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Selected Publications

Below are selected publications by Cornell researchers who have conducted research using Center or Center-supported resources.

2014

Code-Assisted Discovery of TAL Effector Targets in in Bacterial Leaf Streak of Rice
R. Cernadas et al.
PLOS Pathogens

Elastic Strain Engineering of Ferroic Oxides
D. Schlom, L. Chen, C. Fennie et al.
Materials Research Society

Estimating the Number of Species in Microbial Diversity Studies
J. Bunge, A. Willis, F. Walsh
Annual Review of Statistics and Its Applications

Financing of Innovation Strategies in Emerging Economies
A. Leiponen, S. Poczter
Social Science Research Network

Large-Scale Brain Dynamics in Disorders of Consciousness
N. Schiff, T. Nauvel, J. Victor
Current Opinion in Neurobiology

Many-Objective Reservoir Policy Identification and Refinement to Reduce Policy Inertia and Myopia in Water Management
M. Giuliani, J. Herman, A. Castelletti, P. Reed
Water Management Resources

Numerical Study of Collisional Particle Dynamics in Cluster-Induced Turbulence
J. Capecelatro, O. Desjardins, R. Fox
Journal of Fluid Mechanics

Smart Farmers, Happy Cows
K. Klein
Cornell's EZRA Magazine: Julio Giordano

The Low-Lying Electronic States of Pentacene and Their Roles in Singlet Fission
T. Zeng, R. Hoffman, N. Ananth
Journal of the American Chemical Society

TRAIL-Coated Leukocytes that Kill Cancer Cells in the Circulation
M. Mitchell, E. Wayne, K. Rana, C. Schaffer, M. King
Proceedings of the National Academy of Sciences

2013

A Model of Electrophysiological Heterogeneity in Periglomerular Cells
P. Sethupathy, D. Rubin, G. Li, T. Cleland
Frontiers in Computational Neuroscience

An Euler-Lagrange Strategy for Simulating Particle-Laden Flows
J. Capecelatro, O. Desjardins
Journal of Computational Physics

Assessing the Natural Rate of Unemployment
J. Abowd, T. Goel, L. Vilhuber
Cornell University Technical Report

A Two-Layer Biophysical Model of Cholinergic Neuromodulation in Olfactory Bulb
G. Li, T. Cleland
Journal of Neuroscience

Bilayer Thickness Mismatch Controls Domain Size in Model Membranes
F. Heberle, R. Petruzielo, J. Pan, P. Drazba, N. Kucerka, R. Standaert, G. Feigenson, J. Katsaras
Journal of the American Chemical Society

Bulk Coupling of Polarization and Magnetism in the Hexagonal Ferrites
H. Das, A. Wysocki, C. Fennie
arXiv.org

Computational and Experimental Models of Cancer Cell Response to Fluid Shear Stress
M. Mitchell, M. King
Frontiers in Oncology

Cornell Log Analysis and Monitoring Project (CLAMP)
M. Padula, L. Walle
Cornell University Technical Report

Data Management of Confidential Data
C. Lagoze, W. Block, J. Williams, J. Abowd, L. Vilhuber
International Journal of Digital Curation

Evaluating Cloud Computing Techniques for Smart Power Grid Design Using Parallel Scripting
Proceedings of IEEE/ACM CCGrid 2013

Hybrid and Nonhybrid Lipids Exert Common Effects on Membrane Raft Size and Morphology
F. Heberle, M. Doktorova, S. Goh, R. Standaert, J. Katsaras, G. Feigenson
Journal of the American Chemical Society

Kenneth Geddes Wilson, 1936-2013: An Appreciation
L. Kadanoff
arXiv.org

Large-Scale Parallel Simulations of Turbulent Combustion using Combined Dimension Reduction and Tabulation of Chemistry
V. Hiremath, S. Lantz, H. Wang, S. Pope
Proceedings of the Combustion Institute

Multiscale Model of Platelet Translocation and Collision
W. Wang, N. Mody, M. King
Journal of Computational Physics

Science with an Energy Recovery Linac
Editors: D. Bilderback, J. Brock, E. Fontes, G. Hoffstaetter
Cornell University Report

Survey of Software for Fitting Capture-Recapture Models
J. Bunge
Computational Statistics

Toward a Reliable, Secure and Fault Tolerant Smart Grid State Estimation in the Cloud
K. Maheshwari, M. Lim, L. Wan, K. Birman, R. van Renesse
Proceedings of IEEE/PES ISGT 3013

Why There Are So Few Perovskite Ferroelectrics?
N. Benedek, C. Fennie
The Journal of Physical Chemistry

XSEDE Cloud Survey Report
D. Lifka, I. Foster, S. Mehringer, M. Parashar, P. Redfern, C. Stewart, S. Tuecke
EDUCAUSE and XSEDE Achive

2012

A Proposed Solution to the Archiving and Curation of Confidential Scientific Inputs
J. Abowd, L. Vilhuber, W. Block
Privacy in Statistical Databases 2012

Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data
J. Crawford, B. Lazzaro
Frontiers in Evolutionary and Population Genetics

Computationally-Efficient and Scalable Parallel Implementation of Chemistry in Simulations of Turbulent Combustion
V. Hiremath, S. Lantz, H. Wang, S. Pope
Combustion and Flame

Did the Housing Price Bubble Clobber Local Labor Markets When It Burst?
J. Abowd, L. Vilhuber
American Economic Review Papers and Proceedings

Electrical Properties of Improper Ferroelectrics from First Principles
M. Stengel, C. Fennie, P. Ghosez
Physical Review B

Energy Recovery Linac 2012 Report
G. Hoffstaetter, S. Gruner, M. Tigner, et. al.
Cornell Technical Report

Estimating Population Diversity with CatchAll
J. Bunge, L. Woodard, D. Bohning, J. Foster, S. Connolly, H, Allen
Bioinformatics

Global Mapping of Translation Initiation Sites in Mammalian Cells at Single-Nucleotide Resolution
S. Lee, B. Liu, S. Lee. S. Huang, B. Shen, S. Qian
Proceedings of the National Academy of Science

