Michael Bales | Columbia University (original) (raw)

Papers by Michael Bales

Research paper thumbnail of Understanding interdisciplinary health sciences collaborations: a campus-wide survey of obesity experts

Abstract This paper reports a campus-wide survey of obesity experts that allowed us to understand... more Abstract This paper reports a campus-wide survey of obesity experts that allowed us to understand organizational factors and collaboration patterns affiliated with health sciences research. By combining Google and PubMed searches and the snowball sampling method, we identified and then surveyed 113 obesity experts on their collaborators, research interests, and affiliations with academic departments and research centers. The response rate was 61%.

Research paper thumbnail of Epidemiologic Response to Anthrax Outbreaks: Field Investigations, 1950-2001

Research paper thumbnail of Evaluating the Restrict to MeSH Algorithm

Research paper thumbnail of Research Paper: Topological Analysis of Large-scale Biomedical Terminology Structures

Journal of The American Medical Informatics Association, Jan 1, 2007

Research paper thumbnail of Epidemiologic responses to anthrax outbreaks: A review of field investigations conducted by the Centers for Disease Control and Prevention, 1950 to August 2001

The 130th Annual …, Jan 1, 2002

We used unpublished reports, published manuscripts, and communication with investigators to ident... more We used unpublished reports, published manuscripts, and communication with investigators to identify and summarize 49 anthrax-related epidemiologic field investigations conducted by the Centers for Disease Control and Prevention from 1950 to August 2001. Of 41 investigations in which Bacillus anthracis caused human or animal disease, 24 were in agricultural settings, 11 in textile mills, and 6 in other settings. Among the other investigations, two focused on building decontamination, one was a response to bioterrorism threats, and five involved other causes. Knowledge gained in these investigations helped guide the public health response to the October 2001 intentional release of B. anthracis, especially by addressing the management of anthrax threats, prevention of occupational anthrax, use of antibiotic prophylaxis in exposed persons, use of vaccination, spread of B. anthracis spores in aerosols, clinical diagnostic and laboratory confirmation methods, techniques for environmental sampling of exposed surfaces, and methods for decontaminating buildings.

Research paper thumbnail of Extending a medical language processing system to the functional status domain

AMIA Annual …, Jan 1, 2005

The World Health Organization&amp... more The World Health Organization's International Classification of Functioning, Disability, and Health (ICF) provides a common framework for describing functional status information (FSI) in health records. Given the expense of manual coding, we are investigating the use of natural language processing (NLP) for automated FSI coding. We used an existing NLP system that was originally designed to encode clinical information. The system's lexicon and coding table were modified and preprocessing and postprocessing programs were created, allowing for automated assignment of selected ICF codes.

Research paper thumbnail of Sciologer: Visualizing and exploring scientific communities

UMI, ProQuest ® Dissertations & Theses. The world's most comprehensive collectio... more UMI, ProQuest ® Dissertations & Theses. The world's most comprehensive collection of dissertations and theses. Learn more... ProQuest, Sciologer: Visualizing and exploring scientific communities. by Bales, Michael Eliot, Ph ...

Research paper thumbnail of Evolution of Coauthorship in Public Health Services and Systems Research

American Journal of …, Jan 1, 2011

Background-Public health systems and services research (PHSSR) examines the organization, financi... more Background-Public health systems and services research (PHSSR) examines the organization, financing, and delivery of public health services and the impact of these activities on population health. An accurate description of this PHSSR is needed to empower funding agencies and other stakeholders, to coordinate PHSSR activities, and to foster the development of the field.

Research paper thumbnail of Evaluation of a Prototype Search and Visualization System for Exploring Scientific Communities

AMIA Annual Symposium …, Jan 1, 2009

Searches of bibliographic databases generate lists of articles but do little to reveal connection... more Searches of bibliographic databases generate lists of articles but do little to reveal connections between authors, institutions, and grants. As a result, search results cannot be fully leveraged. To address this problem we developed Sciologer, a prototype search and visualization system. Sciologer presents the results of any PubMed query as an interactive network diagram of the above elements. We conducted a cognitive evaluation with six neuroscience and six obesity researchers. Researchers used the system effectively. They used geographic, color, and shape metaphors to describe community structure and made accurate inferences pertaining to a) collaboration among research groups; b) prominence of individual researchers; and c) differentiation of expertise. The tool confirmed certain beliefs, disconfirmed others, and extended their understanding of their own discipline. The majority indicated the system offered information of value beyond a traditional PubMed search and that they would use the tool if available.

