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Items: 41

1.

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesøe RL, Richman AR, Kowalczyk MS, Abdelrahman S, Geduldig JE, Charbonneau S, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon NJ, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suvà ML, Wucherpfennig KW, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA.

Nature. 2019 Jan;565(7738):234-239. doi: 10.1038/s41586-018-0792-9. Epub 2018 Dec 19.

2.

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

Costello M, Fleharty M, Abreu J, Farjoun Y, Ferriera S, Holmes L, Granger B, Green L, Howd T, Mason T, Vicente G, Dasilva M, Brodeur W, DeSmet T, Dodge S, Lennon NJ, Gabriel S.

BMC Genomics. 2018 May 8;19(1):332. doi: 10.1186/s12864-018-4703-0.

3.

Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.

Taylor DL, Walters WA, Lennon NJ, Bochicchio J, Krohn A, Caporaso JG, Pennanen T.

Appl Environ Microbiol. 2016 Nov 21;82(24):7217-7226. Print 2016 Dec 15.

4.

Technological considerations for genome-guided diagnosis and management of cancer.

Lennon NJ, Adalsteinsson VA, Gabriel SB.

Genome Med. 2016 Oct 26;8(1):112. Review.

5.

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM.

PLoS Pathog. 2016 May 10;12(5):e1005619. doi: 10.1371/journal.ppat.1005619. eCollection 2016 May.

6.

Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease.

Blumenstiel B, DeFelice M, Birsoy O, Bleyer AJ, Kmoch S, Carter TA, Gnirke A, Kidd K, Rehm HL, Ronco L, Lander ES, Gabriel S, Lennon NJ.

J Mol Diagn. 2016 Jul;18(4):566-71. doi: 10.1016/j.jmoldx.2016.03.003. Epub 2016 May 5.

7.

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine.

Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Ansong D, Aponte JJ, Asante KP, Bejon P, Birkett AJ, Bruls M, Connolly KM, D'Alessandro U, Dobaño C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi P, Kariuki S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ogutu BR, Otieno W, Otieno L, Otieno K, Owusu-Agyei S, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarlal J, Sogoloff B, Sorgho H, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF.

N Engl J Med. 2015 Nov 19;373(21):2025-2037. doi: 10.1056/NEJMoa1505819. Epub 2015 Oct 21.

8.

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA Jr, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S; Viral Hemorrhagic Fever Consortium, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC.

Cell. 2015 Aug 13;162(4):738-50. doi: 10.1016/j.cell.2015.07.020.

9.

Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations.

Ahronian LG, Sennott EM, Van Allen EM, Wagle N, Kwak EL, Faris JE, Godfrey JT, Nishimura K, Lynch KD, Mermel CH, Lockerman EL, Kalsy A, Gurski JM Jr, Bahl S, Anderka K, Green LM, Lennon NJ, Huynh TG, Mino-Kenudson M, Getz G, Dias-Santagata D, Iafrate AJ, Engelman JA, Garraway LA, Corcoran RB.

Cancer Discov. 2015 Apr;5(4):358-67. doi: 10.1158/2159-8290.CD-14-1518. Epub 2015 Feb 11.

10.

Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

Timling I, Walker DA, Nusbaum C, Lennon NJ, Taylor DL.

Mol Ecol. 2014 Jul;23(13):3258-72. doi: 10.1111/mec.12743. Epub 2014 Apr 30.

PMID:
24689939
11.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.

Nat Biotechnol. 2014 Apr;32(4):381-386. doi: 10.1038/nbt.2859. Epub 2014 Mar 23.

12.

Characterizing and measuring bias in sequence data.

Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, Nusbaum C, Jaffe DB.

Genome Biol. 2013 May 29;14(5):R51. doi: 10.1186/gb-2013-14-5-r51.

13.

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR.

J Infect Dis. 2013 Jul;208(1):17-31. doi: 10.1093/infdis/jis679. Epub 2012 Nov 6.

14.

De novo assembly of highly diverse viral populations.

Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR.

BMC Genomics. 2012 Sep 13;13:475. doi: 10.1186/1471-2164-13-475.

15.

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.

Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, Carneiro MO, Carter SL, Cibulskis K, Erlich RL, Greulich H, Lawrence MS, Lennon NJ, McKenna A, Meldrim J, Ramos AH, Ross MG, Russ C, Shefler E, Sivachenko A, Sogoloff B, Stojanov P, Tamayo P, Mesirov JP, Amani V, Teider N, Sengupta S, Francois JP, Northcott PA, Taylor MD, Yu F, Crabtree GR, Kautzman AG, Gabriel SB, Getz G, Jäger N, Jones DT, Lichter P, Pfister SM, Roberts TM, Meyerson M, Pomeroy SL, Cho YJ.

Nature. 2012 Aug 2;488(7409):106-10. doi: 10.1038/nature11329.

16.

Reemergence and decline of dengue virus serotype 3 in Puerto Rico.

Santiago GA, McElroy-Horne K, Lennon NJ, Santiago LM, Birren BW, Henn MR, Muñoz-Jordán JL.

J Infect Dis. 2012 Sep 15;206(6):893-901. doi: 10.1093/infdis/jis426. Epub 2012 Jun 27.

17.

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.

McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PI; International HIV Controllers Study.

Hum Mol Genet. 2012 Oct 1;21(19):4334-47. doi: 10.1093/hmg/dds226. Epub 2012 Jun 19.

18.

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Duong V, Henn MR, Simmons C, Ngan C, Y B, Gavotte L, Viari A, Ong S, Huy R, Lennon NJ, Ly S, Vong S, Birren BW, Farrar JJ, Deubel V, Frutos R, Buchy P.

Infect Genet Evol. 2013 Apr;15:77-86. doi: 10.1016/j.meegid.2012.05.012. Epub 2012 Jun 5.

PMID:
22677620
19.

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Parameswaran P, Charlebois P, Tellez Y, Nunez A, Ryan EM, Malboeuf CM, Levin JZ, Lennon NJ, Balmaseda A, Harris E, Henn MR.

J Virol. 2012 Aug;86(16):8546-58. doi: 10.1128/JVI.00736-12. Epub 2012 May 30.

20.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR.

PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417. Epub 2012 Mar 15.

21.

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM.

PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529. Epub 2012 Mar 8.

22.

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice.

Pesko KN, Fitzpatrick KA, Ryan EM, Shi PY, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD.

Virology. 2012 May 25;427(1):10-7. doi: 10.1016/j.virol.2012.01.028. Epub 2012 Feb 23.

23.

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.

OhAinle M, Balmaseda A, Macalalad AR, Tellez Y, Zody MC, Saborío S, Nuñez A, Lennon NJ, Birren BW, Gordon A, Henn MR, Harris E.

Sci Transl Med. 2011 Dec 21;3(114):114ra128. doi: 10.1126/scitranslmed.3003084.

24.

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.

Thai KT, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, Simmons CP.

J Virol. 2012 Jan;86(2):835-43. doi: 10.1128/JVI.05985-11. Epub 2011 Nov 16.

25.

A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation.

Schmidt DJ, Pickett BE, Camacho D, Comach G, Xhaja K, Lennon NJ, Rizzolo K, de Bosch N, Becerra A, Nogueira ML, Mondini A, da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R, Gehrke L, Lefkowitz EJ, Birren BW, Henn MR, Bosch I.

Infect Genet Evol. 2011 Dec;11(8):2011-9. doi: 10.1016/j.meegid.2011.09.010. Epub 2011 Sep 23.

26.

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Duong V, Simmons C, Gavotte L, Viari A, Ong S, Chantha N, Lennon NJ, Birren BW, Vong S, Farrar JJ, Henn MR, Deubel V, Frutos R, Buchy P.

Infect Genet Evol. 2013 Apr;15:59-68. doi: 10.1016/j.meegid.2011.06.019. Epub 2011 Jul 2.

PMID:
21757030
27.

Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008.

Armstrong PM, Vossbrinck CR, Andreadis TG, Anderson JF, Pesko KN, Newman RM, Lennon NJ, Birren BW, Ebel GD, Henn MR.