High-Throughput Single Nucleotide Polymorphism Genotyping for Breeding Applications in Rice using the BeadXpress Platform
M. Thompson, K. Zhao, M. Wright, et. al.
Molecular Breeding

HOM Studies of the Cornell ERL Prototype Cavity in a Horizontal Test Cryomodule
N. Valle, M. Biling, G. Hoffstaetter, C. Mayes
Proceedings of IPAC2012

Large-Scale Parallel Simulations of Turbulent Combustion using Combined Dimension Reduction and Tabulation of Chemistry
V. Hiremath, S. Lantz, H. Wang, S. Pope
Proceedings of the Combustion Institute

Measuring the Microbiome: Perspectives on Advances in DNA-based Techniques for Exploring Microbial Life
J. Foster, J. Bunge, J. Gilbert, J. Moore
Briefings in Bioinformatics

Minimum Requirements for Detecting a Stochastic Gravitational Wave Background Using Pulsars
J. Cordes, R. Shannon
Astrophysics Journal

Multiwavelength Constraints on Pulsar Populations in the Galactic Center
R. Wharton, S. Chatterjee, J. Cordes, J. Deneva, T. Lazio
Astrophysics Journal

On-Center/Inhibitory-Surround Decorrelation via Intraglomerular Inhibition in the Olfactory Bulb Glomerular Layer
T. Cleland, C. Linster
Frontiers in Integrative Neuroscience

Optimal Control of Financial Contagion
H. Amini, A. Minca
Social Sciences Research Network

Polar Octahedral Rotations: A Path to New Multifunctional Materials
N. Benedek, A. Mulder, C. Fennie
Journal of Solid State Chemistry

The Xen-Blanket: Virtualize Once, Run Everywhere
D. Williams, H. Jamjoom, H. Weatherspoon
Proceedings of 7th ACM Eurosys

Towards Unrestricted Public Use Business Microdata: The Synthetic Longitudinal Business Database
S. Kinney, J. Reiter, A. Reznek, J. Miranda, R. Jarmin, J. Abowd
International Statistic Review

Twenty Questions with Noise: Bayes Optimal Policies for Entropy Loss
B. Jedynak, P. Frazier, R. Sznitman
Journal of Applied Probability

2011

A Case Study on the Use of Adapt-N
J. LaGioia, H. van Es, J. Melkonian, B. Moebius-Clune, D. Shearing
Computational Agriculture Institute Case Study

Absence of Tec Family Kinases Interleukin-2 Inducible T Cell Kinase and Bruton’s Tyrosine Kinase Severely Impairs Fc EpsilonRI-Dependent Mast Cell Responses
A. Iyer, J. Morales, W. Huang, F. Ojo, G.Ning, E. Wills, J. Baines, A. August
Journal of Biological Chemistry

Computational and Experimental Analysis Reveals a Requirement for Eosinophil-Derived IL-13 for the Development of Allergic Airway Responses in C57BL/6 Mice
E. Walsh, J. Thakar, K. Stokes, F. Huang, R. Albert, A. August
Journal of Immunology

Demographic History and Rare Allele Sharing Among Human Populations
S. Gravel, B. Henn, R. Gutenkunst, A. Indap, G. Marth, A. Clark, et al.
Proceedings of the National Academy of Sciences

Functional Octahedral Rotations: A Path to New Multifunctional Electronic, Magnetic, and Orbital Materials
N. Benedek, C. Fennie
Cornell University Technical Report

Hybrid Improper Ferroelectricity: A Mechanism for Controllable Polarization-Magnetization Coupling
N. Benedek, C. Fennie
Physical Review Letters

Large Eddy Simulation/Probability Density Function Modeling of a Turbulent CH4/H2/N2 Jet Flame
H. Wang, S. Pope
Proceedings of the Combustion Institute

Magnetic Phase Diagram of Spatially Anisotropic, Frustrated Spin-1/2 Heisenberg Antiferromagnet on a Stacked Square Lattice
K. Majumdar
Journal of Physics

Making Time-Stepped Applications Tick in the Cloud
T. Zou, G. Wang, M. Vaz Salles, D. Bindel, A. Demers, J. Gehrke, W. White
ACM Symposium on the Cloud

Maximizing Computational Learning for Faculty and Student Scientists: The Ranger Virtual Workshop
S. Mehringer, N. Woody, A. Dolgert, S. Lantz
TeraGrid Conference (updated)

National Estimates of Gross Employment and Job Flows
J. Abowd, L. Vilhuber
Journal of Econometrics

Phase Separation in Lipid Membranes
F. Heberle, G. Feigenson
Cold Spring Harbor Perspectives in Biology

Protistan Microbial Observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger Insights into Species Richness
V. Edgcomb, W. Orsi, J. Bunge, S. Jeon, et. al.
International Society for Microbial Ecology

Spin-Wave Energy Dispersion of a Frustrated Spin-1/2 Heisenberg Antiferromagnet on a Stacked Square Lattice
K. Majumdar
Journal of Physics: Condensed Matter

Translational Regulation in Nutrigenomics
B. Liu, S. Qian
Advances in Nutrition Journal

2010

A Plausible Role for the Presence of Internal Shine-Dalgarno Sites
L. Ponnala
Bioinformatics and Biology Insights

A Probability-Based Method for Calculating Effective Diffusion Coefficients of Composite Media
R. Keskin, M. Grigoriu
Probabilistic Engineering Mechanics

A Variational Bayes Algorithm for Fast and Accurate Multiple Locus Genome-Wide Association Analysis
B. Logsdon, G. Hoffman, J. Mezey
BMC Bioinformatics

Adapt-N Tool Helps Farmers Deal with Climate Change, Energy Consumption and Greenhouse Gas Emissions
H. van Es, J. Melkonian, B. Moebius-Clune, B. Schindelbeck, L. Joseph, A. DeGaetano
What’s Cropping Up - New York Field Crops & Soils Newsletter

