Leduc A, Khoury L., Cantlon J., Khan S, Slavov N.^✉ (2024)
Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP
Nature Protocols   preprint   |   PDF   |   Web   |   Blog   |   Primer Video

Galatidou S, Petelski A, Pujol A, Lattes K,... Slavov N^✉, Barragan M (2024)
Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes
Molecular Human Reproduction   doi: 10.1093/molehr/gaae023   |   PDF   |   Data

Rogers ZJ, Colombani T, Khan S, et al. (2024)
Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions
Adv Sci. e2402557.   doi: 10.1002/advs.202402557   |   PDF

Khan S, Conover R, Asthagiri AR, Slavov N.^✉ (2024)
Dynamics of single-cell protein covariation during epithelial-mesenchymal transition
J. Proteome Res.   doi: 10.1021/acs.jproteome.4c00277   |   PDF   |   Data Web

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.^✉, Botstein D.^✉ (2013)
Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression
Mol. Biol. Cell, vol. 24, 157-168   PDF   |   Data Web   |   Highlight

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

Slavov N.^✉ (2010)
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks
JMLR, W&CP vol. 9   preprint  |   PDF   |   Code on GitHub  |   Summary

Slavov N.^✉, David Botstein (2010)
Universality, specificity and regulation of S. cerevisiae growth rate response in different carbon sources and nutrient limitations
Dissertation   PDF

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

Slavov N.^✉, Dawson, K. (2009)
Correlation Signature of the Macroscopic States of the Gene Regulatory Network in Cancer
PNAS, vol. 106, no. 11   PDF   |   Summary

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, Elcheikhali M, Leduc A, Huffman R, Derks J, Franks A, Slavov N.^✉ (2024)
Inferring post-transcriptional regulation within and across cell types in human testis
bioRxiv   doi: 10.1101/2024.10.08.617313   |   PDF   |   Data Web   |   BayesPG SCP2024 Talk

Iwamoto-Stohl LK, Petelski AA, ... Slavov N.^✉, Zernicka-Goetz N (2024)
Proteome asymmetry in mouse and human embryos before fate specification
bioRxiv   doi: 10.1101/2024.08.26.609777   |   PDF   |   Web   |   Video

Tsour S, Machne R, Leduc A, Widmer S, Slavov N.^✉ (2024)
Alternate RNA decoding results in stable and abundant proteins in mammals
bioRxiv   doi: 10.1101/2024.08.26.609665   |   PDF   |   Web   |   Video

Leduc A, Luke Khoury, Joshua Cantlon, Slavov N^✉ (2024)
Limiting the impact of protein leakage in single-cell proteomics
bioRxiv   doi: 10.1101/2024.07.26.605378   |   PDF   |   SI Web

Derks J, Jonson T, Leduc A, Khan S, Khoury L, Rafiee M, Slavov N^✉ (2024)
Single-nucleus proteomics identifies regulators of protein transport
bioRxiv   doi: 10.1101/2024.06.17.599449   |   PDF   |   Data Web   |   Talk

Galatidou S, Petelski A, Pujol A, Lattes K, Latorraca L, Fair T, Popovic M, Vassena R, Slavov N^✉, Barragan M (2024)
Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes
bioRxiv   doi: 10.1101/2024.05.23.595547   |   PDF   |   Data Web

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, Khoury 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   |   Talk

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

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments
arXiv   preprint   |   PDF   |   Guidelines Web   |   Primer on single-cell 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

Specht H, Slavov N.^✉ (2020)
Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers
bioRxiv   10.1101/2020.08.24.264994   PDF   |   WebSite   |   SCP2020 talk   |   Code

Petelski AA, Slavov N.^✉ (2020)
Analyzing ribosome remodeling in health and disease
arXiv   arXiv:2007.05839   PDF

Slavov N.^✉ (2020)
Single-cell protein analysis by mass spectrometry
arXiv   arXiv:2004.02069   PDF

Specht H, Emmott E, Koller T, Slavov N.^✉ (2019)
High-throughput single-cell proteomics quantifies the emergence of macrophage heterogeneity
bioRxiv   DOI: 10.1101/665307   PDF   |   Data   |   SCP2019 talk   |   SCoPE2 Web   |   Nature Methods's feature

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

Specht H, Slavov N.^✉ (2018)
Routinely quantifying single cell proteomes: A new age in quantitative biology and medicine
PeerJ, 6:e26821v1   PDF   |   Quantifying proteins in single cells   |   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.^✉ (2015)
From differential transcription of ribosomal proteins to differential structure of ribosomes
PeerJ PrePrints 3:e1878   PDF

Slavov N.^✉, Semrau S., Airoldi E.M., Budnik B., van Oudenaarden A. (2014)
Differential stoichiometry among core ribosomal proteins
bioRxiv, PDF   |   Summary   |   Data Web   |  

Slavov N.^✉, Botstein D., Caudy A. (2014)
Extensive Regulation of Metabolism and Growth during the Cell Division Cycle
bioRxiv   DOI: 10.1101/005629   PDF

Malioutov D.^✉, Slavov N.^✉ (2014)
Convex Total Least Squares
arXiv, arXiv:1406.0189,   PDF  |   Code on GitHub  |   Summary

Slavov N.^✉ (2010)
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks
arXiv, arXiv:1406.0193 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.^✉ (2014)
Discoveries lie hidden behind the façade of popular assumptions
Cell Press   PDF

Slavov N.^✉ (2013)
The Best Projects Are Least Obvious
The Scientist   PDF

Slavov N.^✉ (2013)
A Wonderful Christmas with Mysterious Oscillations
PubChase   PDF

Slavov N.^✉ (2012)
The Mission of MIT
The MIT Tech, Volume 132, Feb. 7, 2012   PDF