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Items: 35

1.

Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation.

Mukherjee S, Perumal TM, Daily K, Sieberts SK, Omberg L, Preuss C, Carter GW, Mangravite LM, Logsdon BA.

Bioinformatics. 2019 Jul 15;35(14):i568-i576. doi: 10.1093/bioinformatics/btz365.

2.

Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age.

Wingo AP, Dammer EB, Breen MS, Logsdon BA, Duong DM, Troncosco JC, Thambisetty M, Beach TG, Serrano GE, Reiman EM, Caselli RJ, Lah JJ, Seyfried NT, Levey AI, Wingo TS.

Nat Commun. 2019 Apr 8;10(1):1619. doi: 10.1038/s41467-019-09613-z.

3.

Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model.

Wang H, Li Y, Ryder JW, Hole JT, Ebert PJ, Airey DC, Qian HR, Logsdon B, Fisher A, Ahmed Z, Murray TK, Cavallini A, Bose S, Eastwood BJ, Collier DA, Dage JL, Miller BB, Merchant KM, O'Neill MJ, Demattos RB.

Mol Neurodegener. 2018 Dec 17;13(1):65. doi: 10.1186/s13024-018-0296-y.

4.

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease.

Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, Ming C, Neff R, Ma W, Fullard JF, Hauberg ME, Bendl J, Peters MA, Logsdon B, Wang P, Mahajan M, Mangravite LM, Dammer EB, Duong DM, Lah JJ, Seyfried NT, Levey AI, Buxbaum JD, Ehrlich M, Gandy S, Katsel P, Haroutunian V, Schadt E, Zhang B.

Sci Data. 2018 Sep 11;5:180185. doi: 10.1038/sdata.2018.185.

5.

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia.

Lee SI, Celik S, Logsdon BA, Lundberg SM, Martins TJ, Oehler VG, Estey EH, Miller CP, Chien S, Dai J, Saxena A, Blau CA, Becker PS.

Nat Commun. 2018 Jan 3;9(1):42. doi: 10.1038/s41467-017-02465-5.

6.

Gene expression elucidates functional impact of polygenic risk for schizophrenia.

Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P.

Nat Neurosci. 2016 Nov;19(11):1442-1453. doi: 10.1038/nn.4399. Epub 2016 Sep 26.

7.

Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases.

Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, Serie D, Wang C, Nguyen T, Lincoln S, Malphrus K, Bisceglio G, Li M, Golde TE, Mangravite LM, Asmann Y, Price ND, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N.

Sci Data. 2016 Oct 11;3:160089. doi: 10.1038/sdata.2016.89.

8.

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer.

Celik S, Logsdon BA, Battle S, Drescher CW, Rendi M, Hawkins RD, Lee SI.

Genome Med. 2016 Jun 10;8(1):66. doi: 10.1186/s13073-016-0319-7.

9.

Identifying Network Perturbation in Cancer.

Grechkin M, Logsdon BA, Gentles AJ, Lee SI.

PLoS Comput Biol. 2016 May 4;12(5):e1004888. doi: 10.1371/journal.pcbi.1004888. eCollection 2016 May.

10.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S; Alzheimer's Disease Neuroimaging Initiative.

Alzheimers Dement. 2016 Jun;12(6):645-53. doi: 10.1016/j.jalz.2016.02.006. Epub 2016 Apr 11.

11.

SPINE: SParse eIgengene NEtwork linking gene expression clusters in Dehalococcoides mccartyi to perturbations in experimental conditions.

Mansfeldt CB, Logsdon BA, Debs GE, Richardson RE.

PLoS One. 2015 Feb 25;10(2):e0118404. doi: 10.1371/journal.pone.0118404. eCollection 2015.

12.

Sparse expression bases in cancer reveal tumor drivers.

Logsdon BA, Gentles AJ, Miller CP, Blau CA, Becker PS, Lee SI.

Nucleic Acids Res. 2015 Feb 18;43(3):1332-44. doi: 10.1093/nar/gku1290. Epub 2015 Jan 12.

13.

Rare variation facilitates inferences of fine-scale population structure in humans.

O'Connor TD, Fu W; NHLBI GO Exome Sequencing Project; ESP Population Genetics and Statistical Analysis Working Group, Emily Turner, Mychaleckyj JC, Logsdon B, Auer P, Carlson CS, Leal SM, Smith JD, Rieder MJ, Bamshad MJ, Nickerson DA, Akey JM.

Mol Biol Evol. 2015 Mar;32(3):653-60. doi: 10.1093/molbev/msu326. Epub 2014 Nov 21.

14.

A variational Bayes discrete mixture test for rare variant association.

Logsdon BA, Dai JY, Auer PL, Johnsen JM, Ganesh SK, Smith NL, Wilson JG, Tracy RP, Lange LA, Jiao S, Rich SS, Lettre G, Carlson CS, Jackson RD, O'Donnell CJ, Wurfel MM, Nickerson DA, Tang H, Reiner AP, Kooperberg C; NHLBI GO Exome Sequencing Project.

Genet Epidemiol. 2014 Jan;38(1):21-30.

15.

Altered residues in key proteins influence the expression and activity of the nitrogenase complex in an adaptive CO2 fixation-deficient mutant strain of Rhodobacter sphaeroides.