Research paper thumbnail of Social network analysis of interdisciplinarity in obesity research

AMIA Annual Symposium …, Jan 1, 2008

Transdisciplinary research accelerates scientific progress. Despite the value of social network a... more Transdisciplinary research accelerates scientific progress. Despite the value of social network analysis to characterize interdepartmental collaboration, institutions have been slow to adopt the approach. We use the approach to characterize collaboration among obesity researchers at our institution, identifying cores of researchers engaged in frequent collaborations. Providing an objective view of research across an institution, social network analysis is a baseline for efforts to facilitate transdisciplinary collaboration.

Research paper thumbnail of Topological analysis of large-scale biomedical terminology structures

Journal of the American Medical …, Jan 1, 2007

Research paper thumbnail of Qualitative assessment of the International Classification of Functioning, Disability, and Health with respect to the desiderata for controlled medical vocabularies

International Journal of …, Jan 1, 2006

Background: The International Classification of Functioning, Disability, and Health (ICF), a clas... more Background: The International Classification of Functioning, Disability, and Health (ICF), a classification system published in 2001 by the World Health Organization (WHO), provides a common language and framework for describing functional status information (FSI) in health records. Methods: Informed by ongoing research in coding FSI in patient records, this paper qualitatively assesses the ICF framework with respect to the desiderata for controlled medical vocabularies, an enumerated a list of desirable qualities for controlled medical vocabularies proposed by Cimino [J.J. Cimino, Desiderata for controlled medical vocabularies in the twenty-first century, Meth. Inform. Med. 37 (1998) 394-403]. Results: The ICF satisfies 5 of the 12 desiderata. Five points were not satisfied and two points could not be evaluated. Conclusion: The ICF is a rich source of relevant terms, concepts, and relationships, but it was not developed in consideration of requirements for formal terminologies. Therefore, it could serve as a base from which to develop a formal terminology of functioning and disability. This assessment is a key next step in the development of the ICF as a sensitive, universal measure of functional status.

Research paper thumbnail of Human and automated coding of rehabilitation discharge summaries according to the International Classification of Functioning, Disability, and Health

Journal of the American …, Jan 1, 2006

Research paper thumbnail of Graph theoretic modeling of large-scale semantic networks

Journal of biomedical informatics, Jan 1, 2006

During the past several years, social network analysis methods have been used to model many compl... more During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Research paper thumbnail of Epidemiologic Responses to Anthrax Outbreaks: A Review of Field Investigations, 1950–2001

Emerging infectious …, Jan 1, 2002

We used unpublished reports, published manuscripts, and communication with investigators to ident... more We used unpublished reports, published manuscripts, and communication with investigators to identify and summarize 49 anthrax-related epidemiologic field investigations conducted by the Centers for Disease Control and Prevention from 1950 to August 2001. Of 41 investigations in which Bacillus anthracis caused human or animal disease, 24 were in agricultural settings, 11 in textile mills, and 6 in other settings. Among the other investigations, two focused on building decontamination, one was a response to bioterrorism threats, and five involved other causes. Knowledge gained in these investigations helped guide the public health response to the October 2001 intentional release of B. anthracis, especially by addressing the management of anthrax threats, prevention of occupational anthrax, use of antibiotic prophylaxis in exposed persons, use of vaccination, spread of B. anthracis spores in aerosols, clinical diagnostic and laboratory confirmation methods, techniques for environmental sampling of exposed surfaces, and methods for decontaminating buildings.

