May 11
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Karandeep Singh

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I direct the Machine Learning for Learning Health Systems lab, whose work focuses on developing, validating, and evaluating the effectiveness of machine learning models within health systems. This includes projects such as a machine learning-supported patient educational platform (https://ask.musicurology.com) to support decision-making for patients with urological conditions. In additional to my predictive modeling research, I study patient-facing mobile apps and have published on this topic in Health Affairs, the Journal of General Internal Medicine, and the Clinical Journal of the American Society of Nephrology, among others. I have additional leadership roles that recognize my expertise in machine learning at a local and regional level. I chair the Michigan Medicine Clinical Intelligence Committee, which oversees implementation of predictive models across our health system, and I serve on the Michigan Economic Development Corporation’s Artificial Intelligence Advisory Board, where I contribute to the state of Michigan’s vision on artificial intelligence. I also teach a health data science and machine learning course to over 60 graduate students per year.

May 01
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Akbar Waljee

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I use machine-learning techniques to implement decision support systems and tools that facilitate more personalized care for disease management and healthcare utilization to ultimately deliver efficient, effective, and equitable therapy for chronic diseases. To test and advance these general principles, I have built operational programs that are guiding—and improving—patient care in costly in low resource settings, including emerging countries.

May 01
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Thomas Valley

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Dr. Valley’s research focuses on understanding and improving decision-making in the intensive care unit (ICU). His primary line of research seeks to identify the patients most likely to benefit from intensive care, allowing clinicians to safely triage patients between the ICU and the general ward. Ultimately, he hopes to identify ICU-based therapies that can be transferred to the general ward to improve hospital efficiency and reduce healthcare costs. Dr. Valley’s research interests also include enhancing diagnosis in critical illness, improving the ICU experience for family members of ICU patients, and reducing barriers to cost-effective pulmonary and critical care.

May 01
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Andrew J. Admon, MD, MPH, MSc

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I am a pulmonary and critical care physician who is passionate about improving critical care delivery by applying advanced methods for causal inference to observational data. My prior work has leveraged real-world data clinical and administrative data to study the epidemiology of critical illness, the organization of critical care, and health care financing.

My current work leverages real-world clinical data to understand whether and how care team fragmentation (transitions of physicians and other providers while a patient is still hospitalized) influences clinical outcomes like survival and recovery. Answering these questions correctly requires methods that are attentive to the complex causal structure underlying the relationship, depicted here. It features time-varying exposures (A), confounders (L), and mediators (M), all of which can influence clinical outcomes (Y). Arrows in the figure identify directional (i.e., causal) relationships between variables.

Apr 30
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Terrence Wong

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Terrence Wong is a Assistant Professor of Internal Medicine and Cancer Biology. The long-term goal of his research is to understand how altered hematopoiesis resulting from somatic mutations and/or epigenetic dysregulation impacts both malignant and non-malignant disease. During his PhD training at The University of Chicago, he worked with Dr. Tao Pan to investigate how the transcriptional process impacts in vivo RNA folding. After graduate school, he completed his residency in internal medicine and fellowship in hematology/oncology at Washington University in St. Louis. He performed my post-doctoral research with Dr. Daniel Link, studying how aging-associated somatic mutations impact the behavior of hematopoietic stem cells (HSCs) under cellular stress. One of their seminal findings was that HSCs harboring aging-associated TP53 mutations gain a competitive fitness advantage under the selective pressure of cytotoxic therapy, allowing them to clonally expand and potentially progress to therapy-related AML/MDS. Since starting his own independent research program at the University of Michigan, he has continued to investigate how somatic mutations impact hematopoiesis and how mutant hematopoietic populations impact human health. Clinically, he primarily treats patients with hematologic malignancies on the inpatient leukemia and bone marrow transplant wards.

