Fast and sensitive multiple alignment of large genomic sequences. - Michael Brudno; Michael Chapman; Berthold Göttgens; Serafim Batzoglou; Burkhard Morgenstern (BMC Bioinform., 2003)

TFBScluster: a resource for the characterization of transcriptional regulatory networks. - Ian John Donaldson; Michael Chapman; Berthold Göttgens (Bioinform., 2005)

TFBScluster web server for the identification of mammalian composite regulatory elements. - Ian John Donaldson; Berthold Göttgens (Nucleic Acids Res., 2006)

BloodExpress: a database of gene expression in mouse haematopoiesis. - Diego Miranda-Saavedra; Subhajyoti De; Matthew W. B. Trotter; Sarah A. Teichmann; Berthold Göttgens (Nucleic Acids Res., 2009)

Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate. - Jatin Narula; Aileen M. Smith; Berthold Göttgens; Oleg A. Igoshin (PLoS Comput. Biol., 2010)

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. - Nicola Bonzanni; Abhishek Garg; K. Anton Feenstra; Judith Schütte; Sarah Kinston; Diego Miranda-Saavedra; Jaap Heringa; Ioannis Xenarios; Berthold Göttgens (Bioinform., 2013)

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. - Florian Buettner 002; Victoria Moignard; Berthold Göttgens; Fabian J. Theis (Bioinform., 2014)

TRES predicts transcription control in embryonic stem cells. - Christopher Pooley; David Ruau; Patrick Lombard; Berthold Göttgens; Anagha Joshi (Bioinform., 2014)

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. - Manuel Sánchez-Castillo; David Ruau; Adam C. Wilkinson; Felicia S. L. Ng; Rebecca Hannah; Evangelia Diamanti; Patrick Lombard; Nicola K. Wilson; Berthold Göttgens (Nucleic Acids Res., 2015)

BTR: training asynchronous Boolean models using single-cell expression data. - Chee Yee Lim; Huange Wang; Steven Woodhouse; Nir Piterman; Lorenz Wernisch; Jasmin Fisher; Berthold Göttgens (BMC Bioinform., 2016)

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data. - Daphne Ezer; Victoria Moignard; Berthold Göttgens; Boris Adryan (PLoS Comput. Biol., 2016)

A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles. - Felicia S. L. Ng; David Ruau; Lorenz Wernisch; Berthold Göttgens (Briefings Bioinform., 2018)

SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data. - Steven Woodhouse; Nir Piterman; Christoph M. Wintersteiger; Berthold Göttgens; Jasmin Fisher (BMC Syst. Biol., 2018)

A single-cell molecular map of mouse gastrulation and early organogenesis. - Blanca Pijuan-Sala; Jonathan A. Griffiths; Carolina Guibentif; Tom W. Hiscock; Wajid Jawaid; Fernando J. Calero-Nieto; Carla Mulas; Ximena Ibarra-Soria; Richard C. V. Tyser; Debbie Lee Lian Ho; Wolf Reik; Shankar Srinivas; et al. (Nat., 2019)

Decoding human fetal liver haematopoiesis. - Dorin-Mirel Popescu; Rachel A. Botting; Emily Stephenson; Kile Green; Simone Webb; Laura Jardine; Emily F. Calderbank; Krzysztof Polanski; Issac Goh; Mirjana Efremova; Meghan Acres; Daniel Maunder; et al. (Nat., 2019)

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets. - M. S. Vijayabaskar; Debbie K. Goode; Nadine Obier; Monika Lichtinger; Amber M. L. Emmett; Fatin N. Zainul Abidin; Nisar Shar; Rebecca Hannah; Salam A. Assi; Michael Lie-A.-Ling; Berthold Göttgens; Georges Lacaud; et al. (PLoS Comput. Biol., 2019)