Publications
2025
Expansion and Revision of the Genus Xanthobacter and Proposal of Roseixanthobacter gen. nov. Soltysiak, Maximillian PM, Amogh P. Jalihal, Caroline E. Christophersen, Audrey LH Ory, Andrew D. Lee, Jessica Boulton, and Michael Springer. IJSEM 75, no. 9 (2025):006909 https://doi.org/10.1099/ijsem.0.006909
groovDB in 2025: A community-editable database of small molecule biosensors. Love, Joshua D., Brady M. Rafferty, Michael Thomas, Michael Springer, Pamela A. Silver, and Simon d’Oelsnitz. bioRxiv (2025): 2025-08. https://doi.org/10.1101/2025.08.18.670880
Continuous accelerated rock weathering by marine bacteria with enhanced siderophore production. Dalvie, Neil C., Amogh P. Jalihal, Jan-Tobias Böhnke, Quincey A. Justman, Pamela A. Silver, and Michael Springer. bioRxiv (2025): 2025-04. https://doi.org/10.1101/2025.04.08.647837
XanthoMoClo─ A Robust Modular Cloning Genetic Toolkit for the Genera Xanthobacter and Roseixanthobacter. Soltysiak, Maximillian PM, Audrey LH Ory, Andrew D. Lee, Caroline E. Christophersen, Amogh P. Jalihal, and Michael Springer. ACS Synthetic Biology 14, no. 4 (2025): 1173-1190. https://doi.org/10.1021/acssynbio.4c00806
Using enantioselective biosensors to evolve asymmetric biocatalysts. d'Oelsnitz, Simon, Wantae Kim, Haley Hardtke, Svetlana Ikonomova, Nina Alperovich, Olga Vasilyeva, Michael James et al. Research Square (Preprint). (2025). https://doi.org/10.21203/rs.3.rs-5861295/v1
The galactokinase enzyme of yeast senses metabolic flux to stabilize galactose pathway regulation. Palme, Julius, Ang Li, and Michael Springer. Nature Metabolism 7, no. 1 (2025): 137-147. https://doi.org/10.1038/s42255-024-01181-x
2024
Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission During the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study Using Genomic Epidemiology. Banga, Jaspreet, Taylor Brock-Fisher, Brittany A. Petros, Eric Y. Dai, Ariana T. Leonelli, Sabrina T. Dobbins, Katelyn S. Messer et al. In Open Forum Infectious Diseases, vol. 11, no. 11, p. ofae591. US: Oxford University Press, 2024. https://doi.org/10.1093/ofid/ofae631.142
Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study. Paull, Jillian S., Brittany A. Petros, Taylor M. Brock-Fisher, Samantha A. Jalbert, Victoria M. Selser, Katelyn S. Messer, Sabrina T. Dobbins et al. The Lancet Microbe 5, no. 5 (2024): e468-e477. https://doi.org/10.1016/S2666-5247(23)00399-3
Microbial Catalysis for CO2 Sequestration: A Geobiological Approach. Van Den Berghe, Martin, Nathan G. Walworth, Neil C. Dalvie, Chris L. Dupont, Michael Springer, M. Grace Andrews, Stephen J. Romaniello et al. Cold Spring Harbor Perspectives in Biology 16, no. 5 (2024): a041673. https://doi.org/10.1101/cshperspect.a041673
LanTERN: a fluorescent sensor that specifically responds to lanthanides. Jones, Ethan M., Yang Su, Chris Sander, Quincey A. Justman, Michael Springer, and Pamela A. Silver. ACS Synthetic Biology 13, no. 3 (2024): 958-962. https://doi.org/10.1021/acssynbio.3c00600
2023
Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics. Liu, Andrew Bo, Daniel Lee, Amogh Prabhav Jalihal, William P. Hanage, and Michael Springer. Nature Communications 14, no. 1 (2023): 8479. https://doi.org/10.1038/s41467-023-44199-7
Systematic profiling of subtelomeric silencing factors in budding yeast. Juárez-Reyes, Alejandro, J. Abraham Avelar-Rivas, Jhonatan A. Hernandez-Valdes, Bo Hua, Sergio E. Campos, James González, Alicia González, Michael Springer, Eugenio Mancera, and Alexander DeLuna. G3: Genes, Genomes, Genetics 13, no. 10 (2023): jkad153. https://doi.org/10.1093/g3journal/jkad153
