Slavov lab | Quantitative Biology
Seeking  principles
in the coordination among protein synthesis, metabolism, cell growth and differentiation
      We strongly support preprinting and open access.
Wallmann G., Leduc A., Slavov N. (2023)
Data-Driven Optimization of DIA Mass-Spectrometry by DO-MS
J. Proteome Res. 22(10):3149-3158   OA   |   preprint   |   PDF   |   Code   |   Web
Slavov N. (2023)
Single-cell proteomics: quantifying post-transcriptional regulation
Development 150, dev201492   PDF   |   Web Resources
van den Berg P., Bérenger-Currias NM, Budnik B., Slavov N., Semrau S. (2023)
Integration of a multi-omics stem cell differentiation dataset using a dynamical model
PLoS Genet 19(5): e1010744   PDF   |   preprint   |   Data Web
Huffman RG, Leduc A, Wichmann C, ... and Slavov N. (2023)
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics
Nature Methods   preprint   |   PDF   |   pSCoPE web   |   Data web   |   Talk   |   Nature Research Briefing (PDF)
MacCoss MJ, Alfaro J, Faivre, D, Wu C, Wanunu M, Slavov N. (2023)
Sampling proteomes by emerging single-molecule and mass-spectrometry methods
Nature Methods 20, 339–346   preprint   |   PDF   |   SCP2022 Talk
Gatto L, Aebersold R, Cox J, Demichev V, Derks J, ..., Slavov N. (2023)
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments
Nature Methods 20, 375–386   preprint   |   PDF   |   Guidelines Web   |   Blog
Derks J, Slavov N. (2022)
Strategies for increasing the depth and throughput of protein analysis by plexDIA
J. Proteome Res.   OA   |   preprint   |   PDF   |   Code   |   Web   |   ASMS Talk
Leduc A, Huffman RG, Cantlon J, Khan S, Slavov N. (2022)
Exploring functional protein covariation across single cells using nPOP
Genome Biol 23, 261   preprint   |   PDF   |   nPOP Web   |   Data   |   Tutorials   |   Highlight by GEN   |   Perspective   |   Conference Talk
Derks J, Leduc A, Wallmann G, Huffman G, Willetts M, Khan S, Specht H, Ralser M, Demichev V, Slavov N. (2022)
Increasing the throughput of sensitive proteomics by plexDIA
Nature Biotech   preprint   |   OA   |   PDF   |   plexDIA web   |   SCP2022 Talk   |   Nature Research Briefing (PDF)   |   Nature Blog   |   Highlight by Nature Methods
Slavov N. (2022)
Counting protein molecules for single-cell proteomics
Cell 185 (2) :232-234   PDF   |   OA   |   SCP2022 Talk
Slavov N. (2022)
Learning from natural variation across the proteomes of single cells
PLoS Biology 20(1): e3001512   PDF   |   Website   |   Videos
Slavov N. (2021)
Scaling up single-cell proteomics
Molecular & Cellular Proteomics   PDF   |   Website   |   Recorded Workshop
Petelski A, Emmott E, Leduc A, Huffman RG, Specht H, Perlman D, Slavov N. (2021)
Multiplexed single-cell proteomics using SCoPE2
Nature Protocols   preprint   |   OA   |   PDF   |   Data web   |   Video Tutorials
Slavov N. (2021)
Driving Single Cell Proteomics Forward with Innovation
J. of Proteome Res., 20, 4915   |   PDF   |   Website   |   Video
Slavov N. (2021)
Increasing proteomics throughput
Nature Biotechnology, 39, 809–810, doi: 10.1038/s41587-021-00881-z   |   PDF
Slavov N. et al. (2021)
Voices of biotech research: Single-cell proteomics
Nature Biotechnology, 39, 281–286   PDF
Specht H, Emmott E, Petelski A, Huffman RG, Perlman D, Serra M, Kharchenko P, Koller A, Slavov N. (2021)
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2
Genome Biology   preprint   |   PDF   |   Data   |   SCP2019 talk   |   SCoPE2 Web  |   Highlight by Nature Methods
Specht H, Slavov N. (2020)
Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers
J. of Proteome Res.   Preprint   |   PDF   |   WebSite   |   SCP2020 talk   |   Code
Petelski AA, Slavov N. (2020)
Analyzing ribosome remodeling in health and disease
Proteomics, 20, 2000039   preprint   PDF
Slavov N. (2020)
Single-cell protein analysis by mass-spectrometry
Current Opinion in Chemical Biology, 60, 1-9   preprint   PDF   |   Summary
Slavov N. (2020)
Unpicking the proteome in single cells
