887 citations · 2k across the 14 of their papers we have counts for
14 papers
Modeling and interpretation of single-cell proteogenomic data
Andrew Leduc, Hannah Harens, Nikolai Slavov
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell…
Sampling the proteome by emerging single-molecule and mass-spectrometry methods
Michael J. MacCoss, Javier Alfaro, Meni Wanunu +2
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications i…
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments
Laurent Gatto, Ruedi Aebersold, Juergen Cox +18
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of pro…
New views of old proteins: clarifying the enigmatic proteome
Participants in a NIH Workshop on Functional, Integrative Proteomics, : +20
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition…
Analyzing ribosome remodeling in health and disease
Aleksandra A. Petelski, Nikolai Slavov
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequa…
Single-cell protein analysis by mass-spectrometry
Nikolai Slavov
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughp…
Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Bogdan Budnik, Ezra Levy, Guillaume Harmange +1
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of e…
Routinely quantifying single cell proteomes: A new age in quantitative biology and medicine
Harrison Specht, Nikolai Slavov
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our…
Quantifying homologous proteins and proteoforms
Dmitry Malioutov, Tianchi Chen, Jacob Jaffe +4
Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteof…
Post-transcriptional regulation across human tissues
Alexander Franks, Edoardo Airoldi, Nikolai Slavov
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining pr…
Extensive regulation of metabolism and growth during the cell division cycle
Nikolai Slavov, David Botstein, Amy Caudy
Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures re…
Differential stoichiometry among core ribosomal proteins
Nikolai Slavov, Sefan Semrau, Edoardo Airoldi +2
Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixe…
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks
Nikolai Slavov
Networks are a unifying framework for modeling complex systems and network inference problems are frequently encountered in many fields. Here, I develop and apply a generative appr…
Convex Total Least Squares
Dmitry Malioutov, Nikolai Slavov
We study the total least squares (TLS) problem that generalizes least squares regression by allowing measurement errors in both dependent and independent variables. TLS is widely u…