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Items: 1 to 50 of 119

1.

RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis.

Peterson KA, Yoshigi M, Hazel MW, Delker DA, Lin E, Krishnamurthy C, Consiglio N, Robson J, Yandell M, Clayton F.

Aliment Pharmacol Ther. 2018 Jun 4. doi: 10.1111/apt.14825. [Epub ahead of print]

PMID:
29863285
2.

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato.

Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH.

Plant Cell. 2018 May 9. pii: tpc.00194.2018. doi: 10.1105/tpc.18.00194. [Epub ahead of print]

3.

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE.

Bioinformatics. 2018 Apr 25. doi: 10.1093/bioinformatics/bty324. [Epub ahead of print]

PMID:
29701825
4.

Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT.

Nat Genet. 2018 May;50(5):768. doi: 10.1038/s41588-018-0075-2.

PMID:
29674745
5.

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia).

Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, T Domyan E, Suh A, Warren WC, Yandell M, Gilbert MTP, Shapiro MD.

G3 (Bethesda). 2018 May 4;8(5):1391-1398. doi: 10.1534/g3.117.300443.

6.

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L, G Reese M, Yandell M.

BMC Bioinformatics. 2018 Feb 20;19(1):57. doi: 10.1186/s12859-018-2056-y.

7.

POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women.

Moriwaki M, Moore B, Mosbruger T, Neklason DW, Yandell M, Jorde LB, Welt CK.

J Endocr Soc. 2017 Feb 7;1(3):162-173. doi: 10.1210/js.2016-1014. eCollection 2017 Mar 1.

8.

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT.

Nat Genet. 2018 Feb;50(2):270-277. doi: 10.1038/s41588-017-0036-1. Epub 2018 Jan 22. Erratum in: Nat Genet. 2018 Apr 19;:.

PMID:
29358652
9.

XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MAT, Yandell M, Huff CD.

Nucleic Acids Res. 2018 Apr 6;46(6):e32. doi: 10.1093/nar/gkx1280.

10.

Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation.

Al-Agha AE, Ahmed IA, Nuebel E, Moriwaki M, Moore B, Peacock KA, Mosbruger T, Neklason DW, Jorde LB, Yandell M, Welt CK.

J Clin Endocrinol Metab. 2018 Feb 1;103(2):555-563. doi: 10.1210/jc.2017-01966.

PMID:
29240891
11.

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands.

Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA Jr, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M.

Nat Genet. 2017 Nov;49(11):1593-1601. doi: 10.1038/ng.3970. Epub 2017 Oct 9.

12.

Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia.

Schlaberg R, Ampofo K, Tardif KD, Stockmann C, Simmon KE, Hymas W, Flygare S, Kennedy B, Blaschke A, Eilbeck K, Yandell M, McCullers JA, Williams DJ, Edwards K, Arnold SR, Bramley A, Jain S, Pavia AT.

J Infect Dis. 2017 Sep 15;216(6):688-696. doi: 10.1093/infdis/jix352.

PMID:
28934425
13.

Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus.

Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H.

Genome Biol Evol. 2017 Sep 1;9(9):2211-2225. doi: 10.1093/gbe/evx157.

14.

Settling the score: variant prioritization and Mendelian disease.

Eilbeck K, Quinlan A, Yandell M.

Nat Rev Genet. 2017 Oct;18(10):599-612. doi: 10.1038/nrg.2017.52. Epub 2017 Aug 14. Review.

15.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

16.

Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779.

Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, TerBush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C.

PLoS Genet. 2017 May 23;13(5):e1006802. doi: 10.1371/journal.pgen.1006802. eCollection 2017 May.

17.

The Venom Repertoire of Conus gloriamaris (Chemnitz, 1777), the Glory of the Sea.

Robinson SD, Li Q, Lu A, Bandyopadhyay PK, Yandell M, Olivera BM, Safavi-Hemami H.

