Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

My NCBI Filters
Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1993 2
1994 3
1995 2
1996 1
1997 1
1998 1
2000 1
2001 3
2002 6
2003 13
2004 21
2005 11
2006 15
2007 21
2008 19
2009 22
2010 19
2011 23
2012 27
2013 25
2014 40
2015 45
2016 26
2017 24
2018 28
2019 30
2020 35
2021 36
2022 3
Text availability
Article attribute
Article type
Publication date

Search Results

464 results
Results by year
Filters applied: . Clear all
Page 1
The Cosmos Collaborative: A Vendor-Facilitated Electronic Health Record Data Aggregation Platform.
Tarabichi Y, Frees A, Honeywell S, Huang C, Naidech AM, Moore JH, Kaelber DC. Tarabichi Y, et al. Among authors: moore jh. ACI open. 2021 Jan;5(1):e36-e46. doi: 10.1055/s-0041-1731004. ACI open. 2021. PMID: 35071993 Free PMC article.
Limitations are being vendor-specific, an "all or none" contribution model, and the lack of control over queries run on an institution's healthcare data. CONCLUSION: Cosmos provides a model for within-vendor data standardization and aggregation and a steppingstone for broa …
Limitations are being vendor-specific, an "all or none" contribution model, and the lack of control over queries run on an institution's
Estimating prevalence of human traits among populations from polygenic risk scores.
Graham BE, Plotkin B, Muglia L, Moore JH, Williams SM. Graham BE, et al. Among authors: moore jh. Hum Genomics. 2021 Dec 13;15(1):70. doi: 10.1186/s40246-021-00370-z. Hum Genomics. 2021. PMID: 34903281 Free PMC article.
The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause disparities, from variation in environments to divergent population genetic structure. We hypothesized that a population-level polygen …
The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause d …
Multi-task learning based structured sparse canonical correlation analysis for brain imaging genetics.
Kim M, Min EJ, Liu K, Yan J, Saykin AJ, Moore JH, Long Q, Shen L. Kim M, et al. Among authors: moore jh. Med Image Anal. 2022 Feb;76:102297. doi: 10.1016/j.media.2021.102297. Epub 2021 Nov 13. Med Image Anal. 2022. PMID: 34871929
In this study, we propose a novel multi-task learning based structured sparse canonical correlation analysis (MTS2CCA) to deliver interpretable results and improve integration in imaging genetics studies. We perform comparative studies with state-of-the-art competing metho …
In this study, we propose a novel multi-task learning based structured sparse canonical correlation analysis (MTS2CCA) to deliver interpreta …
The promise of automated machine learning for the genetic analysis of complex traits.
Manduchi E, Romano JD, Moore JH. Manduchi E, et al. Among authors: moore jh. Hum Genet. 2021 Oct 28. doi: 10.1007/s00439-021-02393-x. Online ahead of print. Hum Genet. 2021. PMID: 34713318 Review.
The goal of automated machine learning (AutoML) is to let a computer algorithm identify the right algorithms and hyperparameters thus taking the guesswork out of the optimization process. ...It is our hope that this review will motivate studies to develop and evalua …
The goal of automated machine learning (AutoML) is to let a computer algorithm identify the right algorithms and hyperparamete …
Plasma biomarkers associated with adverse outcomes in patients with calcific aortic stenosis.
Vidula MK, Orlenko A, Zhao L, Salvador L, Small AM, Horton E, Cohen JB, Adusumalli S, Denduluri S, Kobayashi T, Hyman M, Fiorilli P, Magro C, Singh B, Pourmussa B, Greczylo C, Basso M, Ebert C, Yarde M, Li Z, Cvijic ME, Wang Z, Walsh A, Maranville J, Kick E, Luettgen J, Adam L, Schafer P, Ramirez-Valle F, Seiffert D, Moore JH, Gordon D, Chirinos JA. Vidula MK, et al. Among authors: moore jh. Eur J Heart Fail. 2021 Dec;23(12):2021-2032. doi: 10.1002/ejhf.2361. Epub 2021 Oct 21. Eur J Heart Fail. 2021. PMID: 34632675
International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study.