Author Identifiers in Scholarly Repositories
S. Warner
Cornell University Technical Report

Behavioral Simulations in MapReduce
G. Wang, M. Vaz Salles, B. Sowell, X. Wang, T. Cao, A. Demers, J. Gehrke, W. White
Proceedings of the VLDB Endowment

Coherent Synchrotron Radiation Simulations for the Cornell Energy Recovery Linac
C. Mayes, G. Hoffstaetter
Proceedings of IPAC’10

Construction of an rsmX Co-Variance Model and Identification of Five rsmX non-coding RNAs in Pseudomonas Syringae pv. Tomato DC3000
S. Moll, D. Schneider, P. Stodghill, C. Myers, S. Cartinhour, M. Filiatrault
RNA Biology

How Adapt-N Calculates Field-Specific Sidedress N Recommendations for Corn
B. Moebius-Clune, H. van Es, J. Melkonian
Cornell Adaptive N Management Fact Sheet

How to Build a Parallel MATLAB Cluster
B. Lapp, S. Lee, L. Walle
Cornell University Technical Report

Large Eddy Simulation/Probability Density Function Modeling of a Turbulent CH4/H2/N2 Jet Flame
H. Wang, S. Pope
Proceedings of the Combustion Institute

Local Ionosphere Model Estimation From Dual-Frequency GNSS Observables
R. Mitch, M. Psiaki
Proceedings ION GNSS 2010

Megadalton Complexes in the Chloroplast Stroma of Arabidopsis thaliana
P. Olinares, L. Ponnala, K. van Wijk
Molecular and Cellular Proteomics

Microbial Eukaryotes in the Hypersaline Anoxic L’Atalante Deep-Sea Basin
E. Alexander, A. Stock, H-W Breiner, A. Behnke, J. Bunge, et. Al
Environmental Microbiology

National Estimates of Gross Employment and Job Flows from the Quarterly Workforce Indicators
J. Abowd, L. Vihuber
Journal of Econometrics

NNY Research Supports Precision Farming Tool for Corn Growers
J. Melkonian, H. van Es, M. Davis
Northern New York Agricultural Program

Overview of the Cornell University Center for Advanced Computing Sustainable Funding Model
D. Lifka, R. Alvord, S. Mehringer, P. Redfern
NSF Workshop on Sustainable Funding for HPC Centers White Paper

Population Dynamics of PIWI-RNAs (piRNAs) and their Targets in Drosophila
J. Lu, A. Clark
Genome Research

Pulsar Discovery by Global Volunteer Computing
B. Knispel, B. Allen, J. Cordes
Science

Sustainable Funding and Business Models for Academic Cyberinfrastructure Facilities
S. Ahalt, A. Apon, D. Lifka, H. Neeman
National Science Foundation Workshop Report

Weak Second-Order Splitting Schemes for Lagrangian Monte Carlo Methods for the Composition PDF/FDF Transport Equations
H. Wang, P. Popov, S. Pope
Journal of Computational Physics

2009

An Investigation into Solr and the Full-Text Indexing of Digitized Books
T. Ternquist, J. Yu
Cornell University Technical Report

Analyzing the Orientation Dependence of Stresses in Polycrystals
H. Ritz, P. Dawson, T. Marin
Journal of Mechanics and Physics of Solids

Bioeconomics Meets Biocomplexity: The Gypsy Moth
X. Yang, J. Conrad
Cornell University Technical Report

Computationally Efficient Implementation of Combustion Chemistry in Parallel PDF Calculations
L. Lu, S. Lantz, Z. Ren, S. Pope
Journal of Computational Physics

Constraining the Bulk Properties of Dense Matter by Measuring Millisecond Pulsar Masses
Whitepaper for Decadal Survey CFP Panel

Discovery of Three Pulsars from a Galactic Center Pulsar Population
J. Deneva, J. Cordes, T. Lazio
Astrophysical Journal

Dynamic Modeling of Workforce Requirements for Mass Prophylaxis under Highly Uncertain Conditions
M. Castorena, C. Hawkins, N. Hupert, K. King, J. Muckstadt, C. Wu, W. Xiong
Cornell University Technical Report

Efficient Extraction of Individual Pages from a Complete Web Crawl
O. Krokhin
Cornell University Technical Report

EScience in Practice: Lessons from the Cornell Web Lab
W. Arms, M. Calimlim, L. Walle
D-Lib Magazine

Extending the Recursive Jensen-Shannon Segmentation of Biological Sequences
S. Cheong, P. Stodghill, D. Schneider, S. Cartinhour, C. Myers
Cornell University Technical Report

Extreme Astrophysics with Neutron Stars
D. Lai, M. van Kerkwijk, J. Arons, E. Brown, J. Cordes, et al.
Whitepaper for Astro 2010 Decadal Survey Committee

Flapping Wing Flight Can Save Aerodynamic Power
U. Pesavento, Z. Wang
Physical Review

Fruit Flies Modulate Passive Wing Pitching to Generate In-Flight Turns
A. Bergou, L. Ristroph, J. Guckenheimer, I. Cohen, Z. Wang
Cornell University Technical Report

Gravitational Wave Astronomy Using Pulsars: Massive Black Hole Mergers & the Early Universe
Whitepaper for Decadal Survey CFP Panel

Intergenerational Resource Transfers with Random Offspring Numbers
K. Arrow, S. Levin
Proceedings of the National Academy of Sciences

Landmark Classification in Large-Scale Image Collections
Y. Li, D. Crandall, D. Huttenlocher
Cornell University Technical Report

Mapping the World's Photos
D. Crandall, L. Backstrom, D. Huttenlocher, J. Kleinberg
Cornell University Technical Report

Minimum Cost Data Aggregation with Localized Processing for Statistical Inference
A. Anandkumar, L. Tong, A. Swami, A. Ephremides
IEEE INFOCOM

Microbial Community Structure in the North Pacific Ocean
M. Brown, G. Philip, J. Bunge, et al.
ISME Journal