Science, 367 (6477) :512–513   PDF   |   Science Highlight   |   Summary
Slavov N. et al. (2019)
Voices in methods development: Single-cell proteomics
Nature Methods, 16, 945–951   PDF
Huffman RG, Specht H, Chen AT, Slavov N. (2019)
DO-MS: Data-Driven Optimization of Mass Spectrometry Methods
J. of Proteome Res.,   preprint   |   PDF   |   GitHub   |   DO-MS web   |   DO-MS Talk
Chen AT, Franks A, Slavov N. (2019)
DART-ID increases single-cell proteome coverage
PLoS Comput Biol.   preprint   |   PDF   |   RAW Data   |   GitHub   |   DART-ID web
Emmott EP, Jovanovic M, Slavov N. (2019)
Approaches for Studying Ribosome Specialization
Trends in Biochemical Sciences   PDF   |   Summary
Emmott EP, Jovanovic M, Slavov N. (2018)
Ribosome stoichiometry: from form to function
Trends in Biochemical Sciences   preprint   |   PDF   |   Summary
Malioutov D., Chen T., Jaffe J., Airoldi E., Budnik B., Slavov N. (2018)
Quantifying homologous proteins and proteoforms
Molecular & Cellular Proteomics   preprint   |   PDF   |   HIquant code
Budnik B, Levy E, Harmange G, Slavov N. (2018)
SCoPE-MS: mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Genome Biology 19:161   preprint   |   PDF   |   Data   |   CSHL Talk   |   C&EN Highlight
Levy E, Slavov N. (2018)
Single cell protein analysis for systems biology
Essays in Biochemistry   preprint   |   PMC   |   PDF   |   Summary
Specht H, Slavov N. (2018)
Transformative opportunities for single cell proteomics
J. of Proteome Res., 17 (8), 2565 - 2571   preprint   |   PMC   |   PDF   |   Highlight
Franks A., Airoldi E., Slavov N. (2017)
Post-transcriptional regulation across human tissues
PLoS Comput Biol, 13(5): e1005535   preprint   |   PDF   |   Data Web   |   Highlight
Slavov N. (2015)
Making the most of peer review
eLife, 4:e12708   PDF
Slavov N., Semrau S., Airoldi E., Budnik B., van Oudenaarden A. (2015)
Differential stoichiometry among core ribosomal proteins
Cell Reports, vol. 13   PDF   |   SI   |   preprint   |   Data Web   |   TiBS Spotlight   |  
Malioutov D., Slavov N. (2014)
Convex Total Least Squares
JMLR, W&CP vol. 32,   PDF  |   preprint  |   Code on GitHub  |   Summary
Slavov N., Budnik B., Schwab D., Airoldi E., van Oudenaarden A. (2014)
Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis
Cell Reports, vol. 7,   PDF   |   SI   |   Data   |   Summary   |   Cell Press Q & A
Slavov N., Carey, J., Linse S. (2013)
Calmodulin transduces Ca+2 oscillations into differential regulation of its target proteins
ACS Chemical Neuroscience, vol. 4 (4)   PDF   |   Highlight Summary
Slavov N., van Oudenaarden A. (2012)
How to Regulate a Gene: To Repress or to Activate?
Mol. Cell, vol. 46, issue 5, 551-552   PDF
Slavov N., Airoldi E.M., van Oudenaarden A., Botstein D. (2012)
A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes
Mol. Biol. Cell, vol. 23, no. 10   PDF   |   Summary
Slavov N., Macinskas J., Caudy A., Botstein D. (2011)
Metabolic Cycling without Cell Division Cycling in Respiring Yeast
PNAS, vol. 108, 19090-19095   PDF   |   SI   |   Data Web   |   Behind the paper   |   Summary
Slavov N., Botstein D. (2011)
Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast
Mol. Biol. Cell, vol. 22   PDF   |   Data Web   |   MBoC Highlight
Silverman SJ., Slavov N., Petti A., Parsons L., Briehof R., Thiberge S., Zenklusen D., Gandhi SJ., Larson D., Singer R., Botstein D. (2010)
Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
PNAS, vol. 107   PDF   |   Summary   |   F1000
Tagkopoulos I., Slavov N., Kung S. (2005)
Multi-Class Biclustering and Classification Based on Modeling of Gene Regulatory Networks
IEEE Symposium on Bioinformatics and Bioengineering   PDF

Khan S, Conover R, Asthagiri AR, Slavov N. (2023)
Dynamics of single-cell protein covariation during epithelial-mesenchymal transition
bioRxiv   doi: 10.1101/2023.12.21.572913   |   PDF   |   Data Web
Leduc A, Koury L., Cantlon J., Slavov N. (2023)