Virology. 2011 Aug 15;417(1):203-10. doi: 10.1016/j.virol.2011.06.006. Epub 2011 Jul 1.

28.

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP.

PLoS Pathog. 2011 Jun;7(6):e1002064. doi: 10.1371/journal.ppat.1002064. Epub 2011 Jun 2.

29.

Next-generation sequencing for HLA typing of class I loci.

Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI.

BMC Genomics. 2011 Jan 18;12:42. doi: 10.1186/1471-2164-12-42.

30.

Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007.

McElroy KL, Santiago GA, Lennon NJ, Birren BW, Henn MR, Muñoz-Jordán JL.

Emerg Infect Dis. 2011 Jan;17(1):64-71. doi: 10.3201/eid1701.100961.

31.

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Yu Q, Ryan EM, Allen TM, Birren BW, Henn MR, Lennon NJ.

Bioinformatics. 2011 Jan 15;27(2):266-7. doi: 10.1093/bioinformatics/btq624. Epub 2010 Nov 9.

32.

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults.

Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT, Mai LN, Farrar JJ, Hibberd ML, Simmons CP.

J Virol. 2010 Dec;84(24):12982-94. doi: 10.1128/JVI.01224-10. Epub 2010 Oct 13.

33.

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

Vu TT, Holmes EC, Duong V, Nguyen TQ, Tran TH, Quail M, Churcher C, Parkhill J, Cardosa J, Farrar J, Wills B, Lennon NJ, Birren BW, Buchy P, Henn MR, Simmons CP.

PLoS Negl Trop Dis. 2010 Jul 20;4(7):e757. doi: 10.1371/journal.pntd.0000757.

34.

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, Giannoukos G, Green L, Hollinger A, Hoover CA, Jaffe DB, Juhn F, McCarthy D, Perrin D, Ponchner K, Powers TL, Rizzolo K, Robbins D, Ryan E, Russ C, Sparrow T, Stalker J, Steelman S, Weiand M, Zimmer A, Henn MR, Nusbaum C, Nicol R.

Genome Biol. 2010;11(2):R15. doi: 10.1186/gb-2010-11-2-r15. Epub 2010 Feb 5.

35.

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.

Taylor DL, Booth MG, McFarland JW, Herriott IC, Lennon NJ, Nusbaum C, Marr TG.

Mol Ecol Resour. 2008 Jul;8(4):742-52. doi: 10.1111/j.1755-0998.2008.02094.x.

PMID:
21585882
36.

Dysferlin interacts with annexins A1 and A2 and mediates sarcolemmal wound-healing.

Lennon NJ, Kho A, Bacskai BJ, Perlmutter SL, Hyman BT, Brown RH Jr.

J Biol Chem. 2003 Dec 12;278(50):50466-73. Epub 2003 Sep 23.

37.

Impaired Ca2+-sequestration in dilated cardiomyopathy (review).

Lennon NJ, Ohlendieck K.

Int J Mol Med. 2001 Feb;7(2):131-41. Review.

PMID:
11172615
38.

Impaired Ca2+-ATPase oligomerization and increased phospholamban expression in dilated cardiomyopathy.

Lennon NJ, O'Reilly C, Ohlendieck K.

Int J Mol Med. 2000 Nov;6(5):533-8.

PMID:
11029519
39.

Oligomerization of the sarcoplasmic reticulum Ca2+-ATPase SERCA2 in cardiac muscle.

Lennon NJ, Harmon S, Mackey A, Ohlendieck K.

Mol Cell Biol Res Commun. 1999 Jun;1(3):182-7.

PMID:
10425224
40.

Oligomerisation of calsequestrin from rabbit skeletal muscle.

Maguire PB, Lennon NJ, Ohlendieck K.

Biochem Soc Trans. 1998 Aug;26(3):S292. No abstract available.

PMID:
9766011
41.

Oligomerization is an intrinsic property of calsequestrin in normal and transformed skeletal muscle.

Maguire PB, Briggs FN, Lennon NJ, Ohlendieck K.

Biochem Biophys Res Commun. 1997 Nov 26;240(3):721-7.

PMID:
9398633

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