Daniel Parente, MD, PhD
Family Medicine and Community Health
PhD: University of Kansas Medical Center
MD: University of Kansas Medical Center
Residency, Family Medicine: University of Kansas Medical Center
Research Focus: Precision Medicine, Genomic Medicine, Preventive Care
Board Certification: American Board of Family Medicine
Clinical Responsibilities: Care of hospitalized patients
Non-clinical responsibilities: In-patient clinical informatics committee, Committee for Continuous Improvement Driven by Data (Quality Improvement)
Precision medicine and primary care
We are very interested in how preventive care is implemented and how advanced technologies like machine learning and pharmacogenomics can be used to improve patient outcomes.
- 2020 - BRCA-related cancer genetic counseling is indicated in many women seeking primary care. DJ Parente. J Am Board Fam Med. Nov-Dec 2020;33(6):885-893 [PubMed] [PDF (Open Access)] [Article (Open Access)]
Genomic medicine and rare disease
Multidisciplinary teams are needed to understand the clinical impact of novel or rare monogenic diseases. We have used exome sequencing to describe monogenic pathology in neurodevelopment.
- 2019 - Sorting nexin 27 (SNX27) variants associated with seizures, developmental delay, behavioral disturbance, and subcortical brain abnormalities. DJ Parente, SM Morris, RC McKinstry, T Brandt, E Gabau, A Ruiz, and M Shinawi. Clin Genet. 2019 Nov 13 [PubMed] [Article (Wiley)]
- 2016 - Neuroligin 2 nonsense variant associated with anxiety, autism, intellectual disability, hyperphagia, and obesity. DJ Parente, C Garriga, B Baskin, G Douglas, MT Cho, GC Araujo and M Shinawi. Am J Med Genet A 173(1):213-216 [PubMed] [Article (Wiley)]
Evolutionary architecture of proteins
Understanding the fundamental rules that constrain protein evolution is crucial for interpreting variants observed in patient genomes. Our interdisciplinary teams have used several model systems to interrogate these fundamental rules.
- 2020 - Identification of biochemically neutral positions in liver pyruvate kinase. TA Martin, T Wu, Q Tang, LL Dougherty, DJ Parente, L Swint-Kruse, and AW Fenton. Proteins. 2020 Oct;88(10):1340-1350 [PubMed] [Article (Wiley)] [Preprint PDF] [Preprint Article]
- 2016 - Data on publications, structural analyses, and queries used to build and utilize the AlloRep database. FL Sousa, DJ Parente, JA Hessman, A Chazelle A, SA Teichmann and L Swint-Kruse. Data Brief, 8:948-957 [PubMed] [Article (Open Access)] [PDF (PubMed Central)]
- 2015 - Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores. DJ Parente and L Swint-Kruse. Proteins, 83: 2293–2306 [PubMed] [PDF] [Article (PubMed Central)] [Article (Wiley)]
- 2015 - AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators. FL Sousa, DJ Parente, DL Shis, JA Hessman, A Chazelle, MR Bennett, SA Teichmann and L Swint-Kruse. J Mol Biol, 428(4):671-678 [PubMed] [Article (Open Access)] [PDF (PubMed Central)]
- 2014 - Dissertation: Mining evolutionary data to reveal the layered architecture of protein function. DJ Parente. [University of Kansas ScholarWorks] [PDF (166.7 Mb)]
- 2013 - Multiple co-evolutionary networks are supported by the common tertiary scaffold of the LacI/GalR proteins. DJ Parente and L Swint-Kruse. PLoS ONE, 8, 12:e84398. [PubMed] [Article (Open Access)] [PDF (Open Access)] [PDF (PubMed Central)]
- 2013 - Rheostats and toggle switches for modulating protein function. S Meinhardt, MW Manley Jr, DJ Parente and L Swint-Kruse. PLoS ONE, 8, 12:e83502. [PubMed] [Article (Open Access)] [PDF (Open Access)] [PDF (PubMed Central)]
- 2011 - Functionally important positions can comprise the majority of a protein's architecture. S Tungtur, DJ Parente and L Swint-Kruse. Proteins, 79, 1589-1608. [PubMed] [Article (PubMed Central)] [PDF (PubMed Central] [Article (Wiley)]
- PolyBoost- PolyBoost is a machine learning-based, post-analysis tool for the batch processing output of PolyPhen-2 that replaces the naive Bayes classifier with an extreme gradient boosting XGBoost classifier. Source code on Github or available through the Python Package Index (PyPI) as polyboost. The research publication describing this software is currently in peer review.
- Co-evolution utilities - Protein co-evolutionary analysis utilities; relevant to our 2013 [PDF] and 2015 [PDF] papers on protein co-evolution. Source code on Github
- MARS-Prot (Maintainer of Alignments using Reference Sequences for Proteins) - Maintenance tool for protein multiple sequence alignments (MSAs) that allows for the incorporating of new sequences into existing (hand-optimized) alignments. Source code on Github
- AlloRep - A repository of sequence, structural and mutagenesis data for the LacI/GalR transcription repressor families. This is an important dataset for the development and validation of new bioinformatics analyses. Explore the database at allorep.org.
If you would like to collaborate on topics within precision medicine, genomic medicine, preventive care or understanding the evolutionary architecture of protein function, I would love to hear from you. Please contact me at firstname.lastname@example.org.