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  1. Cho, C.Y., Kelliher, C.M., and Haase, S.B. (2019) The cell-cycle transcriptional network generates and transmits a pulse of transcription once each cell cycle. Cell Cycle 18, 363-378.
  2. Kelliher, C.M., Foster, M.W., Motta, F.C., Deckard, A., Soderblom, E.J., Moseley, M.A., and Haase, S.B. (2018) Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. Mol Bio Cell 29, 2644-2655.
  3. Cho, C.Y., Motta, F.C., Kelliher, C.M., Deckard, A., and Haase, S.B. (2017) Reconciling conflicting models for global control of cell-cycle transcription. Cell Cycle 16, 1965-1978.
  4. Kelliher, C.M., and Haase, S.B. (2017). Connecting virulence pathways to cell-cycle progression in the fungal pathogen Cryptococcus neoformans. Curr Genet.
  5. McGoff, K.A., Guo, X., Deckard, A., Kelliher, C.M., Leman, A.R., Francey, L.J., Hogenesch, J.B., Haase, S.B., and Harer, J.L. (2016). The Local Edge Machine: inference of dynamic models of gene regulation. Genome Biol 17, 214.
  6. Kelliher, C.M., Leman, A.R., Sierra, C.S., and Haase, S.B. (2016). Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans. PLoS Genet 12, e1006453.
  7. Perea, J.A., Deckard, A., Haase, S.B., and Harer, J. (2015). SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. BMC Bioinformatics 16, 257.
  8. Leman, A.R., Bristow, S.L., and Haase, S.B. (2014). Analyzing transcription dynamics during the budding yeast cell cycle. Methods Mol Biol 1170, 295-312.
  9. Haase, S.B., and Wittenberg, C. (2014). Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics 196, 65-90.
  10. Bristow, S.L., Leman, A.R., Simmons Kovacs, L.A., Deckard, A., Harer, J., and Haase, S.B. (2014). Checkpoints couple transcription network oscillator dynamics to cell-cycle progression. Genome Biol 15, 446.
  11. Bristow, S.L., Leman, A.R., and Haase, S.B. (2014). Cell cycle-regulated transcription: effectively using a genomics toolbox. Methods Mol Biol 1170, 3-27.
  12. Guo, X., Bernard, A., Orlando, D.A., Haase, S.B., and Hartemink, A.J. (2013). Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. Proc Natl Acad Sci U S A.
  13. Deckard, A., Anafi, R.C., Hogenesch, J.B., Haase, S.B., and Harer, J. (2013). Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. Bioinformatics 29, 3174-3180.
  14. Simmons Kovacs, L.A., Mayhew, M.B., Orlando, D.A., Jin, Y., Li, Q., Huang, C., Reed, S.I., Mukherjee, S., and Haase, S.B. (2012). Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network. Mol Cell 45, 669-679.
  15. Mayhew, M.B., Guo, X., Haase, S.B., and Hartemink, A.J. (2012). Close Encounters of the Collaborative Kind. Computer 45, 24-30.
  16. Ho, H.J., Lin, T.I., Chang, H.H., Haase, S.B., Huang, S., and Pyne, S. (2012). Parametric modeling of cellular state transitions as measured with flow cytometry. BMC Bioinformatics 13 Suppl 5, S5.
  17. Chee, M.K., and Haase, S.B. (2012). New and Redesigned pRS Plasmid Shuttle Vectors for Genetic Manipulation of Saccharomyces cerevisiae. G3: Genes|Genomes|Genetics 2, 515-526.
  18. Mayhew, M.B., Robinson, J.W., Jung, B., Haase, S.B., and Hartemink, A.J. (2011). A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. Bioinformatics 27, i295-303.
  19. Simmons Kovacs, L.A., and Haase, S.B. (2010). Cohesin: it’s not just for chromosomes anymore. Cell Cycle 9, 1750-1753.
  20. Chee, M.K., and Haase, S.B. (2010). B-cyclin/CDKs regulate mitotic spindle assembly by phosphorylating kinesins-5 in budding yeast. PLoS Genet 6, e1000935.
  21. Orlando, D.A., Iversen, E.S., Jr., Hartemink, A.J., and Haase, S.B. (2009). A Branching Process Model for Flow Cytometry and Budding Index Measurements in Cell Synchrony Experiments. Ann Appl Stat 3, 1521-1541.
  22. Simmons Kovacs, L.A., Orlando, D.A., and Haase, S.B. (2008). Transcription networks and cyclin/CDKs: the yin and yang of cell cycle oscillators. Cell Cycle 7, 2626-2629.
  23. Simmons Kovacs, L.A., Nelson, C.L., and Haase, S.B. (2008). Intrinsic and cyclin-dependent kinase-dependent control of spindle pole body duplication in budding yeast. Mol Biol Cell 19, 3243-3253.
  24. Orlando, D.A., Lin, C.Y., Bernard, A., Wang, J.Y., Socolar, J.E., Iversen, E.S., Hartemink, A.J., and Haase, S.B. (2008). Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 453, 944-947.
  25. Orlando, D.A., Lin, C.Y., Bernard, A., Iversen, E.S., Hartemink, A.J., and Haase, S.B. (2007). A probabilistic model for cell cycle distributions in synchrony experiments. Cell Cycle 6, 478-488.
  26. Haase, S.B., and Lew, D.J. (2007). Microtubule organization: cell shape is destiny. Curr Biol 17, R249-251.
  27. Jackson, L.P., Reed, S.I., and Haase, S.B. (2006). Distinct mechanisms control the stability of the related S-phase cyclins Clb5 and Clb6. Mol Cell Biol 26, 2456-2466.
  28. Haase, S.B. (2004). Cell cycle analysis of budding yeast using SYTOX Green. Curr Protoc Cytom Chapter 7, Unit 7 23.
  29. Haase, S.B., and Reed, S.I. (2002). Improved flow cytometric analysis of the budding yeast cell cycle. Cell Cycle 1, 132-136.
  30. Haase, S.B., Winey, M., and Reed, S.I. (2001). Multi-step control of spindle pole body duplication by cyclin-dependent kinase. Nat Cell Biol 3, 38-42.
  31. Haase, S.B., and Clarke, D.J. (2001). A festival of cell-cycle controls. Trends Cell Biol 11, 445-446.
  32. Kiely, J., Haase, S.B., Russell, P., and Leatherwood, J. (2000). Functions of fission yeast orp2 in DNA replication and checkpoint control. Genetics 154, 599-607.
  33. Haase, S.B., and Reed, S.I. (1999). Evidence that a free-running oscillator drives G1 events in the budding yeast cell cycle. Nature 401, 394-397.
  34. Haase, S.B., and Lew, D.J. (1997). Flow cytometric analysis of DNA content in budding yeast. Methods Enzymol 283, 322-332.
  35. Haase, S.B., Heinzel, S.S., and Calos, M.P. (1994). Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol Cell Biol 14, 2516-2524.
  36. Haase, S.B., and Calos, M.P. (1991). Replication control of autonomously replicating human sequences. Nucleic Acids Res 19, 5053-5058.
  37. Krysan, P.J., Haase, S.B., and Calos, M.P. (1989). Isolation of human sequences that replicate autonomously in human cells. Mol Cell Biol 9, 1026-1033.
  38. Haase, S.B., Heinzel, S.S., Krysan, P.J., and Calos, M.P. (1989). Improved EBV shuttle vectors. Mutat Res 220, 125-132.