Weber GM, Zhang HG, L'Yi S, Bonzel CL, Hong C, Avillach P, Gutiérrez-Sacristán A, Palmer NP, Tan ALM, Wang X, Yuan W, Gehlenborg N, Alloni A, Amendola DF, Bellasi A, Bellazzi R, Beraghi M, Bucalo M, Chiovato L, Cho K, Dagliati A, Estiri H, Follett RW, García Barrio N, Hanauer DA, Henderson DW, Ho YL, Holmes JH, Hutch MR, Kavuluru R, Kirchoff K, Klann JG, Krishnamurthy AK, Le TT, Liu M, Loh NHW, Lozano-Zahonero S, Luo Y, Maidlow S, Makoudjou A, Malovini A, Martins MR, Moal B, Morris M, Mowery DL, Murphy SN, Neuraz A, Ngiam KY, Okoshi MP, Omenn GS, Patel LP, Pedrera Jiménez M, Prudente RA, Samayamuthu MJ, Sanz Vidorreta FJ, Schriver ER, Schubert P, Serrano Balazote P, Tan BW, Tanni SE, Tibollo V, Visweswaran S, Wagholikar KB, Xia Z, Zöller D; Consortium For Clinical Characterization Of COVID-19 By EHR (4CE), Kohane IS, Cai T, South AM, Brat GA. Weber GM, et al. J Med Internet Res. 2021 Oct 11;23(10):e31400. doi: 10.2196/31400. J Med Internet Res. 2021. PMID: 34533459 Free PMC article.
Genetic analysis of coronary artery disease using tree-based automated machine learning informed by biology-based feature selection.
Manduchi E, Le T, Fu W, Moore JH. Manduchi E, et al. Among authors: moore jh. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul 26;PP. doi: 10.1109/TCBB.2021.3099068. Online ahead of print. IEEE/ACM Trans Comput Biol Bioinform. 2021. PMID: 34310318
The goals of this study were to assess applicability of TPOT to genomics and to identify combinations of single nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD), with a focus on genes with high likelihood of being good CAD drug targets. We leve …
The goals of this study were to assess applicability of TPOT to genomics and to identify combinations of single nucleotide polymorphisms (SN …
Why Is the Electronic Health Record So Challenging for Research and Clinical Care?
Holmes JH, Beinlich J, Boland MR, Bowles KH, Chen Y, Cook TS, Demiris G, Draugelis M, Fluharty L, Gabriel PE, Grundmeier R, Hanson CW, Herman DS, Himes BE, Hubbard RA, Kahn CE Jr, Kim D, Koppel R, Long Q, Mirkovic N, Morris JS, Mowery DL, Ritchie MD, Urbanowicz R, Moore JH. Holmes JH, et al. Among authors: moore jh. Methods Inf Med. 2021 May;60(1-02):32-48. doi: 10.1055/s-0041-1731784. Epub 2021 Jul 19. Methods Inf Med. 2021. PMID: 34282602
All members of the panel are affiliated with Penn Medicine at the University of Pennsylvania and have experience with a variety of different EHR platforms and systems and how they have evolved over time. ...
All members of the panel are affiliated with Penn Medicine at the University of Pennsylvania and have experience with a variety of di …
International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries.
Bourgeois FT, Gutiérrez-Sacristán A, Keller MS, Liu M, Hong C, Bonzel CL, Tan ALM, Aronow BJ, Boeker M, Booth J, Cruz Rojo J, Devkota B, García Barrio N, Gehlenborg N, Geva A, Hanauer DA, Hutch MR, Issitt RW, Klann JG, Luo Y, Mandl KD, Mao C, Moal B, Moshal KL, Murphy SN, Neuraz A, Ngiam KY, Omenn GS, Patel LP, Jiménez MP, Sebire NJ, Balazote PS, Serret-Larmande A, South AM, Spiridou A, Taylor DM, Tippmann P, Visweswaran S, Weber GM, Kohane IS, Cai T, Avillach P; Consortium for Clinical Characterization of COVID-19 by EHR (4CE). Bourgeois FT, et al. JAMA Netw Open. 2021 Jun 1;4(6):e2112596. doi: 10.1001/jamanetworkopen.2021.12596. JAMA Netw Open. 2021. PMID: 34115127 Free PMC article.