Early introduction and rise of the Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant in highly vaccinated university populations. Petros, Brittany A., Jacquelyn Turcinovic, Nicole L. Welch, Laura F. White, Eric D. Kolaczyk, Matthew R. Bauer, Michael Cleary et al. Clinical Infectious Diseases 76, no. 3 (2023): e400-e408. https://doi.org/10.1093/cid/ciac413
2022
Viral kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron infection in mRNA-vaccinated individuals treated and not treated with nirmatrelvir-ritonavir. Dai, Eric Y., Kannon A. Lee, Audrey B. Nathanson, Ariana T. Leonelli, Brittany A. Petros, Taylor Brock-Fisher, Sabrina T. Dobbins et al. medRxiv (2022). https://doi.org/10.1101/2022.08.04.22278378
Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Arizti-Sanz, Jon, A’Doriann Bradley, Yibin B. Zhang, Chloe K. Boehm, Catherine A. Freije, Michelle E. Grunberg, Tinna-Solveig F. Kosoko-Thoroddsen et al. Nature biomedical engineering 6, no. 8 (2022): 932-943. https://doi.org/10.1038/s41551-022-00889-z
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Welch, Nicole L., Meilin Zhu, Catherine Hua, Juliane Weller, Marzieh Ezzaty Mirhashemi, Tien G. Nguyen, Sreekar Mantena et al. Nature medicine 28, no. 5 (2022): 1083-1094. https://doi.org/10.1038/s41591-022-01734-1
Association of COVID-19 quarantine duration and postquarantine transmission risk in 4 university cohorts. Liu, Andrew Bo, Dan Davidi, Hannah Emily Landsberg, Maria Francesconi, Judy T. Platt, Giang T. Nguyen, Sehyo Yune et al. JAMA network open 5, no. 2 (2022): e220088-e220088. https://doi.org/10.1001/jamanetworkopen.2022.0088
Analytic sensitivity of the Abbott BinaxNOW™ lateral flow immunochromatographic assay for the SARS-CoV-2 Omicron variant. Kanjilal, Sanjat, Sujata Chalise, Adnan Shami Shah, Chi-An Cheng, Yasmeen Senussi, Michael Springer, and David R. Walt. Medrxiv (2022): 2022-01. https://doi.org/10.1101/2022.08.04.22278378
2021
Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation. Hong, Jiayin, Julius Palme, Bo Hua, and Michael Springer. PLoS Computational Biology 17, no. 9 (2021): e1008691. https://doi.org/10.1371/journal.pcbi.1008691
Passive plasma membrane transporters play a critical role in perception of carbon availability in yeast. Jalihal, Amogh Prabhav, Christine DeGennaro, Han-Ying Jhuang, Nicoletta Commins, Spencer Hamrick, and Michael Springer. bioRxiv (2021): 2021-09. https://doi.org/10.1101/2021.09.11.459425
Variation in the modality of a yeast signaling pathway is mediated by a single regulator. Palme, Julius, Jue Wang, and Michael Springer. Elife 10 (2021): e69974. https://doi.org/10.7554/eLife.69974
Accessioning and automation compatible anterior nares swab design. Pettit, Mary E., Sarah A. Boswell, Jason Qian, Richard Novak, and Michael Springer. Journal of Virological Methods 294 (2021): 114153. https://doi.org/10.1016/j.jviromet.2021.114153
A Semi-Quantitative isothermal diagnostic assay utilizing competitive amplification. Mancuso, Christopher P., Zhi-Xiang Lu, Jason Qian, Sarah A. Boswell, and Michael Springer. Analytical chemistry 93, no. 27 (2021): 9541-9548. https://doi.org/10.1021/acs.analchem.1c01576
Amplicon residues in research laboratories masquerade as COVID-19 in surveillance tests. Davidi, Dan, Susan Fitzgerald, Hannah L. Glaspell, Samantha Jalbert, Catherine M. Klapperich, Lena Landaverde, Stylianos Maheras et al. Cell reports methods 1, no. 1 (2021). https://doi.org/10.1016/j.crmeth.2021.100005
Decoupling transcription factor expression and activity enables dimmer switch gene regulation. Ricci-Tam, C., I. Ben-Zion, J. Wang, J. Palme, A. Li, Y. Savir, and M. Springer. Science 372, no. 6539 (2021): 292-295. https://doi.org/10.1126/science.aba7582
2020
The impacts of testing cadence, mode of instruction, and student density on fall 2020 covid-19 rates on campus. Stubbs, Christopher W., Michael Springer, and Tasha S. Thomas. MedRxiv (2020): 2020-12. https://doi.org/10.1101/2020.12.08.20244574