Farmer RM, Laguna R, Panescu J, McCoy A, Logsdon B, Zianni M, Moskvin OV, Gomelsky M, Tabita FR.

Microbiology. 2014 Jan;160(Pt 1):198-208. doi: 10.1099/mic.0.073031-0. Epub 2013 Oct 14.

PMID:
24126349
16.

PUMA: a unified framework for penalized multiple regression analysis of GWAS data.

Hoffman GE, Logsdon BA, Mezey JG.

PLoS Comput Biol. 2013;9(6):e1003101. doi: 10.1371/journal.pcbi.1003101. Epub 2013 Jun 27.

17.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

18.

Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project.

Auer PL, Johnsen JM, Johnson AD, Logsdon BA, Lange LA, Nalls MA, Zhang G, Franceschini N, Fox K, Lange EM, Rich SS, O'Donnell CJ, Jackson RD, Wallace RB, Chen Z, Graubert TA, Wilson JG, Tang H, Lettre G, Reiner AP, Ganesh SK, Li Y.

Am J Hum Genet. 2012 Nov 2;91(5):794-808. doi: 10.1016/j.ajhg.2012.08.031. Epub 2012 Oct 25.

19.

Simultaneously testing for marginal genetic association and gene-environment interaction.

Dai JY, Logsdon BA, Huang Y, Hsu L, Reiner AP, Prentice RL, Kooperberg C.

Am J Epidemiol. 2012 Jul 15;176(2):164-73. doi: 10.1093/aje/kwr521. Epub 2012 Jul 6.

20.

A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging.

Logsdon BA, Carty CL, Reiner AP, Dai JY, Kooperberg C.

Bioinformatics. 2012 Jul 1;28(13):1738-44. doi: 10.1093/bioinformatics/bts261. Epub 2012 May 4.

21.

Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control.

Logsdon BA, Hoffman GE, Mezey JG.

BMC Bioinformatics. 2012 Apr 2;13:53. doi: 10.1186/1471-2105-13-53.

22.

A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.

Qayyum R, Snively BM, Ziv E, Nalls MA, Liu Y, Tang W, Yanek LR, Lange L, Evans MK, Ganesh S, Austin MA, Lettre G, Becker DM, Zonderman AB, Singleton AB, Harris TB, Mohler ER, Logsdon BA, Kooperberg C, Folsom AR, Wilson JG, Becker LC, Reiner AP.

PLoS Genet. 2012;8(3):e1002491. doi: 10.1371/journal.pgen.1002491. Epub 2012 Mar 8.

23.

Gene expression network reconstruction by convex feature selection when incorporating genetic perturbations.

Logsdon BA, Mezey J.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001014. doi: 10.1371/journal.pcbi.1001014.

24.

A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis.

Logsdon BA, Hoffman GE, Mezey JG.

BMC Bioinformatics. 2010 Jan 27;11:58. doi: 10.1186/1471-2105-11-58.

25.

Quantitative trait loci for the circadian clock in Neurospora crassa.

Kim TS, Logsdon BA, Park S, Mezey JG, Lee K.

Genetics. 2007 Dec;177(4):2335-47. Epub 2007 Oct 18.

26.

Neutral evolution of multiple quantitative characters: a genealogical approach.

Griswold CK, Logsdon B, Gomulkiewicz R.

Genetics. 2007 May;176(1):455-66. Epub 2007 Mar 4.

27.

Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity.

Logsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC.

J Virol. 2004 Mar;78(6):3123-32.

28.

HIV-1 protease variants from 100-fold drug resistant clinical isolates: expression, purification, and crystallization.

Vickrey JF, Logsdon BC, Proteasa G, Palmer S, Winters MA, Merigan TC, Kovari LC.

Protein Expr Purif. 2003 Mar;28(1):165-72.

PMID:
12651121
29.

Disappearance of intramolecular stacking due to one-atom movement or increment of a 'propylene linker' in pyrazolo[3,4-d]pyrimidine-based flexible models.

Maulik PR, Avasthi K, Sarkhel S, Chandra T, Rawat DS, Logsdon B, Jacobson RA.

Acta Crystallogr C. 2000 Nov;56 Pt 11:1361-3.

PMID:
11077299
30.
31.

Evaluation of vancomycin use in a pediatric teaching hospital based on CDC criteria.

Logsdon BA, Lee KR, Luedtke G, Barrett FF.

Infect Control Hosp Epidemiol. 1997 Nov;18(11):780-2.

PMID:
9397378
32.

Drug use during lactation.

Logsdon BA.

J Am Pharm Assoc (Wash). 1997 Jul-Aug;NS37(4):407-18. Review.

PMID:
9519651
33.

Prevention of group B Streptococcus infection in neonates.

Logsdon BA, Casto DT.

Ann Pharmacother. 1997 Jul-Aug;31(7-8):897-906. Review.

PMID:
9220054
34.

Correct dosing of vancomycin in infants and children.

Logsdon BA, Lee KR, Barrett FF.

Pediatrics. 1995 Dec;96(6):1177. No abstract available.

PMID:
7491251
35.

A review and critical analysis of treatment research related to articulation and phonological disorders.

Sommers RK, Logsdon BS, Wright JM.

J Commun Disord. 1992 Mar;25(1):3-22. Review.

PMID:
1401228

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