Research paper thumbnail of Planning against biological terrorism: lessons from outbreak investigations

Emerging Infectious …, Jan 1, 2003

We examined outbreak investigations conducted around the world from 1988 to 1999 by the Centers f... more We examined outbreak investigations conducted around the world from 1988 to 1999 by the Centers for Disease Control and Prevention’s Epidemic Intelligence Service. In 44 (4.0%) of 1,099 investigations, identified causative agents had bioterrorism potential. In six investigations, intentional use of infectious agents was considered. Healthcare providers reported 270 (24.6%) outbreaks and infection control practitioners reported 129 (11.7%); together they reported 399 (36.3%) of the outbreaks. Health departments reported 335 (30.5%) outbreaks. For six outbreaks in which bioterrorism or intentional contamination was possible, reporting was delayed for up to 26 days. We confirmed that the most critical component for bioterrorism outbreak detection and reporting is the frontline healthcare profession and the local health departments. Bioterrorism preparedness should emphasize education and support of this frontline as well as methods to shorten the time between outbreak and reporting.

Research paper thumbnail of A Brain Region-Specific Predictive Gene Map for Autism Derived by Profiling a Reference Gene Set

PLoS ONE, Jan 1, 2011

Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) ... more Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) remain largely unresolved. Increasingly, structural variations in discrete chromosomal loci are implicated in ASD, expanding the search space for its disease etiology. We exploited the high genetic heterogeneity of ASD to derive a predictive map of candidate genes by an integrated bioinformatics approach. Using a reference set of 84 Rare and Syndromic candidate ASD genes (AutRef84), we built a composite reference profile based on both functional and expression analyses. First, we created a functional profile of AutRef84 by performing Gene Ontology (GO) enrichment analysis which encompassed three main areas: 1) neurogenesis/projection, 2) cell adhesion, and 3) ion channel activity. Second, we constructed an expression profile of AutRef84 by conducting DAVID analysis which found enrichment in brain regions critical for sensory information processing (olfactory bulb, occipital lobe), executive function (prefrontal cortex), and hormone secretion (pituitary). Disease specificity of this dual AutRef84 profile was demonstrated by comparative analysis with control, diabetes, and non-specific gene sets. We then screened the human genome with the dual AutRef84 profile to derive a set of 460 potential ASD candidate genes. Importantly, the power of our predictive gene map was demonstrated by capturing 18 existing ASDassociated genes which were not part of the AutRef84 input dataset. The remaining 442 genes are entirely novel putative ASD risk genes. Together, we used a composite ASD reference profile to generate a predictive map of novel ASD candidate genes which should be prioritized for future research.

Research paper thumbnail of Understanding interdisciplinary health sciences collaborations: a campus-wide survey of obesity experts

Abstract This paper reports a campus-wide survey of obesity experts that allowed us to understand... more Abstract This paper reports a campus-wide survey of obesity experts that allowed us to understand organizational factors and collaboration patterns affiliated with health sciences research. By combining Google and PubMed searches and the snowball sampling method, we identified and then surveyed 113 obesity experts on their collaborators, research interests, and affiliations with academic departments and research centers. The response rate was 61%.

Research paper thumbnail of Epidemiologic Response to Anthrax Outbreaks: Field Investigations, 1950-2001

Research paper thumbnail of Evaluating the Restrict to MeSH Algorithm

Research paper thumbnail of Research Paper: Topological Analysis of Large-scale Biomedical Terminology Structures

Journal of The American Medical Informatics Association, Jan 1, 2007

Research paper thumbnail of Epidemiologic responses to anthrax outbreaks: A review of field investigations conducted by the Centers for Disease Control and Prevention, 1950 to August 2001

The 130th Annual …, Jan 1, 2002

We used unpublished reports, published manuscripts, and communication with investigators to ident... more We used unpublished reports, published manuscripts, and communication with investigators to identify and summarize 49 anthrax-related epidemiologic field investigations conducted by the Centers for Disease Control and Prevention from 1950 to August 2001. Of 41 investigations in which Bacillus anthracis caused human or animal disease, 24 were in agricultural settings, 11 in textile mills, and 6 in other settings. Among the other investigations, two focused on building decontamination, one was a response to bioterrorism threats, and five involved other causes. Knowledge gained in these investigations helped guide the public health response to the October 2001 intentional release of B. anthracis, especially by addressing the management of anthrax threats, prevention of occupational anthrax, use of antibiotic prophylaxis in exposed persons, use of vaccination, spread of B. anthracis spores in aerosols, clinical diagnostic and laboratory confirmation methods, techniques for environmental sampling of exposed surfaces, and methods for decontaminating buildings.