RESULTS: There were 347 males (52%; 95% CI, 48.5-55.3) and 324 females (48%; 95% CI, 44.4-51.3) in this study's cohort. There was a bimodal age distribution, with the greatest proportion of patients in the 0- to 2-year (199 patients [30%]) and 12- to 17-year (170 patients …
RESULTS: There were 347 males (52%; 95% CI, 48.5-55.3) and 324 females (48%; 95% CI, 44.4-51.3) in this study's cohort. There was a b …
Novel EDGE encoding method enhances ability to identify genetic interactions.
Hall MA, Wallace J, Lucas AM, Bradford Y, Verma SS, Müller-Myhsok B, Passero K, Zhou J, McGuigan J, Jiang B, Pendergrass SA, Zhang Y, Peissig P, Brilliant M, Sleiman P, Hakonarson H, Harley JB, Kiryluk K, Van Steen K, Moore JH, Ritchie MD. Hall MA, et al. Among authors: moore jh. PLoS Genet. 2021 Jun 4;17(6):e1009534. doi: 10.1371/journal.pgen.1009534. eCollection 2021 Jun. PLoS Genet. 2021. PMID: 34086673 Free PMC article.
Assumptions are made about the genetic model of single nucleotide polymorphisms (SNPs) when choosing a traditional genetic encoding: additive, dominant, and recessive. ...Here, we present a novel and flexible encoding for genetic interactions, the elastic dat …
Assumptions are made about the genetic model of single nucleotide polymorphisms (SNPs) when choosing a traditional genetic enc …
The Translational Machine: A novel machine-learning approach to illuminate complex genetic architectures.
Askland KD, Strong D, Wright MN, Moore JH. Askland KD, et al. Among authors: moore jh. Genet Epidemiol. 2021 Jul;45(5):485-536. doi: 10.1002/gepi.22383. Epub 2021 May 3. Genet Epidemiol. 2021. PMID: 33942369
Second, model-free, nonparametric ML-based feature filtering procedures empirically reduce dimensionality and noise of both original genotype calls and engineered features. Third, a powerful ML algorithm for feature selection is used to differentiate risk variant contribut …
Second, model-free, nonparametric ML-based feature filtering procedures empirically reduce dimensionality and noise of both original genotyp …
Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry.
Graff M, Justice AE, Young KL, Marouli E, Zhang X, Fine RS, Lim E, Buchanan V, Rand K, Feitosa MF, Wojczynski MK, Yanek LR, Shao Y, Rohde R, Adeyemo AA, Aldrich MC, Allison MA, Ambrosone CB, Ambs S, Amos C, Arnett DK, Atwood L, Bandera EV, Bartz T, Becker DM, Berndt SI, Bernstein L, Bielak LF, Blot WJ, Bottinger EP, Bowden DW, Bradfield JP, Brody JA, Broeckel U, Burke G, Cade BE, Cai Q, Caporaso N, Carlson C, Carpten J, Casey G, Chanock SJ, Chen G, Chen M, Chen YI, Chen WM, Chesi A, Chiang CWK, Chu L, Coetzee GA, Conti DV, Cooper RS, Cushman M, Demerath E, Deming SL, Dimitrov L, Ding J, Diver WR, Duan Q, Evans MK, Falusi AG, Faul JD, Fornage M, Fox C, Freedman BI, Garcia M, Gillanders EM, Goodman P, Gottesman O, Grant SFA, Guo X, Hakonarson H, Haritunians T, Harris TB, Harris CC, Henderson BE, Hennis A, Hernandez DG, Hirschhorn JN, McNeill LH, Howard TD, Howard B, Hsing AW, Hsu YH, Hu JJ, Huff CD, Huo D, Ingles SA, Irvin MR, John EM, Johnson KC, Jordan JM, Kabagambe EK, Kang SJ, Kardia SL, Keating BJ, Kittles RA, Klein EA, Kolb S, Kolonel LN, Kooperberg C, Kuller L, Kutlar A, Lange L, Langefeld CD, Le Marchand L, Leonard H, Lettre G, Levin AM, Li Y, Li J, Liu Y, Liu Y, Liu S, Lohman K, Lotay V, Lu Y, Maixner W, Manson JE, McKnight