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Corrigendum: A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC.

Gibson KM, Steiner MC, Kassaye S, Maldarelli F, Grossman Z, Pérez-Losada M, Crandall KA.

Front Microbiol. 2019 Nov 12;10:2590. doi: 10.3389/fmicb.2019.02590. eCollection 2019.


Fecal Transplant in Children With Clostridioides difficile Gives Sustained Reduction in Antimicrobial Resistance and Potential Pathogen Burden.

Hourigan SK, Ahn M, Gibson KM, Pérez-Losada M, Felix G, Weidner M, Leibowitz I, Niederhuber JE, Sears CL, Crandall KA, Oliva-Hemker M.

Open Forum Infect Dis. 2019 Aug 26;6(10):ofz379. doi: 10.1093/ofid/ofz379. eCollection 2019 Oct.


Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus.

Iñiguez LP, de Mulder Rougvie M, Stearrett N, Jones RB, Ormsby CE, Reyes-Terán G, Crandall KA, Nixon DF, Bendall ML.

Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21350-21351. doi: 10.1073/pnas.1907705116. Epub 2019 Oct 8. No abstract available.


ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data.

Spurr L, Alomran N, Bousounis P, Reece-Stremtan D, Prashant NM, Liu H, Słowiński P, Li M, Zhang Q, Sein J, Asher G, Crandall KA, Tsaneva-Atanasova K, Horvath A.

Bioinformatics. 2019 Oct 7. pii: btz750. doi: 10.1093/bioinformatics/btz750. [Epub ahead of print]


Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.

Gu S, Zaidi S, Hassan MI, Mohammad T, Malta TM, Noushmehr H, Nguyen B, Crandall KA, Srivastav J, Obias V, Lin P, Nguyen BN, Yao M, Yao R, King CH, Mazumder R, Mishra B, Rao S, Mishra L.

Gastroenterology. 2019 Oct 1. pii: S0016-5085(19)41365-6. doi: 10.1053/j.gastro.2019.09.023. [Epub ahead of print]


Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.

Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, Jones RB, Mulder LCF, Reyes-Terán G, Crandall KA, Ormsby CE, Nixon DF.

PLoS Comput Biol. 2019 Sep 30;15(9):e1006453. doi: 10.1371/journal.pcbi.1006453. eCollection 2019 Sep.


Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis.

Hoque MN, Istiaq A, Clement RA, Sultana M, Crandall KA, Siddiki AZ, Hossain MA.

Sci Rep. 2019 Sep 19;9(1):13536. doi: 10.1038/s41598-019-49468-4.


Baseline human gut microbiota profile in healthy people and standard reporting template.

King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R.

PLoS One. 2019 Sep 11;14(9):e0206484. doi: 10.1371/journal.pone.0206484. eCollection 2019.


Towards a barnacle tree of life: integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution.

Ewers-Saucedo C, Owen CL, Pérez-Losada M, Høeg JT, Glenner H, Chan BKK, Crandall KA.

PeerJ. 2019 Aug 16;7:e7387. doi: 10.7717/peerj.7387. eCollection 2019.


Machine learning approaches to predict lupus disease activity from gene expression data.

Kegerreis B, Catalina MD, Bachali P, Geraci NS, Labonte AC, Zeng C, Stearrett N, Crandall KA, Lipsky PE, Grammer AC.

Sci Rep. 2019 Jul 3;9(1):9617. doi: 10.1038/s41598-019-45989-0.


Gut microbiome differences between wild and captive black rhinoceros - implications for rhino health.

Gibson KM, Nguyen BN, Neumann LM, Miller M, Buss P, Daniels S, Ahn MJ, Crandall KA, Pukazhenthi B.

Sci Rep. 2019 May 28;9(1):7570. doi: 10.1038/s41598-019-43875-3.


A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans.

Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, Bracken-Grissom HD.

Proc Biol Sci. 2019 Apr 24;286(1901):20190079. doi: 10.1098/rspb.2019.0079.


A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC.

Gibson KM, Steiner MC, Kassaye S, Maldarelli F, Grossman Z, Pérez-Losada M, Crandall KA.

Front Microbiol. 2019 Mar 8;10:369. doi: 10.3389/fmicb.2019.00369. eCollection 2019. Erratum in: Front Microbiol. 2019 Nov 12;10:2590.


Transcriptome patterns in hidradenitis suppurativa: support for the role of antimicrobial peptides and interferon pathways in disease pathogenesis.

Shanmugam VK, Jones D, McNish S, Bendall ML, Crandall KA.

