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Items: 26

1.

A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment.

Stevens RC, Steele JL, Glover WR, Sanchez-Garcia JF, Simpson SD, O'Rourke D, Ramsdell JS, MacManes MD, Thomas WK, Shuber AP.

PLoS One. 2019 Apr 18;14(4):e0215441. doi: 10.1371/journal.pone.0215441. eCollection 2019.

2.

Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus.

Stuckert AMM, Moore E, Coyle KP, Davison I, MacManes MD, Roberts R, Summers K.

BMC Evol Biol. 2019 Apr 18;19(1):85. doi: 10.1186/s12862-019-1410-7.

3.

Dynamic pigmentary and structural coloration within cephalopod chromatophore organs.

Williams TL, Senft SL, Yeo J, Martín-Martínez FJ, Kuzirian AM, Martin CA, DiBona CW, Chen CT, Dinneen SR, Nguyen HT, Gomes CM, Rosenthal JJC, MacManes MD, Chu F, Buehler MJ, Hanlon RT, Deravi LF.

Nat Commun. 2019 Mar 1;10(1):1004. doi: 10.1038/s41467-019-08891-x.

4.

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.

Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G, Nielsen R.

Mol Biol Evol. 2018 Dec 1;35(12):2913-2927. doi: 10.1093/molbev/msy185.

5.

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.

MacManes MD.

PeerJ. 2018 Aug 3;6:e5428. doi: 10.7717/peerj.5428. eCollection 2018.

6.

Sex-biased transcriptomic response of the reproductive axis to stress.

Calisi RM, Austin SH, Lang AS, MacManes MD.

Horm Behav. 2018 Apr;100:56-68. doi: 10.1016/j.yhbeh.2017.11.011. Epub 2018 Mar 20.

7.

Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia.

Schuelke TA, Wu G, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes MD.

Genome Biol Evol. 2017 Dec 1;9(12):3312-3327. doi: 10.1093/gbe/evx242.

8.

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.

Jarett JK, MacManes MD, Morrow KM, Pankey MS, Lesser MP.

Sci Rep. 2017 Nov 22;7(1):16039. doi: 10.1038/s41598-017-16371-9.

9.

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis.

MacManes MD, Austin SH, Lang AS, Booth A, Farrar V, Calisi RM.

Sci Rep. 2017 Apr 18;7:45125. doi: 10.1038/srep45125.

10.

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.

MacManes MD.

Am J Physiol Renal Physiol. 2017 Aug 1;313(2):F262-F272. doi: 10.1152/ajprenal.00067.2017. Epub 2017 Apr 5.

11.

Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus.

Kordonowy L, Lombardo KD, Green HL, Dawson MD, Bolton EA, LaCourse S, MacManes MD.

Physiol Rep. 2017 Mar;5(6). pii: e13218. doi: 10.14814/phy2.13218.

12.

PALADIN: protein alignment for functional profiling whole metagenome shotgun data.

Westbrook A, Ramsdell J, Schuelke T, Normington L, Bergeron RD, Thomas WK, MacManes MD.

Bioinformatics. 2017 May 15;33(10):1473-1478. doi: 10.1093/bioinformatics/btx021.

13.

Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish.

Partridge CG, MacManes MD, Knapp R, Neff BD.

PLoS One. 2016 Dec 1;11(12):e0167509. doi: 10.1371/journal.pone.0167509. eCollection 2016.

14.

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse).

Kordonowy LL, MacManes MD.

PeerJ. 2016 Oct 27;4:e2617. doi: 10.7717/peerj.2617. eCollection 2016.

15.

Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis.

Havens LA, MacManes MD.

PeerJ. 2016 Jun 14;4:e2098. doi: 10.7717/peerj.2098. eCollection 2016.

16.

De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease.

Schuelke TA, Westbrook A, Broders K, Woeste K, MacManes MD.

PeerJ. 2016 May 2;4:e1952. doi: 10.7717/peerj.1952. eCollection 2016.

17.
18.

On the optimal trimming of high-throughput mRNA sequence data.

Macmanes MD.

Front Genet. 2014 Jan 31;5:13. doi: 10.3389/fgene.2014.00013. eCollection 2014.

19.

Improving transcriptome assembly through error correction of high-throughput sequence reads.

Macmanes MD, Eisen MB.

PeerJ. 2013 Jul 23;1:e113. doi: 10.7717/peerj.113. Print 2013.

20.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

21.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A.

Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11.

22.
23.

Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?

MacManes MD, Lacey EA.

PLoS One. 2012;7(5):e37562. doi: 10.1371/journal.pone.0037562. Epub 2012 May 23.

24.

Promiscuity in mice is associated with increased vaginal bacterial diversity.

MacManes MD.

Naturwissenschaften. 2011 Nov;98(11):951-60. doi: 10.1007/s00114-011-0848-2. Epub 2011 Oct 1.

25.

Museum genomics: low-cost and high-accuracy genetic data from historical specimens.

Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, Bi K, Moritz CC.

Mol Ecol Resour. 2011 Nov;11(6):1082-92. doi: 10.1111/j.1755-0998.2011.03052.x. Epub 2011 Jul 25.

PMID:
21791033
26.

Isolation and characterization of polymorphic microsatellite loci from Octodon degus.

Quan YF, Macmanes MD, Ebensperger LA, Lacey EA, Hayes LD.

Mol Ecol Resour. 2009 May;9(3):999-1001. doi: 10.1111/j.1755-0998.2009.02536.x. Epub 2009 Feb 10.

PMID:
21564818

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