James H Kaufman

James H Kaufman
Altos Labs · Modeling and Simulation

PhD
Lead for the Modeling and Simulation group. https://altoslabs.com/

About

145
Publications
20,199
Reads
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4,450
Citations
Additional affiliations
January 2004 - present
IBM Research, Almaden
Position
  • SpatioTemporal Epidemiological Modeler (a recent project)
Description
  • http://www.eclipse.org/stem/
January 2004 - December 2012
IBM
January 1989 - present
University of California, Santa Barbara
Description
  • Graduate School
Education
June 1981 - February 1983
September 1980 - June 1981
University of Pennsylvania
Field of study
  • Physics
September 1976 - May 1980
Cornell University
Field of study
  • Physics

Publications

Publications (145)
Patent
For each unique pair of a complete set of data items, a computing device determines a distance between the data items of the unique pair. The computing device repeats the following until no data items remain in the complete set. For each data item remaining in the complete set, the computing device determines a similarity subset including each othe...
Preprint
Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use th...
Article
Full-text available
SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome this limitation, we developed a novel...
Article
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic mat...
Article
Full-text available
Importance Assumption of a well-mixed population during modeling is often erroneously made without due analysis of its validity. Ignoring the importance of the geo-spatial granularity at which the data is collected could have significant implications on the quality of forecasts and the actionable clinical recommendations that are based on it. Obje...
Article
Full-text available
Case description: In Latvia in 2014, acquired idiopathic megaesophagus (AIME) was observed in increased numbers of dogs that consumed varieties of 1 brand of dog food. Within 2 years, 253 dogs were affected. In Australia in November 2017, 6 working dogs that consumed 1 diet of another brand of dog food developed AIME. In total, 145 Australian dogs...
Preprint
Full-text available
Pandemic control measures like lock-down, restrictions on restaurants and gatherings, social-distancing have shown to be effective in curtailing the spread of COVID-19. However, their sustained enforcement has negative economic effects. To craft strategies and policies that reduce the hardship on the people and the economy while being effective aga...
Preprint
SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. In this work, we analyzed a corpus of 66,000 SARS-CoV-2 genome sequences. We developed a novel semi-supervised pipeline for automated gene, protein, and functional domain annotation of SARS-CoV-2 genomes that differentiates i...
Article
Full-text available
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus...
Article
Full-text available
Background Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the fun...
Preprint
Full-text available
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus...
Preprint
Full-text available
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus...
Preprint
Full-text available
Multiple efforts to model the epidemiology of SARS-CoV-2 have recently been launched in support of public health response at the national, state, and county levels. While the pandemic is global, the dynamics of this infectious disease varies with geography, local policies, and local variations in demographics. An underlying assumption of most infec...
Article
Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. Draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest...
Article
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. Due to the increasing available genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks to...
Preprint
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix...
Preprint
Full-text available
We introduce a novel mathematical model to analyze the effect of removing non-pharmaceutical interventions on the spread of COVID19 as a function of disease testing rate. We find that relaxing interventions has a strong impact on the size of the epidemic peak as a function of intervention re- moval time. We show that it is essential for predictive...
Preprint
Full-text available
Horizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied w...
Article
Full-text available
Increasingly available microbial reference data allows interpreting the composition and function of previously uncharacterized microbial communities in detail, via high-throughput sequencing analysis. However, efficient methods for read classification are required when the best database matches for short sequence reads are often shared among multip...
Preprint
Full-text available
Computational learning methods allow researchers to make predictions, draw inferences, and automate generation of mathematical models. These models are crucial to solving real world problems, such as antimicrobial resistance, pathogen detection, and protein evolution. Machine learning methods depend upon ground truth data to achieve specificity and...
Preprint
Full-text available