Clin Exp Dermatol. 2019 Dec;44(8):882-892. doi: 10.1111/ced.13959. Epub 2019 Apr 24.


Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis.

Hahn A, Fanous H, Jensen C, Chaney H, Sami I, Perez GF, Koumbourlis AC, Louie S, Bost JE, van den Anker JN, Freishtat RJ, Zemanick ET, Crandall KA.

Sci Rep. 2019 Feb 22;9(1):2534. doi: 10.1038/s41598-019-38984-y.


Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas.

Pérez-Losada M, Authelet KJ, Hoptay CE, Kwak C, Crandall KA, Freishtat RJ.

Microbiome. 2018 Oct 4;6(1):179. doi: 10.1186/s40168-018-0564-7.


Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity.

Hahn A, Burrell A, Fanous H, Chaney H, Sami I, Perez GF, Koumbourlis AC, Freishtat RJ, Crandall KA.

Heliyon. 2018 Sep 17;4(9):e00795. doi: 10.1016/j.heliyon.2018.e00795. eCollection 2018 Sep.


Kisspeptin/GPR54 System: What Do We Know About Its Role in Human Reproduction?

Trevisan CM, Montagna E, de Oliveira R, Christofolini DM, Barbosa CP, Crandall KA, Bianco B.

Cell Physiol Biochem. 2018;49(4):1259-1276. doi: 10.1159/000493406. Epub 2018 Sep 11. Review.


Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity.

Hahn A, Bendall ML, Gibson KM, Chaney H, Sami I, Perez GF, Koumbourlis AC, McCaffrey TA, Freishtat RJ, Crandall KA.

Front Microbiol. 2018 May 25;9:1069. doi: 10.3389/fmicb.2018.01069. eCollection 2018.


De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu.

Haynsen MS, Vatanparast M, Mahadwar G, Zhu D, Moger-Reischer RZ, Doyle JJ, Crandall KA, Egan AN.

BMC Genomics. 2018 Jun 5;19(1):439. doi: 10.1186/s12864-018-4798-3.


The Evolution of Gene Expression Underlying Vision Loss in Cave Animals.

Stern DB, Crandall KA.

Mol Biol Evol. 2018 Aug 1;35(8):2005-2014. doi: 10.1093/molbev/msy106.


Systematic pan-cancer analysis of somatic allele frequency.

Spurr L, Li M, Alomran N, Zhang Q, Restrepo P, Movassagh M, Trenkov C, Tunnessen N, Apanasovich T, Crandall KA, Edwards N, Horvath A.

Sci Rep. 2018 May 16;8(1):7735. doi: 10.1038/s41598-018-25462-0.


Phototransduction Gene Expression and Evolution in Cave and Surface Crayfishes.

Stern DB, Crandall KA.

Integr Comp Biol. 2018 Sep 1;58(3):398-410. doi: 10.1093/icb/icy029.


Seminal Simian Immunodeficiency Virus in Chronically Infected Cynomolgus Macaques Is Dominated by Virus Originating from Multiple Genital Organs.

Houzet L, Pérez-Losada M, Matusali G, Deleage C, Dereuddre-Bosquet N, Satie AP, Aubry F, Becker E, Jégou B, Le Grand R, Keele BF, Crandall KA, Dejucq-Rainsford N.

J Virol. 2018 Jun 29;92(14). pii: e00133-18. doi: 10.1128/JVI.00133-18. Print 2018 Jul 15.


Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.


Microbial diversity within the airway microbiome in chronic pediatric lung diseases.

Hahn A, Warnken S, Pérez-Losada M, Freishtat RJ, Crandall KA.

Infect Genet Evol. 2018 Sep;63:316-325. doi: 10.1016/j.meegid.2017.12.006. Epub 2017 Dec 7. Review.


Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC.

Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA; DC Cohort Executive Committee.

PLoS One. 2017 Sep 29;12(9):e0185644. doi: 10.1371/journal.pone.0185644. eCollection 2017.


Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end.

Stern DB, Breinholt J, Pedraza-Lara C, López-Mejía M, Owen CL, Bracken-Grissom H, Fetzner JW Jr, Crandall KA.

Evolution. 2017 Oct;71(10):2522-2532. doi: 10.1111/evo.13326. Epub 2017 Sep 20.


DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants.

Stern DB, Castro Nallar E, Rathod J, Crandall KA.

PeerJ. 2017 Apr 25;5:e3234. doi: 10.7717/peerj.3234. eCollection 2017.


Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma.

Pérez-Losada M, Alamri L, Crandall KA, Freishtat RJ.

