This project has been funded in whole or in part with Federal funds from the National Institute of Allergies and Infectious Diseases, National Institutes of Health, Department of Health  ...  Affy MAS5 is the mismatch-subtracted data from GCOS.  ...  Signals from a mismatch probe are subtracted from a perfect match probe and total signal is calculated using a one step Tukey's biweight estimate after the highest and lowest probe values are discarded  ... 
doi:10.1093/nar/gkl1133 pmid:17478523 pmcid:PMC1904274 fatcat:2wf6e7ahwjcopl6l6533ke5fhi

Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus

2005 Molecular Ecology  
We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus .  ...  The inferred phylogeny supports the hypothesized existence of an 'arid corridor' from the Horn of Africa to the Cape region.  ...  This work was supported by a Graduate Thesis Grant from the University of Central Florida (UCF) Department of Biology to MDH, a Graduate Travel Grant from the UCF College of Arts and Sciences to MDH, start-up  ... 
doi:10.1111/j.1365-294x.2005.02630.x pmid:16029477 fatcat:6hydxoirsrh4hp4dzwkg4lmtki

Offering Online Recommendations with Minimum Customer Input Through Conjoint-Based Decision Aids

Arnaud De Bruyn, John C. Liechty, Eelko K. R. E. Huizingh, Gary L. Lilien
2008 Marketing science (Providence, R.I.)  
In an empirical study, stepwise componential regression, relying on many fewer and easier-to-answer questions, achieved predictive accuracy equivalent to a traditional conjoint approach.  ...  Such a system can offer relevant recommendations quickly and with minimal customer input.  ...  Acknowledgments The authors would like to thank the Institute for the Study of Business Markets at The Pennsylvania State University for its financial support.  ... 
doi:10.1287/mksc.1070.0306 fatcat:ssgy4r6lejcsvjdjm5ffll3soq

Automatic generation of primary sequence patterns from sets of related protein sequences

R. F. Smith, T. F. Smith
1990 Proceedings of the National Academy of Sciences of the United States of America  
The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree).  ...  We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family.  ...  As an initial step in this direction, we have developed a method to extract a diagnostic pattern of primary sequence elements from any set of protein sequences displaying a minimum overall group similarity  ... 
doi:10.1073/pnas.87.1.118 pmid:2296575 pmcid:PMC53211 fatcat:n3wozvpk7vf5dhvbnjqnx4bta4

Organism identification using a genome sequence-independent universal microarray probe set

Yuri Y. Belosludtsev, Dawn Bowerman, Ryan Weil, Nishanth Marthandan, Robert Balog, Kevin Luebke, Jonathan Lawson, Stephen A. Johnston, C. Rick Lyons, Kevin O'Brien, Harold R. Garner, Thomas F. Powdrill
2004 BioTechniques  
Each sequence so generated was included into or excluded from the probe set based on Organism identification using a genome sequence-independent universal microarray probe set Yuri Y.  ...  MATERIALS AND METHODS Probe Set Design The probe set contained a combination of 9015 12-mers and 5268 13-mers.  ...  COMPETING INTEREST STATEMENT Y.Y.B. and T.F.P. are the founders of Vitruvius Biosciences, from which the concept described in this report originated and on whose behalf a patent has been filed.  ... 
doi:10.2144/04374rr02 pmid:15517977 fatcat:uk4s7fulgrbgfjg62ljtfz7l6m
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