Computational study on ratio-sensing in yeast galactose utilization pathway. Hong, Jiayin, Bo Hua, Michael Springer, and Chao Tang. PLoS computational biology 16, no. 12 (2020): e1007960. https://doi.org/10.1371/journal.pcbi.1007960
An enhanced isothermal amplification assay for viral detection. Qian, Jason, Sarah A. Boswell, Christopher Chidley, Zhi-xiang Lu, Mary E. Pettit, Benjamin L. Gaudio, Jesse M. Fajnzylber et al. Nature Communications 11, no. 1 (2020): 5920. https://doi.org/10.1038/s41467-020-19258-y
Barcoded microbial system for high-resolution object provenance. Qian, Jason, Zhi-xiang Lu, Christopher P. Mancuso, Han-Ying Jhuang, Rocío del Carmen Barajas-Ornelas, Sarah A. Boswell, Fernando H. Ramírez-Guadiana et al. Science 368, no. 6495 (2020): 1135-1140. https://doi.org/10.1126/science.aba5584
2019
Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. Tye, Blake W., Nicoletta Commins, Lillia V. Ryazanova, Martin Wühr, Michael Springer, David Pincus, and L. Stirling Churchman. elife 8 (2019): e43002. https://doi.org/10.7554/eLife.43002
Evaluation of Dunphy et al.: Suggestions to Solidify, Clarify, and Focus without Substantial New Work. Springer, Michael. Cell Systems 8, no. 1 (2019): 1-2. https://doi.org/10.1016/j.cels.2018.12.011
Widespread cumulative influence of small effect size mutations on yeast quantitative traits. Hua, Bo, and Michael Springer. Cell systems 7, no. 6 (2018): 590-600. https://doi.org/10.1016/j.cels.2018.11.004
2018
Embodying probabilistic inference in biochemical circuits. Katz, Yarden, Michael Springer, and Walter Fontana. arXiv preprint arXiv:1806.10161 (2018). https://doi.org/10.48550/arXiv.1806.10161
Assigning function to natural allelic variation via dynamic modeling of gene network induction. Richard, Magali, Florent Chuffart, Hélène Duplus‐Bottin, Fanny Pouyet, Martin Spichty, Etienne Fulcrand, Marianne Entrevan et al. Molecular Systems Biology 14, no. 1 (2018): e7803. https://doi.org/10.15252/msb.20177803
2017
Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes. Lee, Kayla B., Jue Wang, Julius Palme, Renan Escalante-Chong, Bo Hua, and Michael Springer. PLoS genetics 13, no. 5 (2017): e1006766. https://doi.org/10.1371/journal.pgen.1006766
Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis. Boswell, Sarah A., Andrew Snavely, Heather M. Landry, L. Stirling Churchman, Jesse M. Gray, and Michael Springer. Nature chemical biology 13, no. 5 (2017): 501-507. https://doi.org/10.1038/nchembio.2317
Achieving global perfect homeostasis through transporter regulation. Savir, Yonatan, Alexander Martynov, and Michael Springer. PLoS computational biology 13, no. 4 (2017): e1005458. https://doi.org/10.1371/journal.pcbi.1005458
Aneuploidy causes non-genetic individuality. Beach, Rebecca R., Chiara Ricci-Tam, Christopher M. Brennan, Christine A. Moomau, Pei-hsin Hsu, Bo Hua, Rebecca E. Silberman, Michael Springer, and Angelika Amon. Cell 169, no. 2 (2017): 229-242. https://doi.org/10.1016/j.cell.2017.03.021
Mutation effects predicted from sequence co-variation. Hopf, Thomas A., John B. Ingraham, Frank J. Poelwijk, Charlotta PI Schärfe, Michael Springer, Chris Sander, and Debora S. Marks. Nature biotechnology 35, no. 2 (2017): 128-135. https://doi.org/10.1038/nbt.3769
2016
Probabilistic adaptation in changing microbial environments. Katz, Yarden, and Michael Springer. PeerJ 4 (2016): e2716. https://doi.org/10.7717/peerj.2716
A competitive trade-off limits the selective advantage of increased antibiotic production. Gerardin, Ylaine, Michael Springer, and Roy Kishony. Nature microbiology 1, no. 12 (2016): 1-7. https://doi.org/10.1038/nmicrobiol.2016.175
Take Your Medicine; It’s Good For You. Teaching Quantitative Principles To Biologists. Springer, Michael. The FASEB Journal 30, S1 (2016): 104.1 https://doi.org/10.1096/fasebj.30.1_supplement.104.1