PLoS One. 2017 Jan 20;12(1):e0170543. doi: 10.1371/journal.pone.0170543. eCollection 2017.


Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

Pérez-Losada M, Crandall KA, Freishtat RJ.

Microbiome. 2016 Jun 16;4(1):25. doi: 10.1186/s40168-016-0170-5.


Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.

Sun Y, Huang Y, Li X, Baldwin CC, Zhou Z, Yan Z, Crandall KA, Zhang Y, Zhao X, Wang M, Wong A, Fang C, Zhang X, Huang H, Lopez JV, Kilfoyle K, Zhang Y, Ortí G, Venkatesh B, Shi Q.

Gigascience. 2016 May 3;5:18. doi: 10.1186/s13742-016-0124-7. eCollection 2016.


Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA.

Front Microbiol. 2016 Apr 7;7:484. doi: 10.3389/fmicb.2016.00484. eCollection 2016.


Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America.

Sproul JS, Houston DD, Nelson CR, Evans RP, Crandall KA, Shiozawa DK.

BMC Evol Biol. 2015 Dec 12;15:279. doi: 10.1186/s12862-015-0553-4.


Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD 4th, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12764-9. doi: 10.1073/pnas.1423041112. Epub 2015 Sep 18.


Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.

Castro-Nallar E, Bendall ML, Pérez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA.

PeerJ. 2015 Aug 25;3:e1140. doi: 10.7717/peerj.1140. eCollection 2015.


Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.

Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA.

BMC Med Genomics. 2015 Aug 16;8:50. doi: 10.1186/s12920-015-0121-1.


Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA.

PLoS One. 2015 Jun 30;10(6):e0131819. doi: 10.1371/journal.pone.0131819. eCollection 2015.


Concordance and discordance of sequence survey methods for molecular epidemiology.

Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA.

PeerJ. 2015 Feb 17;3:e761. doi: 10.7717/peerj.761. eCollection 2015.


Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea).

Richman NI, Böhm M, Adams SB, Alvarez F, Bergey EA, Bunn JJ, Burnham Q, Cordeiro J, Coughran J, Crandall KA, Dawkins KL, DiStefano RJ, Doran NE, Edsman L, Eversole AG, Füreder L, Furse JM, Gherardi F, Hamr P, Holdich DM, Horwitz P, Johnston K, Jones CM, Jones JP, Jones RL, Jones TG, Kawai T, Lawler S, López-Mejía M, Miller RM, Pedraza-Lara C, Reynolds JD, Richardson AM, Schultz MB, Schuster GA, Sibley PJ, Souty-Grosset C, Taylor CA, Thoma RF, Walls J, Walsh TS, Collen B.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140060. doi: 10.1098/rstb.2014.0060.


A synthetic phylogeny of freshwater crayfish: insights for conservation.

Owen CL, Bracken-Grissom H, Stern D, Crandall KA.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140009. doi: 10.1098/rstb.2014.0009.


Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency.

Forest F, Crandall KA, Chase MW, Faith DP.

Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662):20140002. doi: 10.1098/rstb.2014.0002.


Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH.

BMC Bioinformatics. 2014 Nov 19;15:350. doi: 10.1186/s12859-014-0350-x.


Characteristics of equipartition for RNA structure.

Li H, Zhu D, Zhang C, Han H, Crandall KA.

BMC Proc. 2014 Oct 13;8(Suppl 6 Proceedings of the Great Lakes Bioinformatics Confer):S3. doi: 10.1186/1753-6561-8-S6-S3. eCollection 2014.


Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha).

Pérez-Losada M, Høeg JT, Simon-Blecher N, Achituv Y, Jones D, Crandall KA.

Mol Phylogenet Evol. 2014 Dec;81:147-58. doi: 10.1016/j.ympev.2014.09.013. Epub 2014 Sep 27.


PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.

Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33. eCollection 2014.


Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.

Toma I, Siegel MO, Keiser J, Yakovleva A, Kim A, Davenport L, Devaney J, Hoffman EP, Alsubail R, Crandall KA, Castro-Nallar E, Pérez-Losada M, Hilton SK, Chawla LS, McCaffrey TA, Simon GL.

J Clin Microbiol. 2014 Nov;52(11):3913-21. doi: 10.1128/JCM.01678-14. Epub 2014 Aug 20.


Characteristics and prediction of RNA structure.

Li H, Zhu D, Zhang C, Han H, Crandall KA.

Biomed Res Int. 2014;2014:690340. doi: 10.1155/2014/690340. Epub 2014 Jul 6.


Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.


Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.

Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R.

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.

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