Research paper thumbnail of Extending a medical language processing system to the functional status domain

AMIA Annual …, Jan 1, 2005

The World Health Organization&amp... more The World Health Organization's International Classification of Functioning, Disability, and Health (ICF) provides a common framework for describing functional status information (FSI) in health records. Given the expense of manual coding, we are investigating the use of natural language processing (NLP) for automated FSI coding. We used an existing NLP system that was originally designed to encode clinical information. The system's lexicon and coding table were modified and preprocessing and postprocessing programs were created, allowing for automated assignment of selected ICF codes.

Research paper thumbnail of Sciologer: Visualizing and exploring scientific communities

UMI, ProQuest ® Dissertations & Theses. The world's most comprehensive collectio... more UMI, ProQuest ® Dissertations & Theses. The world's most comprehensive collection of dissertations and theses. Learn more... ProQuest, Sciologer: Visualizing and exploring scientific communities. by Bales, Michael Eliot, Ph ...

Research paper thumbnail of Evolution of Coauthorship in Public Health Services and Systems Research

American Journal of …, Jan 1, 2011

Background-Public health systems and services research (PHSSR) examines the organization, financi... more Background-Public health systems and services research (PHSSR) examines the organization, financing, and delivery of public health services and the impact of these activities on population health. An accurate description of this PHSSR is needed to empower funding agencies and other stakeholders, to coordinate PHSSR activities, and to foster the development of the field.

Research paper thumbnail of Evaluation of a Prototype Search and Visualization System for Exploring Scientific Communities

AMIA Annual Symposium …, Jan 1, 2009

Searches of bibliographic databases generate lists of articles but do little to reveal connection... more Searches of bibliographic databases generate lists of articles but do little to reveal connections between authors, institutions, and grants. As a result, search results cannot be fully leveraged. To address this problem we developed Sciologer, a prototype search and visualization system. Sciologer presents the results of any PubMed query as an interactive network diagram of the above elements. We conducted a cognitive evaluation with six neuroscience and six obesity researchers. Researchers used the system effectively. They used geographic, color, and shape metaphors to describe community structure and made accurate inferences pertaining to a) collaboration among research groups; b) prominence of individual researchers; and c) differentiation of expertise. The tool confirmed certain beliefs, disconfirmed others, and extended their understanding of their own discipline. The majority indicated the system offered information of value beyond a traditional PubMed search and that they would use the tool if available.

Research paper thumbnail of Social network analysis of interdisciplinarity in obesity research

AMIA Annual Symposium …, Jan 1, 2008

Transdisciplinary research accelerates scientific progress. Despite the value of social network a... more Transdisciplinary research accelerates scientific progress. Despite the value of social network analysis to characterize interdepartmental collaboration, institutions have been slow to adopt the approach. We use the approach to characterize collaboration among obesity researchers at our institution, identifying cores of researchers engaged in frequent collaborations. Providing an objective view of research across an institution, social network analysis is a baseline for efforts to facilitate transdisciplinary collaboration.

Research paper thumbnail of Topological analysis of large-scale biomedical terminology structures

Journal of the American Medical …, Jan 1, 2007

Research paper thumbnail of Qualitative assessment of the International Classification of Functioning, Disability, and Health with respect to the desiderata for controlled medical vocabularies

International Journal of …, Jan 1, 2006

Background: The International Classification of Functioning, Disability, and Health (ICF), a clas... more Background: The International Classification of Functioning, Disability, and Health (ICF), a classification system published in 2001 by the World Health Organization (WHO), provides a common language and framework for describing functional status information (FSI) in health records. Methods: Informed by ongoing research in coding FSI in patient records, this paper qualitatively assesses the ICF framework with respect to the desiderata for controlled medical vocabularies, an enumerated a list of desirable qualities for controlled medical vocabularies proposed by Cimino [J.J. Cimino, Desiderata for controlled medical vocabularies in the twenty-first century, Meth. Inform. Med. 37 (1998) 394-403]. Results: The ICF satisfies 5 of the 12 desiderata. Five points were not satisfied and two points could not be evaluated. Conclusion: The ICF is a rich source of relevant terms, concepts, and relationships, but it was not developed in consideration of requirements for formal terminologies. Therefore, it could serve as a base from which to develop a formal terminology of functioning and disability. This assessment is a key next step in the development of the ICF as a sensitive, universal measure of functional status.

