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ChromSDE specifications

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 Unique identifier OMICS_06676 ChromSDE Package/Module Command line interface None Unix/Linux, Mac OS, Windows Java Advanced Stable Yes

Publication for ChromSDE

library_books

3D chromosome modeling with semi-definite programming and Hi-C data.

2013 J Comput Biol
PMID: 24195706

ChromSDE in publications

(4)
library_books

3D genome structure modeling by Lorentzian objective function

PMCID: 5430849
PMID: 28180292
DOI: 10.1093/nar/gkw1155

[…] \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\alpha$\end{document}., we compared our methods with four methods implemented in () and with chromsde (), shrec3d () and mogen () using the synthetic data sets. the first four methods include two classic multidimensional scaling methods (metric multidimensional scaling – mds2 and non-metric […]

library_books

Impact of data resolution on three dimensional structure inference methods

PMCID: 4744395
PMID: 26852142
DOI: 10.1186/s12859-016-0894-z

[…] obtains a consensus 3d structure by minimizing some objective function, such as the total “differences” between the translated distances and those inferred from the hypothesized 3d architecture [–]. chromsde [] is an example in this category, but it also estimates the degree of the inverse relationship in addition to the 3d coordinates in the optimization step. further, the distances […]

library_books

Reconstruction of 3D genome architecture via a two stage algorithm

PMCID: 4638111
PMID: 26553003
DOI: 10.1186/s12859-015-0799-2

[…] insensitive to link weighting and enjoys good overall performance speed as further described in the ‘’., an intermediary strategy is represented by the methodology of zhang et al. []. this approach, chromsde, (i) invokes a power law relationship between spatial distances and contact frequencies: d ij=(f ij)−α if f ij>0; d ij=∞ if f ij=0, (ii) uses weighted, penalized mds to obtain points […]

library_books

Manifold Based Optimization for Single Cell 3D Genome Reconstruction

PMCID: 4532452
PMID: 26262780
DOI: 10.1371/journal.pcbi.1004396

[…] [], while the adaptation to 3d genome reconstruction was named shrec3d in lesne et al. []. in the following we will refer to this method simply as cmds. in addition, we present comparison with the chromsde method of zhang et al. [], which is based on semidefinite programming and is significantly more computationally demanding than both the cmds method and mbo., the structure considered […]

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ChromSDE institution(s)
1 School of Computing, National University of Singapore, Singapore, Singapore

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