Biosecurity, Food Provenance, and Diagnostic Development
Qian, J., Boswell, S.A., Chidley, C. et al. An enhanced isothermal amplification assay for viral detection. Nat Commun 11, 5920 (2020). https://doi.org/10.1038/s41467-020-19258-y
Qian, J., Lu, Z.-X., Mancuso, C. P., Jhuang, H.-Y., del Carmen Barajas-Ornelas, R., Boswell, S. A., et al. (2020). Barcoded microbial system for high-resolution object provenance. Science, 368(6495), 1135–1140. http://doi.org/10.1126/science.aba5584
[Abstract, Reprint, Full Text]
Environmental Sensing and Signaling
Lee KB, Wang J, Palme J, Escalante-Chong R, Hua B, & Springer M (2017). Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes. PLoS Genetics, 13(5), e1006766. PMID:28542190.
Savir Y, Martynov A, & Springer M (2017). Achieving global perfect homeostasis through transporter regulation. PLoS Computational Biology, 13(4), e1005458. PMID:28414718.
Katz, Y., & Springer, M. (2016). Probabilistic adaptation in changing microbial environments. PeerJ, 4, e2716.
DeGennaro, C. M., Savir, Y., & Springer, M. (2016). Identifying Metabolic Subpopulations from Population Level Mass Spectrometry. PloS One, 11(3), e0151659. PMID:26986964.
Savir Y, Tu BP, Springer M (2015). Competitive Inhibition Can Linearize Dose-Response and Generate a Linear Rectifier. Cell Systems 1(3): 238-245. PMID: 26495436.
Escalante-Chong R*, Savir Y*, Carroll SM, Ingraham JB, Wang J, Marx CJ, Springer M (2015). Galactose metabolic genes in yeast respond to a ratio of galactose and glucose. PNAS 112: 1636–1641. PMCID: PMC4321281.
Wang J, Atolia E, Hua B, Savir Y, Escalante-Chong R, Springer M (2015). Natural Variation in Preparation for Nutrient Depletion Reveals a Cost-Benefit Tradeoff. PLoS Biology 13: e1002041. PMCID: PMC4308108
Byrne M, Miller N, Springer M, O’Shea EK. (2004). A distal, high-affinity binding site on the cyclin-CDK substrate Pho4 is important for its phosphorylation and regulation. J. Mol. Biol. 335(1):57-70. PMID: 14659740.
Springer M*, Wykoff D*, Miller N, O’Shea E. (2003). Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes. PLoS Biology 1(2): E28. PMCID: PMC261874.
Jeffery, DA*, Springer M*, King DS, O’Shea E. (2001). Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference. J. Mol Biol. 306(5):997-1010. PMID: 11237614.
Systems Biology of Gene Expression
Ricci-Tam C, Ben-Zion I, Wang J, Palme J, Li A, Savir Y, Springer M. Decoupling transcription factor expression and activity enables dimmer switch gene regulation. Science. 2021 Apr 16;372(6539):292-295. doi: 10.1126/science.aba7582. PMID: 33859035.
Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S (2014). A chromatin-based mechanism for limiting divergent noncoding transcription. Cell , 157(7), 1712-1723. PMCID: PMC4090027.
Gray JM, Harmin DA, Boswell SA, Cloonan N, Mullen TE, Ling JJ, … & Springer M (2014). SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample. PloS ONE, 9(2), e89673. PMCID: PMC3935918.
Busby M ,Gray J, Costa A, Stewart C, Stromberg M, Barnett D, Chuang J, Springer M, Marth G (2011). Expression divergence measured by transcriptome sequencing of four yeast species. BMC Genomics (12): 635
DeLuna A*, Springer M*, Kirschner MW, Kishony R. (2010). Need-based upregulation of protein levels in response to deletion of their duplicate genes. PLoS Biology 8(3); e1000347. PMCID: PMC2846854.
Springer M, Weissman J, and Kirschner MW. (2010). A general lack of compensation for gene dosage in yeast. Molecular Systems Biology 6:368. PMCID: PMC2890323.
+Kafri R, Springer M, Pilpel Y. (2009). Genetic redundancy: new tricks for old genes. Cell. 136(3):389-92. PMID: 19203571.
Quantitative Proteomics
Muntel J, Boswell, SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M (2014). Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment. Molecular & Cellular Proteomics mcp-M114 PMID: 25473088.
Merbl Y, Refour P, Patel H, Springer M, Kirschner MW (2013). Profiling of ubiquitin-like modifications reveals features of mitotic control. Cell, 152(5), 1160-1172. PMCID: PMC3711129
Singh S*, Springer M*, Steen J, Kirschner MW, Steen H. (2009). FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J Proteome Res. 8(5):2201-10. PMCID: PMC2868505.
Steen JA, Steen H, Georgi A, Parker K, Springer M, Kirchner M, Hamprecht F, Kirschner MW. (2008). Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. PNAS 105(16):6069-74. PMCID: PMC2329673.
Steen H, Jebanathirajah JA, Springer M, Kirschner MW. (2005). Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. PNAS. 102(11):3948-53. PMCID: PMC552780.
Other
Beach, R. R., Ricci-Tam, C., Brennan, C. M., Moomau, C. A., Hsu, P.-H., Hua, B., Silberman, R.E., Springer, M., & Amon, A. (2017). Aneuploidy causes non-genetic individuality. Cell, 169(2), 229–242. PMID:28388408
Boswell, S. A., Snavely, A., Landry, H. M., Churchman, L. S., Gray, J. M., & Springer, M. (2017). Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis. Nature Chemical Biology. Epub ahead of print. PMID:28263964
Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017). Mutation effects predicted from sequence co-variation. Nature Biotechnology, 35(2), 128–135. PMID: 28092658.
Gerardin, Y., Springer, M., & Kishony, R. (2016). A competitive trade-off limits the selective advantage of increased antibiotic production. Nature Microbiology, 1, 16175. PMID:27668360.
Torres, E. M., Springer, M., & Amon, A. (2016). No current evidence for widespread dosage compensation in S. cerevisiae. eLife, 5, 149. PMID:26949255
Jajoo, R., Jung, Y., Huh, D., Viana, M. P., Rafelski, S. M., Springer, M., & Paulsson, J. (2016). Accurate concentration control of mitochondria and nucleoids. Science, 351(6269), 169–172. PMID: 26744405
Stefan MI, Gutlerner JL, Born R, Springer M. (2015) The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences. PLoS Comput Biol. 11(4):e1004208. PMCID: PMC4399943.
Milo R, Jorgensen P, Moran U, Weber G, Springer M. (2010). BioNumbers–the database of key numbers in molecular and cell biology. Nucleic Acids Res. 38:D750-3. PMCID: PMC2808940.
Palazzo AF, Springer M, Shibata Y, Lee CS, Dias AP, Rapoport TA. (2007). The signal sequence coding region promotes nuclear export of mRNA. PLoS Biology 5(12):e322. PMCID: PMC2100149.
Milo R, Hou JH, Springer M, Brenner MP, Kirschner MW. (2007). The relationship between evolutionary and physiological variation in hemoglobin. PNAS. 104(43):16998-7003. PMCID: PMC2040440.
+Springer M, Paulsson J. (2006). Biological physics: Harmonies from noise. Nature. 439(7072):27-8. PMID: 16397487.
Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL. (2003). Viral discovery and sequence recovery using DNA microarrays. PLoS Biology 1(2):E2. PMCID: PMC261870.
*Contributed equally
+Commentary or review