Model-Based Estimates of Right Whale Habit Use in the Gulf of Maine
A. Pershing, N. Record, B. Monger, C. Mayo, M. Bown, T. Cole, R. Kenney, D. Pendleton, L. Woodard
Marine Ecology

Module Evolution and Substrate Specificity of Fungal Nonribosomal Peptide Synthetases
K. Bushley, D. Ripoll, B. Turgeon
BMC Evolutionary Biology

Parallel Stochastic Global Optimization Using Radial Basis Functions
R. Regis, C. Shoemaker
INFORMS Journal on Computing

Pig Latin Evaluation through PageRank Algorithm Implementation
Aditi Vad
Cornell University Web Laboratory Paper

Polymerase Chain Reaction Primers Miss Half of rRNA Microbial Diversity
S. Hong, J. Bunge, et al.
ISME Journal

Positional Effects on Citation and Readership in arXiv
A. Haque, P. Ginsparg
JASIST

PPDB, the Plant Proteomics Database at Cornell
Q. Sun, B. Zybailov, W. Majeran, G. Friso, P. Olinares, K. van Wijk
Nucleic Acids Research

Protistan Community Patterns within the Brine and Halocline of Deep Hypersaline Anoxic Basins
V. Edgcomb, W. Orsi, C. Leslin, S. Epstein, J. Bunge, S. Jeon, M. Yakimov, A. Behnke, T. Stoeck
Extremophiles Journal

Prostistan Diversity in Suboxic and Anoxic Waters of the Baltic Sea as Revealed by 18S rRNA Clone Libraries
A. Stock, K. Jurgens, J. Bunge. T. Stoeck
Aquatic Microbial Ecology

Sensitivity Calculations in PDF Modelling of Turbulent Flames
Z. Ren, S. Pope
Proceedings of the Combustion Institute

Sensitivity to Grain Discretization of the Simulated Crystal Stress Distributions in FCC Polycrystals
H. Ritz, P. Dawson
Modelling and Simulation in Materials Science and Engineering

Surface Mesh Regeneration Considering Curvatures
A. Miranda, L. Martha, P. Wawrzynek, A. Ingraffea
Engineering with Computers

The Context Sensitivity Problem in Biological Sequence Segmentation
S. Cheong, P. Stodghill, D. Schneider, S. Cartinhour, C.Myers
Cornell University Technical Report

The Cornell Energy Recovery Linac: Update on a Future Source of Coherent Hard X-Rays
D. Bilderback, B. Dunham, G. Hoffstaetter, Al Temnykh, S. Gruner
Synchrotron Radiation News

The GALEX Arecibo SDSS Survey
B. Catinella, D. Schiminovich, et al.
Cornell University Technical Report

2008

A Comparison of Finite Element and Atomistic Modelling of Fracture
V. Coffman, J. Sethna, G Heber, M. Liu, A. Ingraffea, N. Bailey, E. Barker
Modelling and Simulation in Materials Science and Engineering

A Direct Multiple Histogram Reweighting Method for Optimal Computation of the Density of States
M. Fenwick
Journal of Chemical Physics

A Multi-Dimensional View on Information Retrieval of CMS Data
A. Dolgert, L. Gibbons, V. Kuznetsov, C.D. Jones, D. Riley
Journal of Physics

A Multi-Length Scale Sensitivity Analysis for the Control of Texture-Dependent Properties in Deformation Processing
V. Sundararaghavan, N. Zabaras
International Journal of Plasticity

A Non-Linear Dimension Reduction Methodology for Generating Data-Driven Stochastic Input Models
B. Ganapathysubramanian, N. Zabaras
Journal of Computational Physics

A Scalable Framework for the Solution of Stochastic Inverse Problems Using a Sparse Grid Collocation Approach
N. Zabaras, B. Ganapathysubramanian
Journal of Computational Physics

A Seamless Approach towards Stochastic Modeling: Sparse Grid Collocation and Data Driven Input Models
B. Ganapathysubramanian, N. Zabaras
Finite Elements in Analysis and Design

A Stochastic Multiscale Framework for Modeling Flow through Random Heterogeneous Porous Media
B. Ganapathysubramanian, N. Zabaras
Journal of Computational Physics

An Improved Algorithm for In Situ Adaptive Tabulation
L. Lu, S. Pope
Journal of Computational Physics

Analysis Environments for CMS
C.D. Jones, L. Luc, B. Hegner
Journal of Physics

Calculating the Jaccard Similarity Coefficient with Map Reduce for Entity Pairs in Wikipedia
J. Bank, B. Cole
Cornell Technical Report

Challenges in Continuum Modeling of Intergranular Fracture
V. Coffman, J. Sethna, G. Heber, A. Liu, A. Ingraffea, N. Bailey, E. Barker
Nature Materials (submitted to)

Characterization of the PvdS-Regulated Promoter Motif in Pseudomonas syringae pv. Tomato DC3000 Reveals Regulon Members and Insights Regarding PvdS Function in other Pseudomonads
B. Swingle, D. Thete, M. Moll, C Myers, D. Schneider, S. Cartinhour
Molecular Microbiology

Combined Monitoring and Modeling Indicate the Most Effective Agricultural Best Management Practice
Z. Easton, M. Walter, T. Steenhuis
Journal of Environmental Quality

Cyberscholarship: High Performance Computing meets Digital Libraries
W. Arms
Journal of Electronic Publishing

Digital Research Data Curation
Cornell University Library Data Working Group Report

Environmental rRNA Inventories Miss Over Half of Protistan Diversity
S. Jeon, J. Bunge, C. Leslin, T. Stoeck, S. Hong, S. Epstein
BMC Microbiology

Evolution of the Electronic Excitation Spectrum with Strongly Diminishing Hole Density in Superconducting Bi2Sr2CaCu2O8+δ
J. Alldredge, J. Lee, K. McElroy, M. Wang, K. Fujita, Y.Kohsaka, C. Taylor, H. Eisaki, S. Uchida, P. Hirschfeld, J. Davis
Nature Physics

