Software

tTt and qTfy enable single- cell tracking and quantification of cellular and molecular properties in time-lapse imaging data. Reference: Hilsenbeck et al, Nat. Biotechnol. 34, 703-706 (2016), DOI: 10.1038/nbt.362 

destiny: An R library for diffusion maps
Reference: Ph. Angerer et al. Bioinformatics, doi: 10.1093/bioinformatics/btv715 (2015)

MCA: A visualization method for correlated subpopulations
Reference: J. Feigelman et al. BMC Bioinformatics 15:240 (2014)
scLVM: A modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation
Reference: Buettner, F. et al. Nat. Biotechnol. 33, 155-160 (2015)
MONA: A new method for investigating biological functions across multiple "omics" levels via integrated GO enrichment
Reference: Sass, S. et al. Bioinformatics 31, 128-130 (2015)
GPLVM for time-structured gene-expression data
Reference: Buettner, F. & Theis, F. J. (2012). Bioinformatics, 28(18), i626-i632
D2D Software: A collection of numerical methods for quantitative dynamic modeling of biochemical processes, which provides reliable and efficient model calibration methods
Reference: Raue A., et al. PLOS ONE, 8(9), e74335, 2013
stochprofML: Parameterize cell-to-cell regulatory heterogeneities using stochastic profiling and maximum likelihood estimation
Reference: S.S. Bajikar, C. Fuchs et al. PNAS 2014, 111(5), E626-635
Odefy: From discrete to continuous models
Reference: Krumsiek J et al. BMC Bioinformatics. 2010, 11:233
PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes
Reference: Ruepp A, et al. Genome Biology 2010, 11:R6
simbTUM: Simulation of stochastic processes and ODE models in biology
Reference: S. Dräxl et al. Nature Commun.  4:2092 (2013), DOI: 10.1038/ncomms309
iVUN: A visualization toolbox which supports uncertainty-aware analysis of static and dynamic attributes of biochemical reaction networks
Reference: C. Vehlow et al. BMC Syst. Biol., 14(Suppl 19):S2, 2013
bioSDP: A Matlab Toolbox for the analysis of uncertain biochemical networks via semidefinite programming
Reference: J. Hasenauer, et al. IET Syst. Biol., 4(2):119-130, 2010
zfishDB uses links between orthologous genes to retrieve hypothetical interactions between zebrafish genes
Reference: K.J. Webb, et al. Genome Biol. 10 (2009) R81. doi:10.1186/gb-2009-10-7-r81
Gepard: A very fast dotplotting tool for the comparisons of two genome sequences
Reference: Krumsiek J, et al. Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896
GraDe: Knowledge-based matrix factorization
Reference: Kowarsch A, et al. BMC Bioinformatics, 11:585, 2010
fuzzyClustering
Reference: M. L. Hartsperger, et al. BMC Bioinformatics 11:522, 2010
CSA: colored subspace analysis
Reference:
Vertex Centralities in Input-Output Networks
Reference: Blöchl F, et al. Phys, Rev. E, 83(4):046127, 2011

miRco: miRco predicts cooperatively targeted mRNAs based on binding site distances
Reference: Rinck, A. et al. RNA Biol. 10, 1125-1135 (2013)