B, Meng Y, Monda KL, Monroe K, Moore JH, Mosley TH, Mudgal P, Murphy AB, Nadukuru R, Nalls MA, Nathanson KL, Nayak U, N'Diaye A, Nemesure B, Neslund-Dudas C, Neuhouser ML, Nyante S, Ochs-Balcom H, Ogundiran TO, Ogunniyi A, Ojengbede O, Okut H, Olopade OI, Olshan A, Padhukasahasram B, Palmer J, Palmer CD, Palmer ND, Papanicolaou G, Patel SR, Pettaway CA, Peyser PA, Press MF, Rao DC, Rasmussen-Torvik LJ, Redline S, Reiner AP, Rhie SK, Rodriguez-Gil JL, Rotimi CN, Rotter JI, Ruiz-Narvaez EA, Rybicki BA, Salako B, Sale MM, Sanderson M, Schadt E, Schreiner PJ, Schurmann C, Schwartz AG, Shriner DA, Signorello LB, Singleton AB, Siscovick DS, Smith JA, Smith S, Speliotes E, Spitz M, Stanford JL, Stevens VL, Stram A, Strom SS, Sucheston L, Sun YV, Tajuddin SM, Taylor H, Taylor K, Tayo BO, Thun MJ, Tucker MA, Vaidya D, Van Den Berg DJ, Vedantam S, Vitolins M, Wang Z, Ware EB, Wassertheil-Smoller S, Weir DR, Wiencke JK, Williams SM, Williams LK, Wilson JG, Witte JS, Wrensch M, Wu X, Yao J, Zakai N, Zanetti K, Zemel BS, Zhao W, Zhao JH, Zheng W, Zhi D, Zhou J, Zhu X, Ziegler RG, Zmuda J, Zonderman AB, Psaty BM, Borecki IB, Cupples LA, Liu CT, Haiman CA, Loos R, Ng MCY, North KE. Graff M, et al. Among authors: moore jh. Am J Hum Genet. 2021 Apr 1;108(4):564-582. doi: 10.1016/j.ajhg.2021.02.011. Epub 2021 Mar 12. Am J Hum Genet. 2021. PMID: 33713608 Free PMC article.
We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with …
We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the …
Effects of Resistance Training on the Redox Status of Skeletal Muscle in Older Adults.
Mesquita PHC, Lamb DA, Godwin JS, Osburn SC, Ruple BA, Moore JH, Vann CG, Huggins KW, Fruge AD, Young KC, Kavazis AN, Roberts MD. Mesquita PHC, et al. Among authors: moore jh. Antioxidants (Basel). 2021 Feb 26;10(3):350. doi: 10.3390/antiox10030350. Antioxidants (Basel). 2021. PMID: 33652958 Free PMC article.
Protein levels of heat shock proteins (HSPs) were also quantified. RT increased mRNA levels of all assayed antioxidant genes, albeit protein levels either did not change or decreased. ...
Protein levels of heat shock proteins (HSPs) were also quantified. RT increased mRNA levels of all assayed antioxidant genes, albeit …
The phenomics and genetics of addictive and affective comorbidity in opioid use disorder.
Freda PJ, Moore JH, Kranzler HR. Freda PJ, et al. Among authors: moore jh. Drug Alcohol Depend. 2021 Apr 1;221:108602. doi: 10.1016/j.drugalcdep.2021.108602. Epub 2021 Feb 22. Drug Alcohol Depend. 2021. PMID: 33652377 Review.
Significant sources of OUD risk include co-occurring lifetime and current diagnoses of both psychiatric disorders, primarily mood disorders, and other substance use disorders, and unique and shared genetic factors. Although there appears to be pleiotropy between OUD and bo …
Significant sources of OUD risk include co-occurring lifetime and current diagnoses of both psychiatric disorders, primarily mood disorders, …
The Role of Genetic Ancestry as a Risk Factor for Primary Open-angle Glaucoma in African Americans.
Cole BS, Gudiseva HV, Pistilli M, Salowe R, McHugh CP, Zody MC, Chavali VRM, Ying GS, Moore JH, O'Brien JM. Cole BS, et al. Among authors: moore jh. Invest Ophthalmol Vis Sci. 2021 Feb 1;62(2):28. doi: 10.1167/iovs.62.2.28. Invest Ophthalmol Vis Sci. 2021. PMID: 33605984 Free PMC article.