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP
bioRxiv 2023.11.27.568927   doi: 10.1101/2023.11.27.568927   |   PDF   |   nPOP Protocol   |   Blog
Leduc A,Harens H, Slavov N. (2023)
Modeling and interpretation of single-cell proteogenomic data
arXiv   doi: 10.48550/arXiv.2308.07465   |   PDF   |   Web Resources
Wallmann G., Leduc A., Slavov N. (2023)
Data-Driven Optimization of DIA Mass-Spectrometry by DO-MS
bioRxiv   preprint   |   PDF   |   Code   |   Web
Derks J, Slavov N. (2022)
Strategies for increasing the depth and throughput of protein analysis by plexDIA
bioRxiv   preprint   |   PDF   |   Code   |   Web   |   YouTube Talk
MacCoss MJ, Alfaro J, Wanunu M, Faivre DA, Slavov N. (2022)
Sampling proteomes by emerging single-molecule and mass-spectrometry methods
arXiv   preprint   |   PDF   |   SCP2022 Talk on single-molecule proteomics
Leduc A, Huffman RG, Cantlon J, Khan S, Slavov N. (2022)
Exploring functional protein covariation across single cells using nPOP
bioRxiv   preprint   |   PDF   |   nPOP Web   |   Data   |   Talk   |   SCP2021 Talk
Huffman RG, Leduc A, Wichmann C, ... and Slavov N. (2022)
Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages
bioRxiv   preprint   |   PDF   |   pSCoPE web   |   Data web
Derks J, Leduc A, Huffman RG, Specht H, Ralser M, Demichev V, Slavov N. (2021)
Increasing the throughput of sensitive proteomics by plexDIA
bioRxiv   preprint   |   PDF   |   Data web   |   Talk
Leduc A, Huffman RG, Slavov N. (2021)
Droplet sample preparation for single-cell proteomics applied to the cell cycle
bioRxiv   preprint   |   PDF   |   nPOP   |   Data   |   Talk   |   SCP2021 Talk
Petelski A, Emmott E, Leduc A, Huffman RG, Specht H, Perlman D, Slavov N. (2021)
Multiplexed single-cell proteomics using SCoPE2
bioRxiv   preprint   |   PDF   |   Data
Huffman G, Specht H, Chen AT, Slavov N. (2019)
DO-MS: Data-Driven Optimization of Mass Spectrometry Methods
bioRxiv   DOI: 10.1101/512152   PDF   |   DO-MS Talk   |   DO-MS web
Chen A, Franks A, Slavov N. (2018)
DART-ID increases single-cell proteome coverage
bioRxiv   DOI: 10.1101/399121   PDF   |   DART-ID talk   |   GitHub   |   DART-ID web
Specht H, Harmange G, Perlman DH, Emmott E, Niziolek Z, Budnik B, Slavov N. Automated sample preparation for high-throughput single-cell proteomics
bioRxiv   DOI: 10.1101/399774   PDF   |   RAW Data @ MassIVE   |   SCP2018 Talk
Emmott EP, Jovanovic M, Slavov N. (2018)
Ribosome stoichiometry: from form to function
PeerJ, 6:e26991v1   PDF   |   Summary
Levy E, Slavov N. (2018)
Single cell protein analysis for systems biology
PeerJ, 6:e26965v1   PDF   |   Summary
Malioutov D., Chen T., Jaffe J., Airoldi E., Carr S., Budnik B., Slavov N. (2017)
Quantifying homologous proteins and proteoforms
bioRxiv   PDF   |   HIquant code
van den Berg P., Budnik B., Slavov N., Semrau S. (2017)
Dynamic post-transcriptional regulation during embryonic stem cell differentiation
bioRxiv   PDF   |   Data Web
Budnik B., Levy E., Harmange G., Slavov N. (2017)
Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
bioRxiv   PDF   |   Data Web   |   CSHL Talk   |   SCoPE-MS   |   Summary
Franks A., Airoldi E., Slavov N. (2016)
Post-transcriptional regulation across human tissues
bioRxiv   PDF   |   Data Web
Slavov N., Semrau S., Airoldi E.M., Budnik B., van Oudenaarden A. (2014)
Differential stoichiometry among core ribosomal proteins
bioRxiv, PDF   |   Summary   |   Data Web   |  
Malioutov D., Slavov N. (2014)
Convex Total Least Squares
arXiv, arXiv:1406.0189,   PDF  |   Code on GitHub  |   Summary

Slavov N. (2018)
We Must Demand Evidence of Peer Review
The Scientist   PDF
Slavov N. (2015)
Making the most of peer review
eLife, 4:e12708   PDF
Slavov N. (2014)
Tell me about the science, not the prizes!
The Scientist   PDF
Slavov N. (2013)
The Best Projects Are Least Obvious
The Scientist   PDF
Slavov N. (2012)
The Mission of MIT
The MIT Tech   PDF

✉ Corresponding Author(s)
☯ These authors contributed equally