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Items: 1 to 50 of 378

1.

Functional characterization of 3D protein structures informed by human genetic diversity.

Hicks M, Bartha I, di Iulio J, Venter JC, Telenti A.

Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):8960-8965. doi: 10.1073/pnas.1820813116. Epub 2019 Apr 15.

2.

Entry of Polarized Effector Cells into Quiescence Forces HIV Latency.

Dobrowolski C, Valadkhan S, Graham AC, Shukla M, Ciuffi A, Telenti A, Karn J.

MBio. 2019 Mar 26;10(2). pii: e00337-19. doi: 10.1128/mBio.00337-19.

3.

Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A.

Sci Rep. 2019 Jan 18;9(1):213. doi: 10.1038/s41598-018-36135-3.

4.

Response to Whiffin et al.

Shah N, Claire Hou YC, Yu HC, Sainger R, Caskey CT, Venter JC, Telenti A.

Am J Hum Genet. 2019 Jan 3;104(1):186. doi: 10.1016/j.ajhg.2018.11.011. No abstract available.

PMID:
30609405
5.

A primer on deep learning in genomics.

Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A.

Nat Genet. 2019 Jan;51(1):12-18. doi: 10.1038/s41588-018-0295-5. Epub 2018 Nov 26. Review.

PMID:
30478442
6.

Integrating metabolomics with genomics.

Telenti A.

Pharmacogenomics. 2018 Dec;19(18):1377-1381. doi: 10.2217/pgs-2018-0155. Epub 2018 Nov 6. No abstract available.

PMID:
30398072
7.

Profound Perturbation of the Metabolome in Obesity Is Associated with Health Risk.

Cirulli ET, Guo L, Leon Swisher C, Shah N, Huang L, Napier LA, Kirkness EF, Spector TD, Caskey CT, Thorens B, Venter JC, Telenti A.

Cell Metab. 2019 Feb 5;29(2):488-500.e2. doi: 10.1016/j.cmet.2018.09.022. Epub 2018 Oct 11.

8.

Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant.

Wang W, Huang H, Halagan M, Vierra-Green C, Heuer M, Brelsford JE, Haagenson M, Scheuermann RH, Telenti A, Biggs W, Pearson NM, Udell J, Spellman S, Maiers M, Kennedy CJ.

Blood Adv. 2018 Oct 9;2(19):2419-2429. doi: 10.1182/bloodadvances.2018019513.

9.

Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders.

Iranmehr A, Stobdan T, Zhou D, Poulsen O, Strohl KP, Aldashev A, Telenti A, Wong EHM, Kirkness EF, Venter JC, Bafna V, Haddad GG.

Eur J Hum Genet. 2019 Jan;27(1):150-159. doi: 10.1038/s41431-018-0270-8. Epub 2018 Sep 25.

PMID:
30254217
10.

IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis.

Chekuri A, Guru AA, Biswas P, Branham K, Borooah S, Soto-Hermida A, Hicks M, Khan NW, Matsui H, Alapati A, Raghavendra PB, Roosing S, Sarangapani S, Mathavan S, Telenti A, Heckenlively JR, Riazuddin SA, Frazer KA, Sieving PA, Ayyagari R.

Hum Genet. 2018 Jul;137(6-7):447-458. doi: 10.1007/s00439-018-1897-9. Epub 2018 Jul 5.

PMID:
29978320
11.

The fecal metabolome as a functional readout of the gut microbiome.

Zierer J, Jackson MA, Kastenmüller G, Mangino M, Long T, Telenti A, Mohney RP, Small KS, Bell JT, Steves CJ, Valdes AM, Spector TD, Menni C.

Nat Genet. 2018 Jun;50(6):790-795. doi: 10.1038/s41588-018-0135-7. Epub 2018 May 28.

12.

The Antiviral Activity of the Cellular Glycoprotein LGALS3BP/90K Is Species Specific.

Lodermeyer V, Ssebyatika G, Passos V, Ponnurangam A, Malassa A, Ewald E, Stürzel CM, Kirchhoff F, Rotger M, Falk CS, Telenti A, Krey T, Goffinet C.

J Virol. 2018 Jun 29;92(14). pii: e00226-18. doi: 10.1128/JVI.00226-18. Print 2018 Jul 15.