METHODS: Subjects recruited to the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study were classified as glaucoma cases or controls by fellowship-trained glaucoma specialists. ...Among POAG cases, higher African ancestry was also associated with thinner c …
METHODS: Subjects recruited to the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study were classified as glaucoma c …
What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask.
Kohane IS, Aronow BJ, Avillach P, Beaulieu-Jones BK, Bellazzi R, Bradford RL, Brat GA, Cannataro M, Cimino JJ, García-Barrio N, Gehlenborg N, Ghassemi M, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Hong C, Klann JG, Loh NHW, Luo Y, Mandl KD, Daniar M, Moore JH, Murphy SN, Neuraz A, Ngiam KY, Omenn GS, Palmer N, Patel LP, Pedrera-Jiménez M, Sliz P, South AM, Tan ALM, Taylor DM, Taylor BW, Torti C, Vallejos AK, Wagholikar KB; Consortium For Clinical Characterization Of COVID-19 By EHR (4CE), Weber GM, Cai T. Kohane IS, et al. Among authors: moore jh. J Med Internet Res. 2021 Mar 2;23(3):e22219. doi: 10.2196/22219. J Med Internet Res. 2021. PMID: 33600347 Free PMC article.
Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data.
Klann JG, Estiri H, Weber GM, Moal B, Avillach P, Hong C, Tan ALM, Beaulieu-Jones BK, Castro V, Maulhardt T, Geva A, Malovini A, South AM, Visweswaran S, Morris M, Samayamuthu MJ, Omenn GS, Ngiam KY, Mandl KD, Boeker M, Olson KL, Mowery DL, Follett RW, Hanauer DA, Bellazzi R, Moore JH, Loh NW, Bell DS, Wagholikar KB, Chiovato L, Tibollo V, Rieg S, Li ALLJ, Jouhet V, Schriver E, Xia Z, Hutch M, Luo Y, Kohane IS; Consortium for Clinical Characterization of COVID-19 by EHR (4CE) (CONSORTIA AUTHOR), Brat GA, Murphy SN. Klann JG, et al. Among authors: moore jh. J Am Med Inform Assoc. 2021 Jul 14;28(7):1411-1420. doi: 10.1093/jamia/ocab018. J Am Med Inform Assoc. 2021. PMID: 33566082 Free PMC article.
International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study.
Weber GM, Hong C, Palmer NP, Avillach P, Murphy SN, Gutiérrez-Sacristán A, Xia Z, Serret-Larmande A, Neuraz A, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Bellasi A, Benoit V, Beraghi M, Boeker M, Booth J, Bosari S, Bourgeois FT, Brown NW, Bucalo M, Chiovato L, Chiudinelli L, Dagliati A, Devkota B, DuVall SL, Follett RW, Ganslandt T, García Barrio N, Gradinger T, Griffier R, Hanauer DA, Holmes JH, Horki P, Huling KM, Issitt RW, Jouhet V, Keller MS, Kraska D, Liu M, Luo Y, Lynch KE, Malovini A, Mandl KD, Mao C, Maram A, Matheny ME, Maulhardt T, Mazzitelli M, Milano M, Moore JH, Morris JS, Morris M, Mowery DL, Naughton TP, Ngiam KY, Norman JB, Patel LP, Pedrera Jimenez M, Ramoni RB, Schriver ER, Scudeller L, Sebire NJ, Serrano Balazote P, Spiridou A, Tan AL, Tan BW, Tibollo V, Torti C, Trecarichi EM, Vitacca M, Zambelli A, Zucco C; Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Kohane IS, Cai T, Brat GA. Weber GM, et al. Among authors: moore jh. medRxiv. 2021 Feb 5:2020.12.16.20247684. doi: 10.1101/2020.12.16.20247684. Preprint. medRxiv. 2021. PMID: 33564777 Free PMC article.
Subgroup analysis was performed to validate a subset of laboratory values as predictive of severity against a published algorithm. A subset of laboratory values (CRP, albumin, LDH, neutrophil count, D-dimer, and procalcitonin) was compared between North American and Europe …
Subgroup analysis was performed to validate a subset of laboratory values as predictive of severity against a published algorithm. A …
A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions.
Orlenko A, Moore JH. Orlenko A, et al. Among authors: moore jh. BioData Min. 2021 Jan 29;14(1):9. doi: 10.1186/s13040-021-00243-0. BioData Min. 2021. PMID: 33514397 Free PMC article.