Identifying metabolic subpopulations from population level mass spectrometry. DeGennaro, Christine M., Yonatan Savir, and Michael Springer. PLoS One 11, no. 3 (2016): e0151659. https://doi.org/10.1371/journal.pone.0151659
No current evidence for widespread dosage compensation in S. cerevisiae. Torres, Eduardo M., Michael Springer, and Angelika Amon. Elife 5 (2016): e10996. https://doi.org/10.7554/eLife.10996
Accurate concentration control of mitochondria and nucleoids. Jajoo, Rishi, Yoonseok Jung, Dann Huh, Matheus P. Viana, Susanne M. Rafelski, Michael Springer, and Johan Paulsson. Science 351, no. 6269 (2016): 169-172. https://doi.org/10.1126/science.aaa8714
2015
Competitive inhibition can linearize dose-response and generate a linear rectifier. Savir, Yonatan, Benjamin P. Tu, and Michael Springer. Cell systems 1, no. 3 (2015): 238-245. https://doi.org/10.1016/j.cels.2015.09.001
The quantitative methods boot camp: teaching quantitative thinking and computing skills to graduate students in the life sciences. Stefan, Melanie I., Johanna L. Gutlerner, Richard T. Born, and Michael Springer. PLOS Computational Biology 11, no. 4 (2015): e1004208. https://doi.org/10.1371/journal.pcbi.1004208
Galactose metabolic genes in yeast respond to a ratio of galactose and glucose. Escalante-Chong, Renan, Yonatan Savir, Sean M. Carroll, John B. Ingraham, Jue Wang, Christopher J. Marx, and Michael Springer. Proceedings of the National Academy of Sciences 112, no. 5 (2015): 1636-1641. https://doi.org/10.1073/pnas.1418058112
Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA)*[S]. Muntel, Jan, Sarah A. Boswell, Shaojun Tang, Saima Ahmed, Ilan Wapinski, Greg Foley, Hanno Steen, and Michael Springer. Molecular & Cellular Proteomics 14, no. 2 (2015): 430-440. https://doi.org/10.1074/mcp.M114.044321
Natural variation in preparation for nutrient depletion reveals a cost–benefit tradeoff. Wang, Jue, Esha Atolia, Bo Hua, Yonatan Savir, Renan Escalante-Chong, and Michael Springer. PLoS biology 13, no. 1 (2015): e1002041. https://doi.org/10.1371/journal.pbio.1002041
2014
A chromatin-based mechanism for limiting divergent noncoding transcription. Marquardt, Sebastian, Renan Escalante-Chong, Nam Pho, Jue Wang, L. Stirling Churchman, Michael Springer, and Stephen Buratowski. Cell 157, no. 7 (2014): 1712-1723. https://doi.org/10.1016/j.cell.2014.04.036
SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample. Gray, Jesse M., David A. Harmin, Sarah A. Boswell, Nicole Cloonan, Thomas E. Mullen, Joseph J. Ling, Nimrod Miller et al. PloS one 9, no. 2 (2014): e89673. https://doi.org/10.1371/journal.pone.0089673
2013
Profiling of ubiquitin-like modifications reveals features of mitotic control. Merbl, Yifat, Phillipe Refour, Hevan Patel, Michael Springer, and Marc W. Kirschner. Cell 152, no. 5 (2013): 1160-1172. https://doi.org/10.1016/j.cell.2013.02.007
2011
Expression divergence measured by transcriptome sequencing of four yeast species. Busby, Michele A., Jesse M. Gray, Allen M. Costa, Chip Stewart, Michael P. Stromberg, Derek Barnett, Jeffrey H. Chuang, Michael Springer, and Gabor T. Marth. BMC genomics 12, no. 1 (2011): 635. https://doi.org/10.1186/1471-2164-12-635
2010
Expression divergence measured by transcriptome sequencing of four yeast species. Busby, Michele A., Jesse M. Gray, Allen M. Costa, Chip Stewart, Michael P. Stromberg, Derek Barnett, Jeffrey H. Chuang, Michael Springer, and Gabor T. Marth. BMC genomics 12, no. 1 (2011): 635. https://doi.org/10.1186/1471-2164-12-635
A general lack of compensation for gene dosage in yeast. Springer, Michael, Jonathan S. Weissman, and Marc W. Kirschner. Molecular systems biology 6, no. 1 (2010): 368. https://doi.org/10.1038/msb.2010.19