13.

Paternally inherited cis-regulatory structural variants are associated with autism.

Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J.

Science. 2018 Apr 20;360(6386):327-331. doi: 10.1126/science.aan2261.

14.

Deep learning of genomic variation and regulatory network data.

Telenti A, Lippert C, Chang PC, DePristo M.

Hum Mol Genet. 2018 May 1;27(R1):R63-R71. doi: 10.1093/hmg/ddy115. Review.

15.

Identification of Misclassified ClinVar Variants via Disease Population Prevalence.

Shah N, Hou YC, Yu HC, Sainger R, Caskey CT, Venter JC, Telenti A.

Am J Hum Genet. 2018 Apr 5;102(4):609-619. doi: 10.1016/j.ajhg.2018.02.019.

16.

Comparison of phasing strategies for whole human genomes.

Choi Y, Chan AP, Kirkness E, Telenti A, Schork NJ.

PLoS Genet. 2018 Apr 5;14(4):e1007308. doi: 10.1371/journal.pgen.1007308. eCollection 2018 Apr.

17.

Rethinking the medical record.

Telenti A, Steinhubl SR, Topol EJ.

Lancet. 2018 Mar 17;391(10125):1013. doi: 10.1016/S0140-6736(18)30538-5. Epub 2018 Mar 15. No abstract available.

PMID:
29565009
18.

Microbial metagenome of urinary tract infection.

Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R, Telenti A.

Sci Rep. 2018 Mar 12;8(1):4333. doi: 10.1038/s41598-018-22660-8.

19.

The human noncoding genome defined by genetic diversity.

di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Shah N, Kirkness EF, Fabani MM, Biggs WH, Ren B, Venter JC, Telenti A.

Nat Genet. 2018 Mar;50(3):333-337. doi: 10.1038/s41588-018-0062-7. Epub 2018 Feb 26.

PMID:
29483654
20.

Acetaminophen (Paracetamol) Use Modifies the Sulfation of Sex Hormones.

Cohen IV, Cirulli ET, Mitchell MW, Jonsson TJ, Yu J, Shah N, Spector TD, Guo L, Venter JC, Telenti A.

EBioMedicine. 2018 Feb;28:316-323. doi: 10.1016/j.ebiom.2018.01.033. Epub 2018 Feb 15.

21.

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.

Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS.

Clin Transl Gastroenterol. 2018 Jan 18;9(1):e132. doi: 10.1038/ctg.2017.58.

22.

A community effort to protect genomic data sharing, collaboration and outsourcing.

Wang S, Jiang X, Tang H, Wang X, Bu D, Carey K, Dyke SO, Fox D, Jiang C, Lauter K, Malin B, Sofia H, Telenti A, Wang L, Wang W, Ohno-Machado L.

NPJ Genom Med. 2017 Oct 27;2:33. doi: 10.1038/s41525-017-0036-1. eCollection 2017. Review.

23.

Retroviruses As Myeloid Cell Riders: What Natural Human Siglec-1 "Knockouts" Tell Us About Pathogenesis.

Martinez-Picado J, McLaren PJ, Telenti A, Izquierdo-Useros N.

Front Immunol. 2017 Nov 21;8:1593. doi: 10.3389/fimmu.2017.01593. eCollection 2017.

24.

Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes.

Tang H, Kirkness EF, Lippert C, Biggs WH, Fabani M, Guzman E, Ramakrishnan S, Lavrenko V, Kakaradov B, Hou C, Hicks B, Heckerman D, Och FJ, Caskey CT, Venter JC, Telenti A.

Am J Hum Genet. 2017 Nov 2;101(5):700-715. doi: 10.1016/j.ajhg.2017.09.013.

25.

Human gene essentiality.

Bartha I, di Iulio J, Venter JC, Telenti A.

Nat Rev Genet. 2018 Jan;19(1):51-62. doi: 10.1038/nrg.2017.75. Epub 2017 Oct 30. Review.

PMID:
29082913
26.

Single-cell analysis identifies cellular markers of the HIV permissive cell.

Rato S, Rausell A, Muñoz M, Telenti A, Ciuffi A.