Genome-Wide Analyses Reveal Lineage Specific Contributions of Positive Selection and Recombination to the Evolution of Listeria Monocytogenes
R. Orsi, Q.Sun, M. Wiedmann
BMC Evolutionary Biology

Global Transcriptional Responses of Pseudomonas Syringae CD3000 to Changes in Iron Bioavailability In Vitro
P. Bronstein, M. Filiatrault, C. Myers, M. Rutzke, D. Schneider, S. Cartinhour
BMC Microbiology

High-Resolution Spatial Interpolation of Weather Generator Parameters Using Local Weighted Regressions
D. Wilks
Agricultural and Forest Meteorology

Homologous Recombination is Very Rare or Absent in Human Influenza A Virus
M. Boni, Y. Zhou, J. Taubenberger, E. Holmes
Journal of Virology

Imaging the Impact on Cuprate Superconductivity of Varying the Interatomic Distances within Individual Crystal Unit Cells
J. Slezak, J. Lee, M. Wang, K. McElroy, K. Fujita, B. Andersen, P. Hirschfeld, H.Eisaki, S. Uchida, J. Davis
Proceedings of the National Academy of Science

Microarray for Molecular Typing of Salmonella Enterica Serovars
J. Saria, R. Palaniappan, D. Chiu, J. Phan, L. Ponnala, et al.
Molecular and Cellular Probes

Microbial Eukaryotes in the Hypersaline Anoxic L'Atalante Deep-Sea Basin
E. Alexander, A. Stock, H-W. Breiner, A. Behnke, J. Bunge, M. Yakimov, T. Stoeck
Environmental Microbiology

Modeling Diffusion in Random Heterogeneous Media: Data-Driven Models, Stochastic Collocation and the Variational Multiscale Method
B. Ganapathysubramanian, N. Zabaras
Physical Reviews B (in preparation)

Modeling the Response of HCP Polycrystals Deforming by Slip and Twinning Using a Finite Element Representation of the Orientation Space
B. Kouchmeshky, N. Zabaras
International Journal of Plasticity (submitted)

Modeling Zooplankton Development Using the Monotonic Upstream Scheme for Conservation Laws
N. Record, A. Pershing
American Society of Limnology and Oceanography

Module Evolution and Substrate Specificity of Funcal Nonribosomal Peptide Synthetases Involved in Siderophore Biosynthesis
K. Bushley, D. Ripoll, B. Turgeon
BMC Evolutionary Biology

Non-Linear Dimension Reduction Methodology for Generating Data-Driven Stochastic Input Models
B. Ganapathysubramanian, N. Zabaras
Journal of Computational Physics (submitted)

Parametric Models for Estimating the Number of Classes
J. Bunge, K. Barger
Biometrical Journal

Proportionally More Deleterious Genetic Variation in European than in African Populations
K. Lohmueller, A. Indap, S. Schmidt, A. Boyko, R. Hernandez, M. Hubisz, J. Sninsky, T. White, S. Sunyaev, R. Nielsen, A. Clark, C. Bustamante
Nature

Provenance in High-Energy Physics Workflows
A. Dolgert, L. Gibbons, L., C. Jones, V. Kuznetsov, M. Riedewald, D. Riley, G. Sharp, P. Wittich
Computing in Science & Engineering

Radar-Guided Interpolation of Climatological Precipitation Data
A. DeGaetano, D. Wilks
International Journal of Climatology

Rapid Web Development Using AJAX and Python
A. Dolgert, L. Gibbons, V. Kuznetsov
Journal of Physics

Re-estimation of Lexical Parameters for Treebank PCFGs
T. Deoskar
Cornell University Technical Report

Roadmap to new virulence determinants in Pseudomonas syringae: Insights from comparative genomics and genome organization
M. Lindeberg, C Myers, A. Collmer, D. Schneider
Molecular Plant-Microbe Interactions

Role of Copper, Zinc-Superoxide Dismutase in Catalyzing, Nitrotyrosine Formation in Murine Liver
Z. Jian-Hong, X. Zhang, C. Roneker, J. McClung, S. Zhang, T. Thannhauser, D. Ripoll, Q. Sun, X. Lei
Free Radical Biology & Medicine

Satisfiability, Sequence Niches, and Molecular Codes in Cellular Signaling
C. Myers
IET Systems Biology

Sloppiness, Robustness and Evolvability in Systems Biology
B. Daniels, Y. Chen, J. Sethna, R. Gutenkunst, C. Myers
Current Opinion in Biotechnology

Structure of the Glucanase Inhibitor Protein (GIP) Family from Phytophthora Species
C. Damasceno, J. Bishop, D. Ripoll, J. Win, S. Kamoun, J. Rose
Molecular Plant-Microbe Interactions

The Arecibo Legacy Fast ALFA Survey: VI. Second HI Source Catalog of the Virgo Cluster Region
B. Kent, R. Giovanelli, M. Haynes, A. Martin, A. Saintonge, S. Stierwalt, T. Balonek, N. Brosch, R. Koopman
The Astronomical Journal

The CMS Dataset Bookkeeping Service
A. Afaq, A. Dolgert, Y. Guo, C. Jones, S. Kosyakov, V. Kuznetsov, L. Lueking, D. Riley, V. Sekhri
Journal of Physics

The Ranger Virtual Workshop
S. Mehringer, N. Woody, A. Dolgert, D. Fuller, S. Lantz, D. Stanzione, J. Zollweg
TeraGrid 2008

Time Averaging Strategies in the Finite-Volume/Particle Hybrid Algorithm for the Joint PDF Equation of Turbulent Reactive Flows
H. Wang, S. Pope
Combustion Theory and Modelling

Turbulent Dispersion from Line Sources in Grid Turbulence
S. Viswanathan, S. Pope
Physics of Fluid

Variational Method for Estimating the Rate of Convergence of Markov-Chain Monte Carlo Algorithms
F. Casey, J. Waterfall, R. Gutenkunst, C. Myers, J. Sethna