Need-based up-regulation of protein levels in response to deletion of their duplicate genes. DeLuna, Alexander, Michael Springer, Marc W. Kirschner, and Roy Kishony. PLoS biology 8, no. 3 (2010): e1000347. https://doi.org/10.1371/journal.pbio.1000347
BioNumbers—the database of key numbers in molecular and cell biology. Milo, Ron, Paul Jorgensen, Uri Moran, Griffin Weber, and Michael Springer. Nucleic acids research 38, no. suppl_1 (2010): D750-D753. https://doi.org/10.1093/nar/gkp88
2009
FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. Singh, Sasha, Michael Springer, Judith Steen, Marc W. Kirschner, and Hanno Steen. Journal of proteome research 8, no. 5 (2009): 2201-2210. https://doi.org/10.1021/pr800654s
Genetic redundancy: new tricks for old genes. Kafri, Ran, Michael Springer, and Yitzhak Pilpel. Cell 136, no. 3 (2009): 389-392. https://doi.org/10.1016/j.cell.2009.01.027
2008
Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. Steen, Judith AJ, Hanno Steen, Ann Georgi, Kenneth Parker, Michael Springer, Marc Kirchner, Fred Hamprecht, and Marc W. Kirschner. Proceedings of the National Academy of Sciences 105, no. 16 (2008): 6069-6074. https://doi.org/10.1073/pnas.0709807104
2007
The signal sequence coding region promotes nuclear export of mRNA. Palazzo, Alexander F., Michael Springer, Yoko Shibata, Chung-Sheng Lee, Anusha P. Dias, and Tom A. Rapoport. PLoS biology 5, no. 12 (2007): e322. https://doi.org/10.1371/journal.pbio.0050322
The relationship between evolutionary and physiological variation in hemoglobin. Milo, Ron, Jennifer H. Hou, Michael Springer, Michael P. Brenner, and Marc W. Kirschner. Proceedings of the National Academy of Sciences 104, no. 43 (2007): 16998-17003. https://doi.org/10.1073/pnas.0707673104
2006
Harmonies from noise. Springer, Michael, and Johan Paulsson. Nature 439, no. 7072 (2006): 27-28. https://doi.org/10.1038/439027a
2005
Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Steen, Hanno, Judith A. Jebanathirajah, Michael Springer, and Marc W. Kirschner. Proceedings of the National Academy of Sciences 102, no. 11 (2005): 3948-3953. https://doi.org/10.1073/pnas.0409536102
2004
A distal, high-affinity binding site on the cyclin-CDK substrate Pho4 is important for its phosphorylation and regulation. Byrne, Meghan, Nicole Miller, Michael Springer, and Erin K. O'Shea. Journal of molecular biology 335, no. 1 (2004): 57-70. https://doi.org/10.1016/j.jmb.2003.10.035
2003
Viral discovery and sequence recovery using DNA microarrays. Wang, David, Anatoly Urisman, Yu-Tsueng Liu, Michael Springer, Thomas G. Ksiazek, Dean D. Erdman, Elaine R. Mardis et al. PLoS biology 1, no. 2 (2003): e2. https://doi.org/10.1371/journal.pbio.0000002
Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. Springer, Michael, Dennis D. Wykoff, Nicole Miller, and Erin K. O'Shea. PLoS Biology 1, no. 2 (2003): e28. https://doi.org/10.1371/journal.pbio.0000028
2001
Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference. Jeffery, Douglas A., Michael Springer, David S. King, and Erin K. O’Shea. Journal of molecular biology 306, no. 5 (2001): 997-1010. https://doi.org/10.1006/jmbi.2000.4417
1995
Measurement of the state‐specific differential cross section for the H+ D2→ HD (v′= 4, J′= 3)+ D reaction at a collision energy of 2.2 eV. Shafer‐Ray, Neil E., Frédéric Merkt, Daniel J. Hughes, Michael Springer, Richard P. Tuckett, and Richard N. Zare. Journal of Chemical Physics 103, no. 12 (1995): 5157-5160. https://doi.org/10.1063/1.470604
1994
Direct Measurement of the Three-Dimensional Product Velocity Distribution from Photoinitiated Bulb Reactions. Shafer, Neil E., Hao Xu, Richard P. Tuckett, Michael Springer, and Richard N. Zare. The Journal of Physical Chemistry 98, no. 13 (1994): 3369-3378. https://doi.org/10.1021/j100064a018