Current Postdoctoral Fellows
David Chartash, PhD
NLM Postdoctoral Fellow: 7/1/18-
Research Supervisor: Cynthia Brandt, MD, MPH (Yale Center for Medical Informatics)
Research: David Chartash is working to understand the adage in medicine that,
The history is the foundation of diagnosis, management and rapport with the patient, and that diagnosis is based on, first, a focused and meticulous history, followed by a focused and confirmatory physical examination and ending with a parsimonious ancillary investigation. — Crombie, D. L. "General Practice Today and Tomorrow. X. Diagnostic Methods." The Practitioner 191 (1963): 539-545.
His research aims to model information within the medical record and clinical encounter through the use of cognitive science, computational linguistic and complex systems science approaches. Currently this involves the modeling of language using both conventional linguistic and distributional semantic technologies; the analysis of clinical reasoning as it is encoded in physician writing in the pediatric rheumatology context; and the examination of the grammaticalization of fever of unknown illness from 1200 to present.
Jacob McPadden, MD
NLM Postdoctoral Fellow: 8/1/18-
Research Supervisor: Wade Schulz, MD
Research: Jacob McPadden is using deep learning models to predict diagnosis and prognosis of nectrotizing enterocolitis for clinical decision support. In addition, he is involved in projects predictive outcome models for cardiothoracic surgery using data mined from the EMR and clinical devices, and predictive models for pharmicogenomics testing and intervention.
Nima Nouri, PhD
NLM Postdoctoral Fellow: 10/1/18-
Research Supervisor: Steven Kleinstein, PhD (Associate Professor of Pathology)
Research: Nima Nouri carries out research related to the development of computational methods for the analysis of large-scale B cell immunoglobulin repertoire sequencing data. He is helping to build out automated analytical pipelines, develop novel algorithms and models, and create novel platforms to analyze large scale data sets, including those from next-generation sequencing platforms. These methods have been integrated and currently made available to the wider scientific community through the Immcantation tool suite (www.immcantation.org). Nima uses his applied mathematics and statistical skills to reduce complex biological systems to their basic principles leading to proper biological interpretation.
Previous Postdoctoral Fellows
Kelson Zawach, PhD (8/6/17 - 5/31/19)
Research: Kelson Zawach is using functional magnetic resonance imaging (fMRI) data to study the relationship between the structure of neurological connections and attention deficit disorder (ADD). fMRI provides a window into the activity of the brain on a region-specific level by measuring blood flow in each region. These measurements effectively provide a time series of brain activity snapshots. The goal then is to use information about how activity of different regions changes in relation to each other to infer their connectivity and then to use this structure to understand the mechanisms underlying ADD.
Current Position: YCCI Postdoctoral Fellow, Yale University
Monique Surles-Zeigler, PhD (6/27/16 - 6/3/19)
Research: Monique Surles-Zeigler is developing techniques to mine the literature for neuronal protein markers and gene expression data; she is integrating this data into the SenseLab databases (senselab.med.yale.edu) and building a web application that enables exploration of this data and data from other neuroinformatics databases in anatomically based interactive diagrams. She is currently earning a Master’s degree in Computational Biology and Bioinformatics.
Current Position: Postdoctoral Fellow, UCSD
Kelsey Corcoran, DC (7/1/17 - 10/31/18)
Current Position: Associate Research Scientist, Yale University, New Haven, CT
Emily Powers, MD (7/1/16 - 6/30/18)
Research: Emily powers is conducting a systematic review of hard-stop alerts to evaluate their use-cases, efficacy, and unintended consequences as represented in the literature. She is also working on developing a dashboard on practice habits for pediatric fellows to include metrics such as procedure counts, mock RVUs, most commonly seen diagnoses, and benchmark these things again local and national standards.
Current Position: Clinical Fellow, Clinical Instruction, Yale Pediatrics, New Haven, CT
Daniel Spakowicz, PhD (6/1/15 - 3/31/18)
Research: Daniel Spakowicz is studying the dynamics of the relationship between humans and their microbiome, particularly during the onset of disease states. In diabetes, the microbiome has been demonstrated to be different between diabetic and healthy individuals; however, to date, no study has documented the transition between the diabetic disease and non-disease state. Longitudinal data are critical to the goal of establishing causal relationships and furthering the understanding of the role of the microbiome in diabetes pathophysiology. Dr. Spakowicz is participating in a project to follow pre-diabetic individuals over time while collecting massive quantities of data about host and microbial states. Samples are being collected from the same individuals over the course of at least three years, with denser sampling during periods of illness or stress. Dr. Spakowicz is developing novel methods to analyze the microbiomes of human fecal and nasal samples and their relationship to host blood glucose levels and other ‘omic data.
