AREM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool AREM

Tool usage distribution map

This map represents all the scientific publications referring to AREM per scientific context
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AREM specifications


Unique identifier OMICS_07424
Alternative name Aligning Reads by Expectation Maximization
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes




No version available


  • person_outline Xiaohui Xie

Additional information

Publication for Aligning Reads by Expectation Maximization

AREM citations


The effect of Nipped B like (Nipbl) haploinsufficiency on genome wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome

Clin Epigenetics
PMCID: 5574093
PMID: 28855971
DOI: 10.1186/s13148-017-0391-x

[…] tes [, , , ]. This is consistent with the close correlation of the presence of other cohesin subunits at identified Rad21-binding sites [] (Fig. b).Fig. 1 Cohesin-binding sites were identified using AREM [], with a significance cutoff based on a p value less than 1 × 10−4, resulting in a FDR below 3.0% (Fig. a). Cohesin-binding peaks ranged from ~ 200 bp to ~ 6 kb in size with the majority less t […]


Transposable elements reveal a stem cell specific class of long noncoding RNAs

Genome Biol
PMCID: 3580499
PMID: 23181609
DOI: 10.1186/gb-2012-13-11-r107
call_split See protocol

[…] e choice of one alignment per read for these meta-feature analyses should mitigate multi-mapping read challenges. Second, we remapped the reads allowing up to 20 alignments and called peaks using the AREM software package, which implements an iterative algorithm to optimally allocate multi-mapping reads built on top of the MACS method [,]. […]

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AREM institution(s)
Department of Biological Chemistry, University of California, Irvine, CA, USA; Department of Computer Science, University of California, Irvine, CA, USA; The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA
AREM funding source(s)
Partly supported by the NSF (grant DBI-0846218) and the NIH (grant HD062951) and the NIH/NLM Bioinformatics (training grant T15LM07443).

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