Mar 03
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Jessica Golbus

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I am interested in using digital health technology for the treatment of cardiovascular disease with a particular emphasis on its application to patients with heart failure. More specific, my interests include (1) using non-invasive sensors and digital health technology to improve the delivery of cardiovascular care and (2) optimizing treatment for patients with advanced systolic heart failure through novel statistical tools and risk-modeling

Mar 08
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Steven J. Katz

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Dr. Katz’s research addresses cancer treatment communication, decision-making, and quality of care. His work aims to examine the dynamics of how precision medicine presents itself in the exam room via provider and patient communication and shared decision-making. Dr. Katz leads the Cancer Surveillance and Outcomes Research Team (CanSORT), an interdisciplinary research program centered at the University of Michigan and focused on population and intervention studies of the quality of care and outcomes of cancer detection and treatment in diverse populations.  Dr. Katz and CanSORT have been collaborating with Surveillance, Epidemiology, and End Results (SEER) cancer registries since 2002 to study breast cancer treatment decision making at the population level. We obtain patient clinical and demographic information from SEER and combine this with surveys of patients and physicians to create comprehensive data sets that enable us to study testing and treatment trends and the challenges of individualizing treatments for breast cancer patients. In 2015 we added a new dimension to our research by partnering with evaluative testing firms to obtain tumor genomic and germline genetic test results for over 30,000 breast and ovarian cancer patients in the states of California and Georgia. We are also pursuing insurance claims data to assist with our analysis of physician network effects.

Steven Katz, MD discusses BRCA and multigene sequence testing at the labs of Ambry Genetics.

Steven Katz, MD discusses BRCA and multigene sequence testing at the labs of Ambry Genetics.

Mar 08
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Brahmajee Nallamothu

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I study quality of care and patient outcomes in healthcare delivery systems, largely focusing on cardiovascular diseases. I use large national and regional data sets to answer fundamental questions about current healthcare delivery systems and how new approaches to designing these systems could save lives and reduce disease burden in large patient populations. My research includes the use of innovative data mining and machine learning tools.

As Director of the Michigan Integrated Center for Health Analytics and Medical Prediction (MiCHAMP), I collaborate with multidisciplinary investigators on predictive modeling and precision medicine initiatives. http://michamp.med.umich.edu/; http://midas.umich.edu/research/health/mchamp/

I have received funding from AHRQ, NIH, VA HSR&D and the BCBS Foundation of Michigan and participated on NIH and VA study sections targeting health services research.

I am Editor-in-Chief of Circulation: Cardiovascular Quality & Outcomes, a leading cardiovascular outcomes research journal published by the American Heart Association.

Mar 08
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Brian Athey

Brian D. Athey

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The Athey Lab in the Department of Computational Medicine and Bioinformatics (DCM&B) University of Michigan Medical School, is led by Dr. Brian Athey (see Atheylab.ccmb.med.umich.edu).

The lab is working on two complementary domains of research and development.

1. The Athey Lab’s recent research interests are in the creation and use of bioinformatics pipelines and machine learning methods to radically improve the efficacy of psychiatric pharmacogenomics—allowing patients to take the most effective drug for their illness and suffer the fewest side effects. This area of research centers on the exploration of the ‘pharmacoepigenome’ in psychiatry, neurology, anesthesia and addiction medicine. This research employs high-throughput 4D microscopic imaging of enhancers, promoters and chromatin features, using fluorescence in situ hybridization (FISH). These methods are coupled with Hi-C chromatin conformation capture, chromatin state annotation, localization in postmortem human brain tissue and induced neuronal pluripotent stem cells, and machine learning for identification of regulatory variants, to provide insight into the genetic and epigenetic mechanisms of inter-individual and inter-cohort differences in psychotropic drug response

2. The Athey Lab is also developing new high-throughput methods to analyze images of genes in the context of the cellular nucleus to better understand the machinery of bioinformatics in context. One main area of research is the application of high resolution fluorescence optical microscopy coupled with high-throughput analysis, 3D imaging and machine learning to explore the chromatin structure and nuclear architecture of cells. This research emphasizes the convergence between 3D structural predictions and 3D structural measurements with microscopy, to provide insight into the transcriptional architecture of the interphase nucleus.