Mar Drugs. 2017 May 20;15(5). pii: E145. doi: 10.3390/md15050145.

18.

Physical interface dynamics alter how robotic exosuits augment human movement: implications for optimizing wearable assistive devices.

Yandell MB, Quinlivan BT, Popov D, Walsh C, Zelik KE.

J Neuroeng Rehabil. 2017 May 18;14(1):40. doi: 10.1186/s12984-017-0247-9.

19.

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.

Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K.

J Infect Dis. 2017 May 1;215(9):1407-1415. doi: 10.1093/infdis/jix148.

20.

Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study.

Manuck TA, Watkins WS, Esplin MS, Biggio J, Bukowski R, Parry S, Zhan H, Huang H, Andrews W, Saade G, Sadovsky Y, Reddy UM, Ilekis J, Yandell M, Varner MW, Jorde LB; Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Genomics and Proteomics Network for Preterm Birth Research (GPN-PBR).

BJOG. 2018 Feb;125(3):343-350. doi: 10.1111/1471-0528.14485. Epub 2017 Jan 31.

PMID:
28139890
21.

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, Yandell M, Reddy TE.

Bioinformatics. 2017 May 15;33(10):1437-1446. doi: 10.1093/bioinformatics/btw799.

22.

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus.

Cone KR, Kronenberg ZN, Yandell M, Elde NC.

J Virol. 2017 Jan 31;91(4). pii: e01428-16. doi: 10.1128/JVI.01428-16. Print 2017 Feb 15.

23.

VARPRISM: incorporating variant prioritization in tests of de novo mutation association.

Hu H, Coon H, Li M, Yandell M, Huff CD.

Genome Med. 2016 Aug 25;8(1):91. doi: 10.1186/s13073-016-0341-9.

24.

Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa.

Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM.

Mol Biol Evol. 2016 Nov;33(11):2924-2934. Epub 2016 Aug 14.

25.

The draft genome sequence and annotation of the desert woodrat Neotoma lepida.

Campbell M, Oakeson KF, Yandell M, Halpert JR, Dearing D.

Genom Data. 2016 Jun 23;9:58-9. doi: 10.1016/j.gdata.2016.06.008. eCollection 2016 Sep.

26.

Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo Ldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 May 27;48(6):700. doi: 10.1038/ng0616-700c. No abstract available.

PMID:
27230688
27.

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.

Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R.

Genome Biol. 2016 May 26;17(1):111. doi: 10.1186/s13059-016-0969-1.

28.

Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

Barber MF, Kronenberg Z, Yandell M, Elde NC.

PLoS Genet. 2016 May 20;12(5):e1006063. doi: 10.1371/journal.pgen.1006063. eCollection 2016 May.

29.

Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate.

Yandell MB, Zelik KE.

Sci Rep. 2016 Mar 18;6:23243. doi: 10.1038/srep23243.

30.

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species.

Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD.

Elife. 2016 Mar 15;5:e12115. doi: 10.7554/eLife.12115.

31.

Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides.

Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3227-32. doi: 10.1073/pnas.1525790113. Epub 2016 Mar 8.

32.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH.

Nat Genet. 2016 Apr;48(4):427-37. doi: 10.1038/ng.3526. Epub 2016 Mar 7.

33.

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R.

J Clin Microbiol. 2016 Apr;54(4):1000-7. doi: 10.1128/JCM.03060-15. Epub 2016 Jan 27.

34.

An Introduction to Genome Annotation.

Campbell MS, Yandell M.

Curr Protoc Bioinformatics. 2015 Dec 17;52:4.1.1-17. doi: 10.1002/0471250953.bi0401s52.

PMID:
26678385
35.

Age-related mutations and chronic myelomonocytic leukemia.

Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Zabriskie MS, Yan D, Pomicter AD, Reynolds KR, Eiring AM, Kronenberg Z, Sherman RL, Tyner JW, Dalley BK, Dao KH, Yandell M, Druker BJ, Gotlib J, O'Hare T, Deininger MW.