Research paper thumbnail of Human and automated coding of rehabilitation discharge summaries according to the International Classification of Functioning, Disability, and Health

Journal of the American …, Jan 1, 2006

Research paper thumbnail of Graph theoretic modeling of large-scale semantic networks

Journal of biomedical informatics, Jan 1, 2006

During the past several years, social network analysis methods have been used to model many compl... more During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Research paper thumbnail of Epidemiologic Responses to Anthrax Outbreaks: A Review of Field Investigations, 1950–2001

Emerging infectious …, Jan 1, 2002

We used unpublished reports, published manuscripts, and communication with investigators to ident... more We used unpublished reports, published manuscripts, and communication with investigators to identify and summarize 49 anthrax-related epidemiologic field investigations conducted by the Centers for Disease Control and Prevention from 1950 to August 2001. Of 41 investigations in which Bacillus anthracis caused human or animal disease, 24 were in agricultural settings, 11 in textile mills, and 6 in other settings. Among the other investigations, two focused on building decontamination, one was a response to bioterrorism threats, and five involved other causes. Knowledge gained in these investigations helped guide the public health response to the October 2001 intentional release of B. anthracis, especially by addressing the management of anthrax threats, prevention of occupational anthrax, use of antibiotic prophylaxis in exposed persons, use of vaccination, spread of B. anthracis spores in aerosols, clinical diagnostic and laboratory confirmation methods, techniques for environmental sampling of exposed surfaces, and methods for decontaminating buildings.

Research paper thumbnail of Planning against biological terrorism: lessons from outbreak investigations

Emerging Infectious …, Jan 1, 2003

We examined outbreak investigations conducted around the world from 1988 to 1999 by the Centers f... more We examined outbreak investigations conducted around the world from 1988 to 1999 by the Centers for Disease Control and Prevention’s Epidemic Intelligence Service. In 44 (4.0%) of 1,099 investigations, identified causative agents had bioterrorism potential. In six investigations, intentional use of infectious agents was considered. Healthcare providers reported 270 (24.6%) outbreaks and infection control practitioners reported 129 (11.7%); together they reported 399 (36.3%) of the outbreaks. Health departments reported 335 (30.5%) outbreaks. For six outbreaks in which bioterrorism or intentional contamination was possible, reporting was delayed for up to 26 days. We confirmed that the most critical component for bioterrorism outbreak detection and reporting is the frontline healthcare profession and the local health departments. Bioterrorism preparedness should emphasize education and support of this frontline as well as methods to shorten the time between outbreak and reporting.

Research paper thumbnail of A Brain Region-Specific Predictive Gene Map for Autism Derived by Profiling a Reference Gene Set

PLoS ONE, Jan 1, 2011

Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) ... more Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) remain largely unresolved. Increasingly, structural variations in discrete chromosomal loci are implicated in ASD, expanding the search space for its disease etiology. We exploited the high genetic heterogeneity of ASD to derive a predictive map of candidate genes by an integrated bioinformatics approach. Using a reference set of 84 Rare and Syndromic candidate ASD genes (AutRef84), we built a composite reference profile based on both functional and expression analyses. First, we created a functional profile of AutRef84 by performing Gene Ontology (GO) enrichment analysis which encompassed three main areas: 1) neurogenesis/projection, 2) cell adhesion, and 3) ion channel activity. Second, we constructed an expression profile of AutRef84 by conducting DAVID analysis which found enrichment in brain regions critical for sensory information processing (olfactory bulb, occipital lobe), executive function (prefrontal cortex), and hormone secretion (pituitary). Disease specificity of this dual AutRef84 profile was demonstrated by comparative analysis with control, diabetes, and non-specific gene sets. We then screened the human genome with the dual AutRef84 profile to derive a set of 460 potential ASD candidate genes. Importantly, the power of our predictive gene map was demonstrated by capturing 18 existing ASDassociated genes which were not part of the AutRef84 input dataset. The remaining 442 genes are entirely novel putative ASD risk genes. Together, we used a composite ASD reference profile to generate a predictive map of novel ASD candidate genes which should be prioritized for future research.