2007

A Non-Intrusive Stochastic Galerkin Approach for Modeling Uncertainty Propagation in Deformation Processes
S. Acharjee, N. Zabaras
Computational Stochastic Mechanics

A Tomato Endo-ß-1, 4-glucanase, SlCel9C1, Represents a Distinct Subclass with a New Family of Carbohydrate Binding Modules
B.R. Urbanowicz, C. Catala, D. Irwin, D.B. Wilson, D.R. Ripoll, J.K.C. Rose
Journal of Biological Chemistry

Cayuga: A General Purpose Event Monitoring System
A. Demers, J. Gehrke, B. Panda, M. Riedewald, V. Sharma, W. White
Conference on Innovative Data Systems Research (CIDR 2007)

Computational Fracture Mechanics of Concrete Structures: A Retrospective through Multiple Lenses
J. Emery, J. Hochhalther, A. Ingraffea
Cornell University Technical Report

Digital Material: A Flexible Atomistic Simulation Code
N. Bailey, T. Cretegny, J. Sethna, V. Coffman, A. Dolgert, C. Myers, J. Schiotz, J. Mortensen
Cornell Technical Report

Dynamically Dimensioned Search Algorithm for Computationally Efficient Watershed Model Calibration
B. Tolson, C.A. Shoemaker
Water Resources Research

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
A.G. Clark and the Rhesus Macaque Genome Sequencing and Analysis Consortium
Science

Extracting Falsifiable Predictions from Sloppy Models
R. Gutenkunst, F. Casey, J. Waterfall, C. Myers, J. Sethna
Annals of the New York Academy of Science

Modeling the Response of HCP Polycrystals Deforming by Slip and Twinning Using a Finite Element Representation of the Orientation Space
B. Kouchmeshky, N. Zabaras
Cornell University Technical Report

Multiscale Modeling of Alloy Solidification Using a Database Approach
L. Tan, N. Zabaras
Journal of Computational Physics

Optimal Experimental Design in an EGFR Signaling and Down-Regulation Model
F. Casey, D. Baird, Q. Feng, R. Gutenkunst, J. Waterfall, C Myers, K. Brown, R. Cerione, J. Sethna
IET Systems Biology

Optimization of Quantum Monte Carlo Wave Functions by Energy Minimization
J. Toulouse, C. Umrigar
Journal of Chemical Physics

Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?
T. Stoeck, J. Kasper, J. Bunge, C. Leslin, V. Ilyin, S. Epstein
PLoS ONE

Python for Education: Computational Methods for Nonlinear Systems
C. Myers, J. Sethna
Computing for Science and Engineering

Python Unleashed on Systems Biology
C. Myers, R. Gutenkunst, J. Sethna
Computing in Science and Engineering

Scalable Framework for the Solution of Stochastic Inverse Problems Using a Sparse Grid Collocation Approach
N. Zabaras, B. Ganapathysubramanian
Cornell University Technical Report

Support Vector Training of Protein Alignment Models
R. Elber, T. Joachims, J. Pillardy, C. Yu
Research in Computational Molecular Biology

Topology of Type II REases Revisted; Structural Classes and the Common Conserved Core
M. Niv, D. Ripoll, J. Vila, A. Liwo, E. Vanamee, A. Aggarwal, H. Weinstein, H. Scheraga
Nucleic Acids Research

Universally Sloppy Parameter Sensitivities in Systems Biology
R. N. Gutenkunst, J.J. Waterfall, F.P. Casey, K.S. Brown, C.R. Myers, J.P. Sethna
Cornell University Technical Report

2006

A Localized Specific Interaction Alters the Unfolding Pathways of Structural Homologues
G. Xu, M. Narayan, I. Kurinov, D.R. Ripoll, E. Welker, M. Khalili, S.E. Ealick, H.A. Scheraga
Journal of American Chemical Society

A Research Library Based on the Historical Collections of the Internet Archive
W. Arms, S. Aya, P Dmitriev, B. Kot, R. Mitchell, L. Walle
D-Lib Magazine

Advanced Computational Techniques for Materials-by-Design
N. Zabaras
Cornell University Technical Report

ALPS: A Software Framework for Parallel Space-Time Adaptive Processing
K. Lee, A.W. Bojanczyk
Applied Parallel Computing

Bayesian Calibration of Computationally Expensive Models Using Optimization and Radial Basic Function Approximation
N. Blizniouk, P. Mugunthan, R. Regis, D. Ruppert, C. Shoemaker, S. Wild
Cornell University Technical Report

Building a Research Library for the History of the Web
W. Arms, S. Aya, P. Dmitriey, B. Kot, R. Mitchell, L Walle
Joint Conference on Digital Libraries

Cluster Assimilation and Collisional Filtering on Metal-Oxide Surfaces
D.A. Freedman, T.A. Arias
Physical Review Letters

Comment on “Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil”
J. Bunge, S.S. Epstein, D.G. Peterson
Science

Efficient Computation of the First Passage Time Distribution of the Generalized Master Equation by Steady-State Relaxation
D. Shalloway, A. Faradkijan
Journal of Chemical Physics

Development and Characterization of a Normalized Canine Retinal cDNA Library for Genomic and Expression Studies
B. Zangerl, Q. Sun, J. Pillardy, J. Johnson, P. Schweitzer, A. Hernandez, L. Liu, G. Acland, G. Aguirre
Investigative Ophthalmology and Visual Science

Distributed System Based on Web Services for Computational Science Simulations
K. Pingali, P. Stodghill
Proceedings of the International Conference on Supercomputing

Efficient Query Processing on Unstructured Tetrahedral Meshes
S. Papadomanolakis, A. Ailamaki, J. Lopez, T. Tu, D.R. O’Hallaron, G. Heber
Proceedings of ACM SIGMOD

Evaluation of the PNM Model for Simulating Drain Flow Nitrate-N Concentration Under Manure-Fertilized Maize
J.M. Sogbedji, H.M. van Es, J.J. Melkonian, R.R. Schindelbeck
Plant and Soil