PLoS Pathog. 2017 Oct 26;13(10):e1006678. doi: 10.1371/journal.ppat.1006678. eCollection 2017 Oct.

27.

Correction: Gustafson et al., Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree. Genes 2017, 8, 210.

Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer KA, Ayyagari R.

Genes (Basel). 2017 Oct 23;8(10). pii: E286. doi: 10.3390/genes8100286.

28.

New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude.

Stobdan T, Akbari A, Azad P, Zhou D, Poulsen O, Appenzeller O, Gonzales GF, Telenti A, Wong EHM, Saini S, Kirkness EF, Venter JC, Bafna V, Haddad GG.

Mol Biol Evol. 2017 Dec 1;34(12):3154-3168. doi: 10.1093/molbev/msx239.

29.

Fine population structure analysis method for genomes of many.

Pan X, Wang Y, Wong EHM, Telenti A, Venter JC, Jin L.

Sci Rep. 2017 Oct 3;7(1):12608. doi: 10.1038/s41598-017-12319-1.

30.

Identification of individuals by trait prediction using whole-genome sequencing data.

Lippert C, Sabatini R, Maher MC, Kang EY, Lee S, Arikan O, Harley A, Bernal A, Garst P, Lavrenko V, Yocum K, Wong T, Zhu M, Yang WY, Chang C, Lu T, Lee CWH, Hicks B, Ramakrishnan S, Tang H, Xie C, Piper J, Brewerton S, Turpaz Y, Telenti A, Roby RK, Och FJ, Venter JC.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10166-10171. doi: 10.1073/pnas.1711125114. Epub 2017 Sep 5. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 2;:.

31.

Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree.

Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer KA, Ayyagari R.

Genes (Basel). 2017 Aug 24;8(9). pii: E210. doi: 10.3390/genes8090210. Erratum in: Genes (Basel). 2017 Oct 23;8(10 ):.

32.

Hepatitis E virus as a cause of acute hepatitis acquired in Switzerland.

Fraga M, Doerig C, Moulin H, Bihl F, Brunner F, Müllhaupt B, Ripellino P, Semela D, Stickel F, Terziroli Beretta-Piccoli B, Aubert V, Telenti A, Greub G, Sahli R, Moradpour D.

Liver Int. 2018 Apr;38(4):619-626. doi: 10.1111/liv.13557. Epub 2017 Sep 7.

33.

Severe viral respiratory infections in children with IFIH1 loss-of-function mutations.

Asgari S, Schlapbach LJ, Anchisi S, Hammer C, Bartha I, Junier T, Mottet-Osman G, Posfay-Barbe KM, Longchamp D, Stocker M, Cordey S, Kaiser L, Riedel T, Kenna T, Long D, Schibler A, Telenti A, Tapparel C, McLaren PJ, Garcin D, Fellay J.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8342-8347. doi: 10.1073/pnas.1704259114. Epub 2017 Jul 17.

34.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.

Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064. doi: 10.1073/pnas.1707945114. Epub 2017 Jul 3.

35.

The blood DNA virome in 8,000 humans.

Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A.

PLoS Pathog. 2017 Mar 22;13(3):e1006292. doi: 10.1371/journal.ppat.1006292. eCollection 2017 Mar.

36.

Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.

Long T, Hicks M, Yu HC, Biggs WH, Kirkness EF, Menni C, Zierer J, Small KS, Mangino M, Messier H, Brewerton S, Turpaz Y, Perkins BA, Evans AM, Miller LA, Guo L, Caskey CT, Schork NJ, Garner C, Spector TD, Venter JC, Telenti A.

Nat Genet. 2017 Apr;49(4):568-578. doi: 10.1038/ng.3809. Epub 2017 Mar 6.

PMID:
28263315
37.

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control.

Bartha I, McLaren PJ, Brumme C, Harrigan R, Telenti A, Fellay J.

PLoS Comput Biol. 2017 Feb 9;13(2):e1005339. doi: 10.1371/journal.pcbi.1005339. eCollection 2017 Feb.

38.

The Human Microbiome and Cancer.

Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE.

Cancer Prev Res (Phila). 2017 Apr;10(4):226-234. doi: 10.1158/1940-6207.CAPR-16-0249. Epub 2017 Jan 17. Review.

