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ChromSDE specifications


Unique identifier OMICS_06676
Name ChromSDE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for ChromSDE

ChromSDE citations


Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] d the liftOver tool of the UCSC Genome Brower to transform the Hi-C data from reference NCBI36/hg18 to reference NCBI37/hg19. The resolution of the Hi-C data processed with HOMER was set to 1 kb, and ChromSDE was used to predict the chromatin 3D structures of enhancers.We determined the enrichment of 466 TFs in eRNA regions and weakly-transcribed enhancers using FIMO with the default parameters. T […]


3D genome structure modeling by Lorentzian objective function

Nucleic Acids Res
PMCID: 5430849
PMID: 28180292
DOI: 10.1093/nar/gkw1155

[…] 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 m […]


Impact of data resolution on three dimensional structure inference methods

BMC Bioinformatics
PMCID: 4744395
PMID: 26852142
DOI: 10.1186/s12859-016-0894-z
call_split See protocol

[…] We compared tREX with its fellow modeling-based methods (BACH [], tPAM [] and PASTIS []) as well as optimization-based methods (ShRec3D [] and ChromSDE []). In fitting tREX, tPAM, and BACH to the simulation data, we normalized the data by incorporating the systematic bias information as covariates to the model. In contrast, we first normaliz […]


Reconstruction of 3D genome architecture via a two stage algorithm

BMC Bioinformatics
PMCID: 4638111
PMID: 26553003
DOI: 10.1186/s12859-015-0799-2
call_split See protocol

[…] ly 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 in 3D co […]


Manifold Based Optimization for Single Cell 3D Genome Reconstruction

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

[…] ap [], 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 in this va […]


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

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