From Wayback Machine to Yesternet: New Opportunities for Social Science
W. Arms, D. Huttenlocher, J. Kleinberg, M. Macy, D Strang
Second International Conference on e-Social Science

Ground State of the Pseudogap in Cuprate Superconductors
T. Valla, A.V. Fedorov, Jinho Lee, J.C. Davis, G.D. Gu
Science

Microfluidic Biomaterials
A.D. Stroock, M. Cabodi
M.R.S. Bulletin

Mobile MPI Programs in Computational Grids
R. Fernandes, K. Pingali, P. Stodghill
ACM 2006 Symposium on Principles and Practice of Parallel Computing

“Propeller” Regime of Disk Accretion to Rapidly Rotating Stars
G.V. Ustyugova, A.V. Kodoba, M.M. Romanova, R.V.E. Lovelace
The Astrophysical Journal

Protein Translocation Through a Tunnel Induces Changes in Folding Kinetics: A Lattice Model Study
L.M. Contreras Martinez, F.J. Martinez-Verachoechea, P. Pohkarel, A.D. Stroock, F.A. Escobedo, M.P. DeLisa
Biotechnology & Bioengineering

Reported Anatomical Variability Naturally Leads to Multimodal Distributions of Denavit-Hartenberg
V. Santos, F. Valero-Cuevas
IEEE Transactions of Biomedical Engineering

Risk Neutral Compatibility with Option Prices
J. Jacod, P. Protter
Cornell University Technical Report

Spatial Interpolation of Daily Maximum and Minimum Air Temperature Based on Meteorological Model Analysis and Independent Observation
A.T. DeGaetano, B.N. Belcher
Cornell University Technical Report

Strategic Design of Distribution Systems with Economies of Scale in Transportation
J.R. Lin, L.K. Nozick, M.A. Turnquist
Annals of Operation Research

Supporting Finite Element Analysis with a Relational Database Backend; Part III
G. Heber, C. Pelkie, A. J. Dolgert. J. Gray, D. Thompson
Microsoft Research Technical Report

Supporting Finite Element Analysis with a Relational Database Backend; Part II
G. Heber, J. Gray
Microsoft Research Technical Report

Synthetic Statistical Approach Reveals a High Degree of Richness of Microbial Eukaryotes in an Anoxic Water Column
S.-O. Jean, J. Bunge, T. Stoeck, K.J.-A. Barger, S.-H. Hong, S.S. Epstein
Applied and Environmental Microbiology

The Sloppy Model Universality Class and Vandermonde Matrix
J.J. Waterfall, F.P. Casey, R.N. Gutenkunst, K.S. Brown, C.R. Myers, P.W. Brouwer, V. Elser, J.P. Sethna
Physical Review Letters

Three Case Studies of Large-Scale Data Flows
W. Arms, S. Aya, M. Calimlim, J. Cordes, P. Deneva, P. Dmitriev, J. Gehrke, L. Gibbons, C.D. Jones, V. Kuznetsov, D. Lifka, M. Riedewald, D. Riley, A. Ryd, G.J. Sharp
IEEE Proceedings on Workflow and Dataflow for Scientific Applications

Whole-Genome Expression Profiling Defines the HrpL Regulon of Pseudomonas syringae pv. Tomato DC3000
A.O. Ferreira, C.R. Myers, J.S. Gordon, G.B. Martin, M. Vencato, A. Collmer, M.D. Wehling, J.R. Alfano, G. Moreno-Hagelsieb, W.F. Lamboy, G. DeClerck, D.J. Schneider, S.W. Cartinhour
Molecular Plant-Microbe Interactions

2005

A Method to Infer Time of Observation at U.S. Cooperative Observer Network Stations Using Model Analyses
B.N. Belcher, A.T. DeGaetano
Cornell University Technical Report

A Surface Loop of the Potato Leafroll Virus Coat Protein is Involved in Virion Assembly, Systemic Movement, and Aphid Transmission
L. Lee, I.B. Kaplan, D.R. Ripoll, D. Liang, P. Palukaitis, S.M. Gray
Journal of Virology

A Variable Temperature EPR Study of Mn2+ -doped NH4C10.9I0.1 Single Crystal at 170 GHz: Zero-Field Splitting Parameter and its Absolute Sign
S. K. Misra, S.I. Andronenko, P. Chand, K.A. Earle, S.V. Paschenko, J.H. Freed
Journal of Magnetic Resonance

Coupling Between Conformation and Proton Binding in Proteins
J. Vila, D.R. Ripoll, Y.A. Arnautova, Y.N. Vorobjev, H.A. Scheraga
Proteins

Detection of Repolarization Alternans With an Implantable Cardioverter Defibrillator Lead in a Porcine Model
Maybhate, S.C. Hao, S. Iwai, J.U. Lee, A.B. Guttigoli, K.Stein, B. Lerman, D. Christini
IEEE Transactions on Biomedical Engineering

Electric Organ Discharge Patterns During Group Hunting by a Mormyrid Fish
M.E. Arnegard, B.A. Carlson
Proceedings of the Royal Society

Evolutionary Robotics and Open-Ended Design Automation
H. Lipson
Biometrics

High-Frequency ESR at ACERT
K.A. Earle, B. Dzikovski. W. Hofbauer, J.K. Moscicki, J.H. Freed
Magnetic Resonance in Chemistry

Insights into Dark Energy: Interplay Between Theory and Observation
R. Bean, S. Carroll, M. Trodden
Cornell University Technical Report

Lattice Strain Partitioning in a Two-Phase Alloy and its Redistribution Upon Yielding
T.S. Han, Paul R. Dawson
Materials Science and Engineering

Measuring and Modeling the Appearance of Finished Wood
S.R. Marchner, S.H. Westin, A. Arbree, J.T. Moon
ACM Transactions on Graphics (SIGGRAPH 2005 Proceedings)

Minimizing CVaR and VaR for a Portfolio of Derivatives
S. Alexander, T.F. Coleman, Y. Li
Journal of Banking and Finance