39.

PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS.

Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp SC, Shimizu C, Burns JC, Wright VJ, Png E, Hibberd ML, Lloyd DD, Yang H, Telenti A, Bloss CS, Fox D, Lauter K, Ohno-Machado L.

Bioinformatics. 2017 Mar 15;33(6):871-878. doi: 10.1093/bioinformatics/btw758.

40.

Exploring viral infection using single-cell sequencing.

Rato S, Golumbeanu M, Telenti A, Ciuffi A.

Virus Res. 2017 Jul 15;239:55-68. doi: 10.1016/j.virusres.2016.10.016. Epub 2016 Nov 2. Review.

41.

Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing.

Branham K, Matsui H, Biswas P, Guru AA, Hicks M, Suk JJ, Li H, Jakubosky D, Long T, Telenti A, Nariai N, Heckenlively JR, Frazer KA, Sieving PA, Ayyagari R.

Physiol Genomics. 2016 Dec 1;48(12):922-927. doi: 10.1152/physiolgenomics.00101.2016. Epub 2016 Oct 7.

42.

Deep sequencing of 10,000 human genomes.

Telenti A, Pierce LC, Biggs WH, di Iulio J, Wong EH, Fabani MM, Kirkness EF, Moustafa A, Shah N, Xie C, Brewerton SC, Bulsara N, Garner C, Metzker G, Sandoval E, Perkins BA, Och FJ, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11901-11906. Epub 2016 Oct 4.

43.

Protecting genomic data analytics in the cloud: state of the art and opportunities.

Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, Ohno-Machado L.

BMC Med Genomics. 2016 Oct 13;9(1):63.

44.

Identification of Siglec-1 null individuals infected with HIV-1.

Martinez-Picado J, McLaren PJ, Erkizia I, Martin MP, Benet S, Rotger M, Dalmau J, Ouchi D, Wolinsky SM, Penugonda S, Günthard HF, Fellay J, Carrington M, Izquierdo-Useros N, Telenti A.

Nat Commun. 2016 Aug 11;7:12412. doi: 10.1038/ncomms12412.

45.

Innate immune defects in HIV permissive cell lines.

Rausell A, Muñoz M, Martinez R, Roger T, Telenti A, Ciuffi A.

Retrovirology. 2016 Jun 27;13(1):43. doi: 10.1186/s12977-016-0275-8.

46.

Dynamics of an Aging Genome.

Telenti A, Perkins BA, Venter JC.

Cell Metab. 2016 Jun 14;23(6):949-950. doi: 10.1016/j.cmet.2016.06.002.

47.

Identifying Adverse Effects of HIV Drug Treatment and Associated Sentiments Using Twitter.

Adrover C, Bodnar T, Huang Z, Telenti A, Salathé M.

JMIR Public Health Surveill. 2015 Jul 27;1(2):e7. doi: 10.2196/publichealth.4488. eCollection 2015 Jul-Dec.

48.

Single-Cell Genomics for Virology.

Ciuffi A, Rato S, Telenti A.

Viruses. 2016 May 4;8(5). pii: E123. doi: 10.3390/v8050123. Review.

49.

Guanylate Binding Protein (GBP) 5 Is an Interferon-Inducible Inhibitor of HIV-1 Infectivity.

Krapp C, Hotter D, Gawanbacht A, McLaren PJ, Kluge SF, Stürzel CM, Mack K, Reith E, Engelhart S, Ciuffi A, Hornung V, Sauter D, Telenti A, Kirchhoff F.

Cell Host Microbe. 2016 Apr 13;19(4):504-14. doi: 10.1016/j.chom.2016.02.019. Epub 2016 Mar 17.

50.

Privacy-preserving genomic testing in the clinic: a model using HIV treatment.

McLaren PJ, Raisaro JL, Aouri M, Rotger M, Ayday E, Bartha I, Delgado MB, Vallet Y, Günthard HF, Cavassini M, Furrer H, Doco-Lecompte T, Marzolini C, Schmid P, Di Benedetto C, Decosterd LA, Fellay J, Hubaux JP, Telenti A.

Genet Med. 2016 Aug;18(8):814-22. doi: 10.1038/gim.2015.167. Epub 2016 Jan 14.

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