Software

• Universal Protein Binding Microarray (PBM) Analysis Suite
  Berger MF, ML Bulyk
  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. (2009) 4(3):393-411

• MEDEA: Motif Enrichment of Differential Elements of Accessibility
  Mariani L*, Weinand K*, Gisselbrecht SS, Bulyk ML.
  MEDEA: analysis of transcription factor binding motifs in accessible chromatin. Genome Research, 2020. 30(5), 736-748. Epub 2020 May 18

• TF-8mer glossary and GENRE background contruction suite
  Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML.
  Identification of human lineage-specific transcriptional co-regulators enabled by a glossary of binding modules and tunable genomic backgrounds. Cell Systems. 2017 Sep 27. 5(3):187–201

• Specificity Inference for TAL Effector Design (SIFTED) Suite
  Rogers JM*, Barrera LA*, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML.
  Context influences on TALE-DNA binding revealed by quantitative profiling. Nature Communications

• Bayesian Hierarchical Model of Protein Binding Microarray (PBM) Data
  Jiang B, Liu JS, Bulyk ML.
  Bayesian hierarchical model of protein binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. Bioinformatics (2013) 29(11):1390-1398. Epub April 4, 2013.

• MultiFinder
  BR Huber and ML Bulyk
  BMC Bioinformatics (2006) 7(1):229 Additional file associated with MultiFinder Software

• PhylCRM
  *Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML.
  Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors)

• Lever
  *Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML.
  Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors)

• Lever + LOESS correction
  Aboukhalil A, Bulyk ML.
  LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics. (2012) Epub Apr 5, 2012. doi: 10.1093/bioinformatics/bts1555D

Legacy Software




The following has been superceded by newer software. A reference is provided here to support part of the Supplementary Material associated with a previous publication.




• ModuleFinder
  AA Philippakis, FS He and ML Bulyk (2005) PSB p.519-530
  *Superceded by PhylCRM

• Universal Protein Binding Microarray (PBM) Analysis Suite
  Berger MF, ML Bulyk
  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. (2009) 4(3):393-411
  *Only includes original array designs (4x44K and 8x15K)