BACKGROUND: Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex diseases such as Alzheimer's, diabetes, and cardiovascular disease. Detecting interactions requires careful selection of analytical metho …
BACKGROUND: Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex dise …
Empowering the data science scientist.
Moore JH. Moore JH. BioData Min. 2021 Jan 23;14(1):8. doi: 10.1186/s13040-021-00246-x. BioData Min. 2021. PMID: 33485343 Free PMC article. No abstract available.
Metabolomics Insights in Early Childhood Caries.
Heimisdottir LH, Lin BM, Cho H, Orlenko A, Ribeiro AA, Simon-Soro A, Roach J, Shungin D, Ginnis J, Simancas-Pallares MA, Spangler HD, Zandoná AGF, Wright JT, Ramamoorthy P, Moore JH, Koo H, Wu D, Divaris K. Heimisdottir LH, et al. Among authors: moore jh. J Dent Res. 2021 Jun;100(6):615-622. doi: 10.1177/0022034520982963. Epub 2021 Jan 9. J Dent Res. 2021. PMID: 33423574
We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study's analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North …
We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence a …
Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.
Li R, Duan R, Zhang X, Lumley T, Pendergrass S, Bauer C, Hakonarson H, Carrell DS, Smoller JW, Wei WQ, Carroll R, Velez Edwards DR, Wiesner G, Sleiman P, Denny JC, Mosley JD, Ritchie MD, Chen Y, Moore JH. Li R, et al. Among authors: moore jh. Nat Commun. 2021 Jan 8;12(1):168. doi: 10.1038/s41467-020-20211-2. Nat Commun. 2021. PMID: 33420026 Free PMC article.
Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for pleiotropy analyses. ...As a result, we introduce Sum-Share, a method designed to efficiently integrate EHR and genetic data from mul …
Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for …
Learning feature spaces for regression with genetic programming.
La Cava W, Moore JH. La Cava W, et al. Among authors: moore jh. Genet Program Evolvable Mach. 2020 Sep;21(3):433-467. doi: 10.1007/s10710-020-09383-4. Epub 2020 Mar 11. Genet Program Evolvable Mach. 2020. PMID: 33343224 Free PMC article.
Genetic programming has found recent success as a tool for learning sets of features for regression and classification. Multidimensional genetic programming is a useful variant of genetic programming for this task because it represents candidate solutions as
Genetic programming has found recent success as a tool for learning sets of features for regression and classification. Multidimensio
Label-Free Quantification of Cell Cycle Synchronicity of Human Neural Progenitor Cells Based on Electrophysiology Phenotypes.
Honrado C, Michel N, Moore JH, Salahi A, Porterfield V, McConnell MJ, Swami NS. Honrado C, et al. Among authors: moore jh. ACS Sens. 2021 Jan 22;6(1):156-165. doi: 10.1021/acssensors.0c02022. Epub 2020 Dec 16. ACS Sens. 2021. PMID: 33325234
The ability to coax human-induced pluripotent stem cells (hiPSCs) into human neural progenitor cells (hNPCs) can lead to novel drug discovery and transplant therapy platforms for neurological diseases. Since hNPCs can form organoids that mimic brain development, there is e …
The ability to coax human-induced pluripotent stem cells (hiPSCs) into human neural progenitor cells (hNPCs) can lead to novel drug discover …
Transfer learning with chest X-rays for ER patient classification.
Stubblefield J, Hervert M, Causey JL, Qualls JA, Dong W, Cai L, Fowler J, Bellis E, Walker K, Moore JH, Nehring S, Huang X. Stubblefield J, et al. Among authors: moore jh. Sci Rep. 2020 Dec 1;10(1):20900. doi: 10.1038/s41598-020-78060-4. Sci Rep. 2020. PMID: 33262425 Free PMC article.
An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder.
Veatch OJ, Butler MG, Elsea SH, Malow BA, Sutcliffe JS, Moore JH. Veatch OJ, et al. Among authors: moore jh. Int J Mol Sci. 2020 Nov 27;21(23):9029. doi: 10.3390/ijms21239029. Int J Mol Sci. 2020. PMID: 33261099 Free PMC article.
