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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1974 3
1977 1
1983 1
1987 3
1988 3
1989 11
1991 5
1992 58
1993 270
1994 204
1995 156
1996 244
1997 254
1998 306
1999 319
2000 424
2001 537
2002 610
2003 950
2004 1104
2005 1181
2006 1226
2007 1178
2008 1144
2009 1245
2010 1432
2011 1650
2012 1810
2013 1547
2014 1903
2015 2218
2016 2456
2017 2454
2018 2506
2019 1299
2020 54
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27,515 results
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Page 1
Single-cell RNA sequencing: Technical advancements and biological applications.
Hedlund E and Deng Q. Mol Aspects Med 2018 - Review. PMID 28754496
Cells are the basic building blocks of organisms and each cell is unique. Single-cell RNA sequencing has emerged as an indispensable tool to dissect the cellular heterogeneity and decompose tissues into cell types and/or cell states, which offers enormous potential for de novo discovery. ...The applications of these methods in different biological contexts are also discussed. We anticipate an ever-increasing role of single-cell RNA sequencing in biology with further improvement in providing spatial information and coupling to other cellular modalities. ...
Cells are the basic building blocks of organisms and each cell is unique. Single-cell RNA sequencing has emerged as
A crash course in sequencing for a microbiologist.
Kozińska A, et al. J Appl Genet 2019 - Review. PMID 30684135 Free PMC article.
The major goal of next-generation sequencing for a microbiologist is not really resolving another circular genomic sequence. NGS started its infancy from basic structural and functional genomics, to mature into the molecular taxonomy, phylogenetic and advanced comparative genomics. ...
The major goal of next-generation sequencing for a microbiologist is not really resolving another circular genomic sequence
Accurate detection of complex structural variations using single-molecule sequencing.
Sedlazeck FJ, et al. Nat Methods 2018. PMID 29713083 Free PMC article.
Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. ...NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings....
Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are
Nanopore sequencing data analysis: state of the art, applications and challenges.
Magi A, et al. Brief Bioinform 2018. PMID 28637243
Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinformatic community comparing performance and reporting limits and advantages of using this new generation of sequences for genomic analyses. Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution. ...
Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehens …
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
Frampton GM, et al. Nat Biotechnol 2013. Among authors: An P. PMID 24142049 Free PMC article.
As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. ...Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests....
As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match
Describing Sequence Variants Using HGVS Nomenclature.
den Dunnen JT. Methods Mol Biol 2017. PMID 27822869
DNA sequencing is usually performed to determine the sequence of a region of interest or even the entire genome of an individual. After sequencing, the sequence obtained is compared to a reference, all differences (the variants) are recorded, and the possible consequences of the changes identified, on both the RNA and protein level, are predicted. ...
DNA sequencing is usually performed to determine the sequence of a region of interest or even the entire genome of an i …
Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.
Stuart T, et al. Methods Mol Biol 2018. PMID 29524143
Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required. Here, we outline a step-by-step approach for the analysis and interpretation of WGBS data. First, sequencing reads must be trimmed, quality checked, and aligned to the genome. Second, DNA methylation levels are estimated at each cytosine position using the aligned sequence reads of the bisulfite treated DNA. ...
Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are requir …
Bioinformatics Analysis of Whole Exome Sequencing Data.
Ulintz PJ, et al. Methods Mol Biol 2019. PMID 30350213
This chapter contains a step-by-step protocol for identifying somatic SNPs and small Indels from next-generation sequencing data of tumor samples and matching normal samples. ...Variants are annotated with population allele frequencies and curated resources such as GnomAD and ClinVar and curated effect predictions from dbNSFP using VCFtools, SnpEff, and SnpSift....
This chapter contains a step-by-step protocol for identifying somatic SNPs and small Indels from next-generation sequencing da …
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
Ellrott K, et al. Cell Syst 2018. PMID 29596782 Free PMC article.
Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. ...
Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybr …
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.
Ainscough BJ, et al. Nat Genet 2018. PMID 30397337 Free PMC article.
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consuming, costly, poorly standardized, and non-reproducible. Here, we systematized and standardized somatic variant refinement using a machine learning approach. ...
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somat …
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