Haystack specifications


Unique identifier OMICS_13326
Name Haystack
Interface Web user interface
Restrictions to use None
Input data Genome-scale data, patterns
Output data Key network regulatory nodes
Programming languages Perl
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Joanne Chory <>

Publication for Haystack

Haystack in publications

PMCID: 5226840
PMID: 28076377
DOI: 10.1371/journal.pone.0169923

[…] was calculated using ms excel and plotted using prism. t-test was used to calculate statistical significance (p value) between troughs and acrophases., the data was initially analyzed using haystack []. haystack is a model-based pattern-matching algorithm, which compares a collection of diurnal/circadian models against microarray time-course data to identify cycling genes. […]

PMCID: 3468600
PMID: 23071677
DOI: 10.1371/journal.pone.0046961

[…] organs/tissues., in this study, we first identified all circadian-regulated transcripts based on a microarray dataset from high-density temporal sampling of the murine liver, using jtk_cycle and haystack . we went on to re-define lcgs and two other datasets—non-liver circadian genes (nlcgs) and liver-expressed non-circadian genes (lncgs)—based on our new analysis strategies. we also […]

PMCID: 3047585
PMID: 21407816
DOI: 10.1371/journal.pone.0017613

[…] showed some special periodic patterns that were non-sinusoidal periodic patterns, such as probe set os.22928.2.s1_at () with a periodic expression value and a spike-shaped pattern according to haystack (http://haystack.cgrb.oregonstate.edu/). this approach appears to be efficient in analyzing short time-series compared with the spectral method and has a simpler computational procedure […]

PMCID: 2990718
PMID: 21124901
DOI: 10.1371/journal.pone.0014101

[…] pca was performed using the pcamethods bioconductor package . the heatmap () was generated in microsoft excel using a macro kindly provided by yves gibon (inra bordeaux, france). haystack algorithm was used to identify circadian regulation of transcripts and metabolites based on either 16/8 or 8/16 hours (peak/trough) models in order to match the long-day light/dark cycles […]

PMCID: 3095283
PMID: 20576144
DOI: 10.1186/1471-2229-10-126

[…] following preprocessing and normalization of the raw hybridization values, genes on the array exhibiting circadian waveforms were identified by two well-established methods known as cosopt and haystack [,]. cosopt is a method that fits gene expression profiles to a series of modified cosine models, with the agreement between the experimental data and the model reported by the mmc-β value […]

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Haystack institution(s)
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
Haystack funding source(s)
This work was supported by the Howard Hughes Medical Institute, National Institutes of Health grants GM56006 and GM67837 and GM52413 and GM62932, and a NSF Plant Genome grant DBI 0605240, Ruth L. Kirschstein NIH Postdoctoral Fellowships, and the National Sciences and Engineering Research Council of Canada Fellowship.

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