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks...
Article
Full-text available
Foodborne diseases are a longstanding worldwide public health concern. Modeling the transmission pathways of foodborne pathogens accurately and effectively can aid in understanding the spread of pathogens and facilitate decision making for intervention. A new compartmental model is reported that integrates the effects of both direct and indirect tr...
Article
Full-text available
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA se...
Article
Full-text available
Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into questi...
Article
Full-text available
The Spatiotemporal Epidemiologic Modeler (STEM) is an open source software project supported by the Eclipse Foundation and used by a global community of researchers and public health officials working to track and, when possible, control outbreaks of infectious disease in human and animal populations. STEM is not a model or a tool designed for a sp...
Presentation
Presentation to PACCARB on January 2019 https://www.youtube.com/watch?v=PV621k2YwwY&list=PLrl7E8KABz1HjPwWvHw08iTKUOodunxJQ&index=3&t=0s
Preprint
Full-text available
To investigate the feasibility of using freeware to model and forecast disease on a local scale, we report the results of modeling measles using a spatial patch model centered around 73 clinics in the North West London Borough of Ealing. MMR1 and MM2 immunization data was extracted for three cohorts, age 1-3, 4-6 and 7-19 and patient population was...
Article
Full-text available
Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in data. In...
Conference Paper
Full-text available
ABSTRACT Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in...
Article
Full-text available
Salmonella is a common food-associated bacterium that has substantial impact on worldwide human health and the global economy. This is the public release of 1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Salmonella genus.
Article
Full-text available
The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associa...
Article
Full-text available
A zoonotic disease is a disease that can be passed from animals to humans. Zoonotic viruses may adapt to a human host eventually becoming endemic in humans, but before doing so punctuated outbreaks of the zoonotic virus may be observed. The Ebola virus disease (EVD) is an example of such a disease. The animal population in which the disease agent i...
Article
Full-text available
The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation an...
Article
Full-text available
Under intense scrutiny for safety and authenticity, our food supply encompasses probiotic supplementation, fermentation organisms, pathogenic bacteria, and microbial toxins - in short, the microbiome and metabolome of food. Recent claims regarding probiotic supplements, additives, and cultured foods highlight the need for widely accepted protocols...
Article
Full-text available
Foodborne disease is a global public health problem that affects millions of people every year. During a foodborne illness outbreak, rapid identification of contaminated food is vital to minimize illness, loss and impact on society. Public health officials face a significant challenge and long delays in obtaining critical information to help identi...
Article
Full-text available
Food safety procedures are critical to reducing pathogen caused food-borne disease (FBD). However there is no way to completely eliminate the risk of consuming contaminated products. When prevention efforts fail, rapid identification of the contaminated product is essential. The medical and economic losses incurred grow with the duration of the out...
Article
Full-text available
Open access at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137482 This paper uses methods drawn from physics to study the life cycle of viruses. The paper analyzes a model of viral infection and evolution using the "grand canonical ensemble" and formalisms from statistical mechanics and thermodynamics. Using this approach we...
Patent
Full-text available
A system facilitates management of public health data. The system includes an input interface, a policy data structure, a notification compliance engine, and a data translator. The input interface receives input data content descriptive of a public health event. The policy data structure stores reporting conditions for a plurality of public health...
Conference Paper
Full-text available
The current outbreak of Ebola virus disease (EVD) in West Africa has caused around 23000 infections by middle of February 2015, with a death rate of 40%. The cases have been imported into developed countries, e.g., Spain and US, through travelers and returning healthcare workers. It is clear that the virus is a threat to public health worldwide. Gi...
Article
Full-text available
Foodborne disease outbreaks of recent years demonstrate that due to increasingly interconnected supply chains these type of crisis situations have the potential to affect thousands of people, leading to significant healthcare costs, loss of revenue for food companies, and-in the worst cases-death. When a disease outbreak is detected, identifying th...
Patent
Full-text available