This area of research centers on the exploration of the ‘pharmacoepigenome’ in psychiatry, neurology, anesthesia and addiction medicine. This research employs high-throughput 4D microscopic imaging of enhancers, promoters and chromatin features, using fluorescence in situ hybridization (FISH). These methods are coupled with Hi-C chromatin conformation capture, chromatin state annotation, localization in postmortem human brain tissue and induced neuronal pluripotent stem cells, and machine learning for identification of regulatory variants, to provide insight into the genetic and epigenetic mechanisms of inter-individual and inter-cohort differences in psychotropic drug response.

Collaborations: The lab works very closely with Assurex Health, Inc. (Mason, Ohio) on project 1. This work is governed by a Regents-approved Master Agreement between U-M and Assurex Health, Inc. Similarly, the lab collaborates closely with the tranSMART Foundation (tF), and this is also governed by a Master Agreement between U-M and tF.

The lab collaborates with the Brady Urological Institute at Johns Hopkins Medical School, lead by Dr. Ken Pienta, to build on their extensive 2D characterization of prostate tumors, by the introduction of simple chromatin dyes, advanced biomarkers, and 3D imaging systems.

The lab works closely with Dr. John Wiley of University of Michigan Health System, studying the effect of glucocorticoids on the neuroblastoma based cell line Sy5y before and after treatment with retinoic acid and BDNF, particularly in their terminally differentiated condition.

The lab also collaborates with Dr. Christoph Cremer from the Institute of Molecular Biology in Mainz, Germany, investigating super-resolution microscopy techniques.

Lithium response network in human brain in bipolar disorder: A regulatory network in human brain mediating lithium response in bipolar patients was revealed by analysis of functional single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWAS) and published gene association studies, followed by epigenome mapping. Noncoding SNPs characterized as altering enhancer and promoter function were imputed using fine epigenetic mapping, followed by bioinformatics analysis. Following gene set enrichment and pathway analysis, these genes were found to be significantly associated (p < 10-27; Fisher’s exact test) with this ionotropic AMPA2 glutamate receptor network in human brain67. Higgins GA, Allyn-Feuer A,Barbour E and Athey BD. “A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.” Accepted, Journal of Pharmacogenomics. August 2015.

Lithium response network in human brain in bipolar disorder: A regulatory network in human brain mediating lithium response in bipolar patients was revealed by analysis of functional single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWAS) and published gene association studies, followed by epigenome mapping. Noncoding SNPs characterized as altering enhancer and promoter function were imputed using fine epigenetic mapping, followed by bioinformatics analysis. Following gene set enrichment and pathway analysis, these genes were found to be significantly associated (p < 10-27; Fisher’s exact test) with this ionotropic AMPA2 glutamate receptor network in human brain67. Higgins GA, Allyn-Feuer A,Barbour E and Athey BD. “A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis.” Accepted, Journal of Pharmacogenomics. August 2015.

Mar 08
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Yuanfang Guan

Yuanfang Guan

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Functional genomic data, such as RNA-seq, microarray, protein-protein interactions, are growing exponentially these days. The research in Guan Lab focuses on developing novel and high-accuracy algorithms that integrate these data for predicting gene functions and networks. We have the following ongoing projects in the lab:

1. Modeling dynamic networks: Biological networks may rewire during cell lineage differentiation, tissue development or a disease course. We are actively developing novel algorithms that capture such dynamics. The algorithm contributed by our group (The GuanLab Team) was one of the six best-performance methods (out of over 100 submissions) in the HPN-DREAM 2013 Competition. We achieved the best performance (along another team) to subchallenge 2A, as well as the best aggregate prediction to subchallenges 2A and 2B: network timecourse prediction.

2. Isoform-level analysis: We are exploring algorithms that allow us to go beyond the traditional gene-level analysis to the isoform level.