Leukemia. 2016 Apr;30(4):906-13. doi: 10.1038/leu.2015.337. Epub 2015 Dec 9.

36.

Wham: Identifying Structural Variants of Biological Consequence.

Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M.

PLoS Comput Biol. 2015 Dec 1;11(12):e1004572. doi: 10.1371/journal.pcbi.1004572. eCollection 2015 Dec.

37.

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.

Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15976-81. doi: 10.1073/pnas.1510461112. Epub 2015 Nov 23. Erratum in: Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):E5364.

38.

Hormone-like peptides in the venoms of marine cone snails.

Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H.

Gen Comp Endocrinol. 2017 Apr 1;244:11-18. doi: 10.1016/j.ygcen.2015.07.012. Epub 2015 Aug 22.

39.

Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.

Bowles NE, Jou CJ, Arrington CB, Kennedy BJ, Earl A, Matsunami N, Meyers LL, Etheridge SP, Saarel EV, Bleyl SB, Yost HJ, Yandell M, Leppert MF, Tristani-Firouzi M, Gruber PJ; Baylor Hopkins Centers for Mendelian Genomics.

Am J Med Genet A. 2015 Dec;167A(12):2975-84. doi: 10.1002/ajmg.a.37297. Epub 2015 Aug 18.

40.

Electron accommodation dynamics in the DNA base thymine.

King SB, Stephansen AB, Yokoi Y, Yandell MA, Kunin A, Takayanagi T, Neumark DM.

J Chem Phys. 2015 Jul 14;143(2):024312. doi: 10.1063/1.4923343.

PMID:
26178110
41.

Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).

Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB.

PLoS One. 2015 Jun 29;10(6):e0131514. doi: 10.1371/journal.pone.0131514. eCollection 2015.

42.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G.

Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.

43.

Muscle stem cells contribute to myofibres in sedentary adult mice.

Keefe AC, Lawson JA, Flygare SD, Fox ZD, Colasanto MP, Mathew SJ, Yandell M, Kardon G.

Nat Commun. 2015 May 14;6:7087. doi: 10.1038/ncomms8087.

44.

Specialized insulin is used for chemical warfare by fish-hunting cone snails.

Safavi-Hemami H, Gajewiak J, Karanth S, Robinson SD, Ueberheide B, Douglass AD, Schlegel A, Imperial JS, Watkins M, Bandyopadhyay PK, Yandell M, Li Q, Purcell AW, Norton RS, Ellgaard L, Olivera BM.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1743-8. doi: 10.1073/pnas.1423857112. Epub 2015 Jan 20.

45.

DisAp-dependent striated fiber elongation is required to organize ciliary arrays.

Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG.

J Cell Biol. 2014 Dec 22;207(6):705-15. doi: 10.1083/jcb.201409123.

46.

Transposable element islands facilitate adaptation to novel environments in an invasive species.

Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, Oettler J.

Nat Commun. 2014 Dec 16;5:5495. doi: 10.1038/ncomms6495.

47.

Genome Annotation and Curation Using MAKER and MAKER-P.

Campbell MS, Holt C, Moore B, Yandell M.

Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-39. doi: 10.1002/0471250953.bi0411s48.

48.

Time-resolved radiation chemistry: dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes.

King SB, Yandell MA, Stephansen AB, Neumark DM.

J Chem Phys. 2014 Dec 14;141(22):224310. doi: 10.1063/1.4903197.

PMID:
25494752
49.

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2015 Jan;167(1):25-39. doi: 10.1104/pp.114.245027. Epub 2014 Nov 10.

50.

Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma.

Darlington TM, Pimentel R, Smith K, Bakian AV, Jerominski L, Cardon J, Camp NJ, Callor WB, Grey T, Singleton M, Yandell M, Renshaw PF, Yurgelun-Todd DA, Gray D, Coon H.

Transl Psychiatry. 2014 Oct 21;4:e471. doi: 10.1038/tp.2014.111.

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