The initial partitioning of a distributed computing problem can be critical, and is often a source of tedium for the user. A method is provided that automatically segments the problem into fixed sized collections of original program cells (OPCs) based on the complexity of the problem specified, and the combination of computing agents of various cal...
Conference Paper
Food safety procedures, such as the recommendations recently published by the FDA, are critical to reducing foodborne illness. However there is no way to completely eliminate the risk of receiving contaminated food. When prevention efforts fail, rapid identification of the source product is essential. The medical and economic losses incurred grow w...
Article
Full-text available
Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of th...
Conference Paper
Full-text available
Dengue is a major international public health concern that impacts one-third of the world's population. There are four serotypes of the dengue virus (DENV). Infection with one serotype affords life-long immunity to that serotype but only temporary cross immunity (CI) to other serotypes. The risk of lethal complications is elevated upon re-infection...
Conference Paper
Full-text available
Over the last decades the globalization of trade has significantly altered the topology of food supply chains. Even though food-borne illness has been consistently on the decline, the hazardous impact of contamination events is larger [1-3]. Possible contaminants include pathogenic bacteria, viruses, parasites, toxins or chemicals. Contamination ca...
Conference Paper
Full-text available
This paper describes the Spatiotemporal Epidemiological Modeler (STEM), an open source disease modeling application available through the Eclipse Foundation. The most distinguishing aspect of STEM is that it provides an open platform for researchers to build, run, share, and reuse models of infectious disease. We give a motivation why we believe an...
Article
Background The role of the Anopheles vector in malaria transmission and the effect of climate on Anopheles populations are well established. Models of the impact of climate change on the global malaria burden now have access to high-resolution climate data, but malaria surveillance data tends to be less precise, making model calibration problematic...
Conference Paper
A community resource for spatial, temporal and food chain epidemiological modelling to assess risks in bio-terroristic or agro-terroristic crisis situations Falenski, A.1, Thoens, C.1, Filter, M.1, Kaesbohrer, A.1, Appel, B.1, Kaufman, J.H.2, Edlund, S.2, Davis,M.2, Douglas, J.V.2, and Hu, K.2, 1Federal Institute for Risk Assessment, Department Bio...
Conference Paper
The SpatioTemporal Epidemiological Modeler: An open source framework for modeling food-borne disease Authors: JH Kaufman*, M Davis, JV Douglas, S Edlund, and K Hu IBM Research Division, Almaden Research Center, San Jose, CA M Filter, J-F Wigger, C Thoens, AA Weiser, A Kaesbohrer, and B Appel Federal Institute for Risk Assessment, Dep. Biologica...
Article
In recent decades, dengue becomes a major international public health concern. Dengue Fever (DF) is now endemic in more than 100 countries and impact one-third of the world's population1. This vector-borne disease is transmitted by the bite of an infectious Aedes mosquito. No specific vaccine and treatment are available. There are four serotypes of...
Article
Full-text available
Rising costs, decreasing quality of care, diminishing productivity, and increasing complexity have all contributed to the present state of the healthcare industry. The interactions between payers (e.g., insurance companies and health plans) and providers (e.g., hospitals and laboratories) are growing and are becoming more complicated. The constant...
Article
This chapter describes the Spatiotemporal Epidemiological Modeler (STEM), now being developed as an open source computer software system for defining and visualizing simulations of the spread of infectious disease in space and time. Part of the Eclipse Technology Project, http://www.eclipse.org/ stem, STEM is designed to offer the research communit...
Article
In this paper we report the use of the open source Spatiotemporal Epidemiological Modeler (STEM, www.eclipse.org/stem) to compare three basic models for seasonal influenza transmission. The models are designed to test for possible differences between the seasonal transmission of influenza A and B. Model 1 assumes that the seasonality and magnitude...
Chapter
For autonomous agents to achieve their full potential they require access to detailed private information about individuals they are designed to assist. The time is rapidly approaching when we can build systems to gather this information and monitor all aspects of an individual’s life. In this chapter we describe Tempus Fugit (Time Flies), an attem...
Article
This paper describes an attempt to model seasonal influenza using the SpatioTemporal Epidemiological Modeler (STEM). Ten years of influenza data collected at 49 locations in Israel by the Israeli Center for Disease Control was used to fit the model, and a deterministic SIR(S) compartmental disease model was extended to account for seasonal variatio...