Modeling Nitrogen Dynamics Under Maize on Ferralsols in Western Africa
J.M. Sogbedji, H.M. van Es, K.L. Agbeko
Nutrient Cycling in Agroecosystems

Multivariate Optimization of a High Brightness DC Gun Photoinjector
I. Bazarov, C.K. Sinclair
Physical Review

Nonlinear Spectroscopy of Resonantly Coupled Classical Mechanical Molecular Vibrations
W.G. Noid, R.F. Loring
Molecular Physics

Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests
S. Lodziej, C. Czaplewski, A. Liwo, M. Chinchio, M. Nanias, JA Vila, M. Khalili, Y.A. Arnautova, A. Jagielska, M. Makowski, H.D. Schafroth, R. Kazmierkiewicz, . D.R. Ripoll, J. Pillardy, J.A. Saunders, Y.K. Kang, K.D. Gibson, H.A. Scheraga
Proceedings of the National Academy of Science

Polar Octahedral Rotations: A Path to New Multifunctional Materials
W. Majeran, Y. Cai, Q. Sun, K.J. van Wijk
Plant Cell

Predicting Microbial Species Richness
S.-H. Hong, J. Bunge, S.-O. Jeon, S.S. Epstein
National Academy of Science

Reducing Communication Time Through Message Prefetching
J. Ke, Martin Burtscher, E. Speight
Proceedings of International Conference on Parallel and Distributed Processing

Scientific Data Management in the Coming Decade
J. Gray, D.T. Liu, M.Nieto-Santisteban, A. Szalay, D.J. DeWitt, G. Heber
ACM SIGMOD

Soil Test, Aerial Image and Yield Data as Inputs for Site-specific Fertility and Hybrid Management Under Maize
A. Magri, H. M. van Es, M.A. Glos, W.J. Cox
Precision Agriculture

Structural Damage Identification Using Co-Evolution and Frequency Response Functions
B. Kouchmeshky, W. Aquino
Cornell University Technical Report

Supporting Finite Element Analysis with a Relational Database Backend; Part I
G. Heber, J. Gray
Microsoft Research Technical Report

The Influence of Chemical Mechanisms on PDF Calculations of Nonpremixed Piloted Jet Flames
R.R. Cao, S.B. Pope
Combustion and Flame Journal

The Maximum Density Droplet to Lower Density Droplet Transition in Quantum Dots
A.D. Guclu, C.J. Umrigar
Physical Review

Three-Dimensional, Parallel, Finite Element Simulation of Fatigue Crack Growth in a Bevel Pinion Gear
A. Ural, G. Heber, P.A. Wawrzynek, A.R. Ingraffea, D.G Lewicki, Joaquim Neto
Engineering Fracture Mechanics Journal

   

2004

A Vision for PetaByte Data Management and Analysis Services for the Arecibo Telescope
M. Calimlim, J. Cordes, A. Demers, J. Deneva, J. Gehrke, D. Kifer, M. Riedewald, J. Shanmugasundaram
IEEE Computer Society

Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution Protein Coding Sequences and for Identifying Positively Selected Sites
W. Wong, Z. Yang, N. Goldman, R. Nielsen
Genetics

Enriching the Sequence Substitution Matrix by Structural Information
O. Teodorescu, T. Galor, J. Pillardy, R. Elber
Protein

Hedging Guarantees in Variable Annuities (Under Both Market and Interest Rate Risks)
T.F. Coleman, Y. Li, M.-C. Patron
Cornell University Technical Report

In-Depth Analysis of the Thylakoid Membrane proteome of Arabidopsis thaliana Chloroplasts: New Proteins, New Functions, and a Plastid Proteome Database
G. Frisco, L. Guacamole, A. J. Sternberg, J.B. Pettier, A. Rubella, Q. Sun, K.J. van Wink
Plant Cell

Implementation and Evaluation of a Scalable Application-Level Checkpoint-Recovery Scheme for MPI Programs
M. Schulz, G. Bronevetsky, R. Fernandes, D. Marques, K. Pingali, P. Stodghill
Supercomputing 2004

Integrated Design, Deployment and Inference for Robot Ecologies
J. Bongard, H. Lipson
Proceedings of Robosphere 2004

Novel Two-Dimensional Photonic Crystals Designed by Evolutionary Algorithms
S.F. Preble, H. Lipson, M. Lipson
Proceedings of the International Society for Optical Engineering 2004

PeerGAD: a Peer-Review-based and Community-Centric Web Application for Viewing and Annotating Prokaryotic Genome Sequences
M.D. D’Ascenzo, A. Collmer, G.B. Martin
Nucleic Acids Research

Performance Analysis of the Pipe Problem, a Multi-Physics Simulation Based on Web Services
P. Stodghill, R. Cronin, K. Pingali, G. Heber
Cornell University Technical Report

Performance Modeling and Optimization Framework for Space-Time Adaptive Processing (STAP)
K. Lee, A. Bojanczyk
IEEE International Parallel and Distributed Processing Symposium

Robustly Hedging Variable Annuities with Guarantees Under Jump and Volatility Risks
T. Coleman, Y. Kim, Y. Li, M.-C. Patron
Cornell University Technical Report

Runtime Compression of MPI Messages to Improve the Performance and Scalability of Parallel Applications
J. Ke, M. Burtscher, E. Speight
Supercomputing 2004

Sam68 Exerts Separable Effects on Cell Cycle Progression and Apoptosis
S.J. Taylor, R.J. Resnick, D. Shalloway
BMC Cell Biology

The Protein Folding Problem: Global Optimization of Force Fields
H.A. Scheraga, A. Liwo, S. Oldziej, C. Czaplewski, J. Pillardy, D.R. Ripoll, J.A. Vila, R. Kazmierkiewicz, J.A. Saunders, Y.A. Arnautova, A. Jagielska, M. Chinchio, M. Nanias
Frontiers of Biology Journal

Vortex-Induced Vibrations
C.H.K. Williamson, R. Govardhan
Annual Review of Fluid Mechanics