Current Position: Assistant Professor, The Ohio State Unviersity Wexner Medical Center, Columbus, Ohio
Kyle McGregor, PhD (2/1/16 - 9/15/17)
Research: Kyle McGregor studied ethical issues related to data science, specifically looking at the development and use of tools informed by clinical data to aid in enhanced identification and diagnosis of diseases impacting vulnerable populations. Work in this area requires careful consideration of risks and benefits to patient populations, development of new methods and procedures to protect patient level data, as well as direct involvement of community members most likely to be impacted by this work. Dr. McGregor worked with a widely interdisciplinary audience to develop an ethically guided framework to working with big data, vulnerable populations, and community partners. He presented his research at the Society for Adolescent Health and Medicine where he gave a platform presentation, National Translational Science meeting, and the Association of Maternal Child health Bureau programs annual meeting. Kyle worked on an ethically guided framework for analyzing social media data from adolescence with current gang involvement or suspected future gang involvement.
Current Position: Assistant Professor, Thomas Jefferson Univeristy. Philadelphia, PA
Rajdeep Brar, MD (07/29/15 - 07/28/17)
Research: Rajdeep Brar is developing a multi-axial, category based knowledge management system for decision support alerts. The initial phase involves developing an ontology for the categories that are believed to be most useful for managing alerts. The ontology will declare formal definitions for inclusion into each proposed category. The hypothesis is that analyzing performance statistics of the alerts (e.g. firing rate, acceptance rate, override rate) aggregated by category will help target areas for improvement. For example, if our patient safety related alerts are performing poorly, we can investigate for underlying reasons such as poor design. The categories can also help maintain the content of the knowledge base underlying the alerts. Dr. Brar has submitted abstracts of the described work to NLM and AMIA. He is also working on developing a tool for visualizing pediatric readmissions using best practices in visual analytics.
Current Position: Internist, Syosset, New York
Robert McDougal, PhD (6/1/2013 - 5/31/2016)
Research: Robert McDougal is developing techniques for studying the interaction of intracellular biochemical processes with electrophysiology in biophysically detailed numerical simulations of neurons and networks of neurons. There are three primary aspects of this research: developing techniques for presenting and analyzing these complicated models, developing a high-level language for specifying such models, and developing an extension to the NEURON simulator to efficiently integrate the corresponding equations. He is also earning a Masters degree in Computational Biology and Bioinformatics. In 2014-15, Dr. McDougal presented posters at the Society for Neuroscience (SfN) meeting in Washington DC, at the Multiscale Modeling meeting of the Interagency Modeling and Analysis Group (IMAG) in Bethesda, and at the Organization for Computational Neurosciences (CNS) meeting in Quebec. He gave tutorials featuring his NEURON extensions at both the CNS and SfN meetings. He gave a podium presentation at the NLM Informatics Training Meeting in Pittsburgh and a talk at the Open Source Brain conference in Alghero.
Current Position: Assistant Professor of Biostatistics, Yale University, New Haven, CT
Liyang Diao, PhD (10/1/14 - 7/15/16)
Research: Liyang Diao is researching community state types in the vaginal microbiome, how they are related to diseases such as bacterial vaginosis, and whether or not shifts in the microbiome can be predicted. While some microbiomes are very diverse between individuals, the vaginal microbiome appears to consist of five well-defined clusters, coined community state types (CSTs). However, the definition of these state types is not entirely clear, and different clustering methods and measures of sample dissimilarity produce varying results, particularly with RNA sequencing data. Liyang recently attended a workshop at the Statistical and Applied Mathematical Sciences Institute (SAMSI), where she is working with a group to predict CST shifts. Other interests of the SAMSI microbiome groups include normalization of microbiome RNA sequencing data and groundtruthing experiments. Liyang is also working on a method to analyze the differential expression of genes in time series data collected on various human and non- human brain regions.
Current Position: Senior Bioinformatics Scientist, Seres Therapeutics, Greater Boston Area
Yauheni Solad, MD (7/1/13 - 10/4/15)
Research: Dr. Solad developed tools for building research disease registries. Using pancreatic cystic neoplasms as a clinical domain, he analyzed practice guidelines for implementability and extracted concepts to build an ontology and concepts map. The concepts map was used as a blueprint for registry development with the EPIC EMR system.
Current Position: Medical Director, Digital Health at Yale New Haven Health, New Haven, CT
Taisha Roman, MD (7/1/13 - 5/8/15)
Research: Dr. Roman developed and implemented a custom specimen tracking system and evaluated its effects on patient safety and quality. She also evaluated a secure mobile application as a viable alternative to current methods of clinician communication.
Current Position: Medical Informatics Specialist, Physician Informatist at Northwell Health, Greater New York City Area