Browsing by Author "Airoldi, Edoardo"
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Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by PostTranscriptional Processes, Largely Determine SteadyState Protein Levels in Yeast
Csárdi, Gábor; Franks, Alexander; Choi, David S.; Airoldi, Edoardo M.; Drummond, D. Allan (Public Library of Science, 2015)Cells respond to their environment by modulating protein levels through mRNA transcription and posttranscriptional control. Modest observed correlations between global steadystate mRNA and protein measurements have been ... 
Aneuploidy Prediction and Tumor Classification with Heterogeneous Hidden Conditional Random Fields
Barutcuoglu, Zafer; Airoldi, Edoardo; Dumeaux, Vanessa; Schapire, Robert E.; Troyanskaya, Olga G. (Oxford University Press, 2008)Motivation: The heterogeneity of cancer cannot always be recognized by tumor morphology, but may be reflected by the underlying genetic aberrations. ArrayCGH methods provide highthroughput data on genetic copy numbers, ... 
Asymptotic and finitesample properties of estimators based on stochastic gradients
Toulis, Panos; Airoldi, Edoardo Maria (Institute of Mathematical Statistics, 2017)Stochastic gradient descent procedures have gained popularity for parameter estimation from large data sets. However, their statis tical properties are not well understood, in theory. And in practice, avoiding numerical ... 
A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes
Slavov, Nikolai; Airoldi, Edoardo Maria; van Oudenaarden, A.; Botstein, D. (American Society for Cell Biology (ASCB), 2012)The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is ... 
Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis
Slavov, Nikolai; Budnik, Bogdan; Schwab, David; Airoldi, Edoardo Maria; van Oudenaarden, Alexander (Elsevier BV, 2014)Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting ... 
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Brauer, M. J.; Huttenhower, Curtis; Airoldi, Edoardo Maria; Rosenstein, R.; Matese, J. C.; Gresham, D.; Boer, V. M.; Troyanskaya, O. G.; Botstein, D. (American Society for Cell Biology (ASCB), 2008)We studied the relationship between growth rate and genomewide gene expression, cell cycle progression, and glucose metabolism in 36 steadystate continuous cultures limited by one of six different nutrients (glucose, ... 
Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis
Solis, Eric John; Pandey, Jai P.; Zheng, Xu; Jin, Dexter X.; Gupta, Piyush B.; Airoldi, Edoardo Maria; Pincus, David Frank; Denic, Vladimir (Elsevier BV, 2016)Despite its eponymous association with the heat shock response, yeast heat shock factor 1 (Hsf1) is essential even at low temperatures. Here we show that engineered nuclear export of Hsf1 results in cytotoxicity associated ... 
Distributed and Multiphase Inference in Theory and Practice: Principles, Modeling, and Computation for HighThroughput Science
Blocker, Alexander Weaver (20130918)The rise of highthroughput scientific experimentation and data collection has introduced new classes of statistical and computational challenges. The technologies driving this data explosion are subject to complex new ... 
An Entropy Approach to Disclosure Risk Assessment: Lessons from Real Applications and Simulated Domains
Airoldi, Edoardo Maria; Bai, Xue; Malin, Bradley (Elsevier, 2011)We live in an increasingly mobile world, which leads to the duplication of information across domains. Though organizations attempt to obscure the identities of their constituents when sharing information for worthwhile ... 
Estimating Latent Processes on a Network From Indirect Measurements
Airoldi, Edoardo Maria; Blocker, Alexander (Informa UK Limited, 2013)In a communication network, pointtopoint traffic volumes over time are critical for designing protocols that route information efficiently and for maintaining security, whether at the scale of an Internet service provider ... 
Getting Started in Probabilistic Graphical Models
Airoldi, Edoardo (Public Library of Science, 2007)Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover ... 
Implicit methods for iterative estimation with large data sets
Toulis, Panagiotis (20160425)The ideal estimation method needs to fulfill three requirements: (i) efficient computation, (ii) statistical efficiency, and (iii) numerical stability. The classical stochastic approximation of (Robbins, 1951) is an iterative ... 
Interpretable and Scalable Bayesian Models for Advertising and Text
Bischof, Jonathan Michael (20140606)In the era of "big data", scalable statistical inference is necessary to learn from new and growing sources of quantitative information. However, many commercial and scientific applications also require models to be ... 
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in NanogDepleted Murine Embryonic Stem Cells
Markowetz, Florian; Mulder, Klaas; Airoldi, Edoardo Maria; Lemischka, Ihor; Troyanskaya, Olga (Public Library of Science, 2010)Embryonic stem cells (ESC) have the potential to selfrenew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for selfrenewal, maintenance of pluripotency and lineage specification ... 
Mixed Membership Stochastic Blockmodels
Airoldi, Edoardo Maria; Blei, David M.; Fienberg, Stephen E.; Xing, Eric P. (2008)Consider data consisting of pairwise measurements, such as presence or absence of links between pairs of objects. These data arise, for instance, in the analysis of protein interactions and gene regulatory networks, ... 
Multiway blockmodels for analyzing coordinated highdimensional responses
Airoldi, Edoardo Maria; Wang, Xiaopei (Institute of Mathematical Statistics, 2013)We consider the problem of quantifying temporal coordination between multiple highdimensional responses. We introduce a family of multiway stochastic blockmodels suited for this problem, which avoids preprocessing steps ... 
Network Sampling and Classification: An Investigation of Network Model Representations
Airoldi, Edoardo Maria; Bai, Xue; Carley, Kathleen (Elsevier, 2011)Methods for generating a random sample of networks with desired properties are important tools for the analysis of social, biological, and information networks. Algorithmbased approaches to sampling networks have received ... 
A NonParametric Perspective on the Analysis of Massive Networks
Costa, Thiago (20150515)This dissertation develops an inferential framework for a highly nonparametric class of network models called graphons, which are the limit objects of converging sequences in the theory of dense graph limits. The theory, ... 
Polytope samplers for inference in illposed inverse problems
Airoldi, Edoardo Maria; Haas, Bertrand (Proceedings of Machine Learning Research, 20180726)We consider linear illposed inverse problems y = Ax, in which we want to infer many count parameters x from few count observations y, where the matrix A is binary and has some unimodularity property. Such problems are ... 
Predicting Cellular Growth from Gene Expression Signatures
Airoldi, Edoardo; Huttenhower, Curtis; Gresham, David; Lu, Charles; Caudy, Amy A.; Dunham, Maitreya J.; Broach, James R.; Botstein, David; Troyanskaya, Olga G. (Public Library of Science, 2009)Maintaining balanced growth in a changing environment is a fundamental systemslevel challenge for cellular physiology, particularly in microorganisms. While the complete set of regulatory and functional pathways supporting ...