Human genetic studies have implicated more than a hundred genes in Autism Spectrum Disorder (ASD). ...Compared with 1000 gene sets, each with a random selection of human protein coding genes, more genes in the ASD set were annotated for each cat …
Human genetic studies have implicated more than a hundred genes in Autism Spectrum Disorder (ASD). ...Compared with 1000 ge
Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers.
Madhavan S, Bastarache L, Brown JS, Butte AJ, Dorr DA, Embi PJ, Friedman CP, Johnson KB, Moore JH, Kohane IS, Payne PRO, Tenenbaum JD, Weiner MG, Wilcox AB, Ohno-Machado L. Madhavan S, et al. Among authors: moore jh. J Am Med Inform Assoc. 2021 Feb 15;28(2):393-401. doi: 10.1093/jamia/ocaa287. J Am Med Inform Assoc. 2021. PMID: 33260207 Free PMC article.
Ten simple rules for writing a paper about scientific software.
Romano JD, Moore JH. Romano JD, et al. Among authors: moore jh. PLoS Comput Biol. 2020 Nov 12;16(11):e1008390. doi: 10.1371/journal.pcbi.1008390. eCollection 2020 Nov. PLoS Comput Biol. 2020. PMID: 33180774 Free PMC article.
Diagnostic biomarkers to differentiate sepsis from cytokine release syndrome in critically ill children.
Diorio C, Shaw PA, Pequignot E, Orlenko A, Chen F, Aplenc R, Barrett DM, Bassiri H, Behrens E, DiNofia AM, Gonzalez V, Koterba N, Levine BL, Maude SL, Meyer NJ, Moore JH, Paessler M, Porter DL, Bush JL, Siegel DL, Davis MM, Zhang D, June CH, Grupp SA, Melenhorst JJ, Lacey SF, Weiss SL, Teachey DT. Diorio C, et al. Among authors: moore jh. Blood Adv. 2020 Oct 27;4(20):5174-5183. doi: 10.1182/bloodadvances.2020002592. Blood Adv. 2020. PMID: 33095872 Free PMC article.
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses.
Manduchi E, Fu W, Romano JD, Ruberto S, Moore JH. Manduchi E, et al. Among authors: moore jh. BMC Bioinformatics. 2020 Oct 1;21(1):430. doi: 10.1186/s12859-020-03755-4. BMC Bioinformatics. 2020. PMID: 32998684 Free PMC article.
We describe applications of this approach to toxicogenomics and schizophrenia gene expression data sets. The TPOT extensions discussed in this work are available at https://github.com/EpistasisLab/tpot/tree/v0.11.1-resAdj . CONCLUSIONS: In this work, we address an importan …
We describe applications of this approach to toxicogenomics and schizophrenia gene expression data sets. The TPOT extensions discusse …
Spatial Pyramid Pooling with 3D Convolution Improves Lung Cancer Detection.
Causey J, Li K, Chen X, Dong W, Walker K, Qualls J, Stubblefield J, Moore JH, Guan Y, Huang X. Causey J, et al. Among authors: moore jh. IEEE/ACM Trans Comput Biol Bioinform. 2020 Sep 29;PP. doi: 10.1109/TCBB.2020.3027744. Online ahead of print. IEEE/ACM Trans Comput Biol Bioinform. 2020. PMID: 32991288
The development of deep learning techniques has the potential to help improve lung cancer screening technology. Here we present the algorithm, DeepScreener, which can predict a patient's cancer status from a volumetric lung CT scan. ...Furthermore, by combining Spat …
The development of deep learning techniques has the potential to help improve lung cancer screening technology. Here we present the algor
International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium.
