Computational Systems Biology Methods and Protocols.7z

(typically<1 Mb), sequence all of the protein-coding regions (whole exome, 30–60 Mb), or sequence the whole genome (3 Gb). In ...

two or three cells can be required to have the same variant at the same location, which is unlikely to occur by chance with the ...

Fig. 4A typical schematic workflow of clonal structure inference and visualization based on single-cell DNA sequencing. (a) The ...

modeled as binomial process [168]. It is a soft clustering approach that provides the probabilities that a cell comes from the d ...

modifications, chromosome conformation, and replication dynam- ics. Like the scRNA-seq and scDNA-seq, the main computational cha ...

on prior assumptions or using unsupervised clustering [63]) and extract for each cell the average epigenetic state in each of th ...

integrated single-cell pipettes. J Am Chem Soc 136(31):10858–10861. https://doi. org/10.1021/ja5053279 Frohlich J, Konig H (200 ...

Picelli S, Bjorklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R (2013) Smart- seq2 for sensitive full-length transcript ...

https://doi.org/10.1016/j.celrep.2015.02. 001 Lorthongpanich C, Cheow LF, Balu S, Quake SR, Knowles BB, Burkholder WF, Solter D ...

Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A (2015) Integrated genome and transcriptome sequencing of the same ce ...

changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol 16.https://doi.org/10.1186/S13059- 015- ...

Campbell KR, Yau C (2017) switchde: infer- ence of switch-like differential expression along single-cell trajectories. Bioinfor ...

Yadav VK, De S (2015) An assessment of computational methods for estimating purity and clonality using genomic data derived fro ...

random monoallelic gene expression in mam- malian cells. Science 343(6167):193–196. https://doi.org/10.1126/science.1245316 Gru ...

structure inference from single-cell tumor sequencing. Nat Methods 13(7):573. https://doi.org/10.1038/Nmeth.3867 Fraley C, Raft ...

Huntsman DG, McAlpine JN, Aparicio S, Shah SP (2014) TITAN: inference of copy number architectures, in clonal cell popula- tions ...

Chapter 20 Progress on Diagnosis of Tuberculous Meningitis Yi-yi Wang and Bing-di Xie Abstract Central nervous system (CNS) dise ...

meningitis is the most common presentation among CNS tubercu- losis, which remains a formidable diagnostic challenge [5]. Mortal ...

(95% CI 23.0–77.0), which is higher than conventional fluores- cence microscope with 35.7% (95% CI 12.8–64.9). Specificity was v ...

2.2 Culture of Mycobacterium tuberculosis Culture of Mycobacterium tuberculosis from the CSF of TBM patients is slow and insuffi ...