Brat GA, Weber GM, Gehlenborg N, Avillach P, Palmer NP, Chiovato L, Cimino J, Waitman LR, Omenn GS, Malovini A, Moore JH, Beaulieu-Jones BK, Tibollo V, Murphy SN, Yi SL, Keller MS, Bellazzi R, Hanauer DA, Serret-Larmande A, Gutierrez-Sacristan A, Holmes JJ, Bell DS, Mandl KD, Follett RW, Klann JG, Murad DA, Scudeller L, Bucalo M, Kirchoff K, Craig J, Obeid J, Jouhet V, Griffier R, Cossin S, Moal B, Patel LP, Bellasi A, Prokosch HU, Kraska D, Sliz P, Tan ALM, Ngiam KY, Zambelli A, Mowery DL, Schiver E, Devkota B, Bradford RL, Daniar M, Daniel C, Benoit V, Bey R, Paris N, Serre P, Orlova N, Dubiel J, Hilka M, Jannot AS, Breant S, Leblanc J, Griffon N, Burgun A, Bernaux M, Sandrin A, Salamanca E, Cormont S, Ganslandt T, Gradinger T, Champ J, Boeker M, Martel P, Esteve L, Gramfort A, Grisel O, Leprovost D, Moreau T, Varoquaux G, Vie JJ, Wassermann D, Mensch A, Caucheteux C, Haverkamp C, Lemaitre G, Bosari S, Krantz ID, South A, Cai T, Kohane IS. Brat GA, et al. Among authors: moore jh. NPJ Digit Med. 2020 Aug 19;3:109. doi: 10.1038/s41746-020-00308-0. eCollection 2020. NPJ Digit Med. 2020. PMID: 32864472 Free PMC article.
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.
Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR; N3C Consortium. Haendel MA, et al. J Am Med Inform Assoc. 2021 Mar 1;28(3):427-443. doi: 10.1093/jamia/ocaa196. J Am Med Inform Assoc. 2021. PMID: 32805036 Free PMC article.
Conservation machine learning.
Sipper M, Moore JH. Sipper M, et al. Among authors: moore jh. BioData Min. 2020 Aug 5;13:9. doi: 10.1186/s13040-020-00220-z. eCollection 2020. BioData Min. 2020. PMID: 32774460 Free PMC article. No abstract available.
Evaluating recommender systems for AI-driven biomedical informatics.
La Cava W, Williams H, Fu W, Vitale S, Srivatsan D, Moore JH. La Cava W, et al. Among authors: moore jh. Bioinformatics. 2021 Apr 19;37(2):250-256. doi: 10.1093/bioinformatics/btaa698. Bioinformatics. 2021. PMID: 32766825 Free PMC article.
Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based AI platform to recommend mo …
Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply …
treeheatr: an R package for interpretable decision tree visualizations.
Le TT, Moore JH. Le TT, et al. Among authors: moore jh. Bioinformatics. 2021 Apr 19;37(2):282-284. doi: 10.1093/bioinformatics/btaa662. Bioinformatics. 2021. PMID: 32702108 Free PMC article.
SUMMARY: treeheatr is an R package for creating interpretable decision tree visualizations with the data represented as a heatmap at the tree's leaf nodes. The integrated presentation of the tree structure along with an overview of the data efficiently illustrates how the …
SUMMARY: treeheatr is an R package for creating interpretable decision tree visualizations with the data represented as a heatmap at the tre …
WellExplorer: an integrative resource linking hydraulic fracturing chemicals with hormonal pathways and geographic location.
Wetherbee O, Meeker JR, DeVoto C, Penning TM, Moore JH, Boland MR. Wetherbee O, et al. Among authors: moore jh. Database (Oxford). 2020 Jan 1;2020:baaa053. doi: 10.1093/database/baaa053. Database (Oxford). 2020. PMID: 32701164 Free PMC article.
We found that wells in Alabama use a disproportionately high number of ingredients targeting estrogen pathways, while Illinois, Ohio and Pennsylvania use a disproportionately high number of ingredients targeting testosterone pathways. ...
We found that wells in Alabama use a disproportionately high number of ingredients targeting estrogen pathways, while Illinois, Ohio and …
H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts.
Pei J, Harakalova M, Treibel TA, Lumbers RT, Boukens BJ, Efimov IR, van Dinter JT, González A, López B, El Azzouzi H, van den Dungen N, van Dijk CGM, Krebber MM, den Ruijter HM, Pasterkamp G, Duncker DJ, Nieuwenhuis EES, de Weger R, Huibers MM, Vink A, Moore JH, Moon JC, Verhaar MC, Kararigas G, Mokry M, Asselbergs FW, Cheng C. Pei J, et al. Among authors: moore jh. Clin Epigenetics. 2020 Jul 14;12(1):106. doi: 10.1186/s13148-020-00895-5. Clin Epigenetics. 2020. PMID: 32664951 Free PMC article.
The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabo …
The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adj …
464 results