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Items: 19


A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

Bik EM, Bird SW, Bustamante JP, Leon LE, Nieto PA, Addae K, Alegría-Mera V, Bravo C, Bravo D, Cardenas JP, Carson GA, Caughey A, Covarrubias PC, Pérez-Donoso J, Gass G, Gupta SL, Harman K, Hongo DMB, Jiménez JC, Kraal L, Melis-Arcos F, Morales EH, Morton A, Navas CF, Nuñez H, Olivares E, Órdenes-Aenishanslins N, Ossandon FJ, Phan R, Pino R, Soto-Liebe K, Varas I, Vera-Wolf P, Walton NA, Almonacid DE, Goddard AD, Ugalde JA, Zneimer S, Richman J, Apte ZS.

PLoS One. 2019 May 1;14(5):e0215945. doi: 10.1371/journal.pone.0215945. eCollection 2019.


Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Almonacid DE, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JP, Bik EM, Goddard AD, Richman J, Apte ZS.

PLoS One. 2019 Feb 12;14(2):e0212474. doi: 10.1371/journal.pone.0212474. eCollection 2019.


The role of a sequencing-based clinical intestinal screening test in patients at high-risk for Clostridium difficile and other pathogens: a case report.

Hitschfeld M, Tovar E, Gupta S, Bik EM, Palmer C, Hoaglin MC, Almonacid DE, Richman J, Apte ZS.

J Med Case Rep. 2019 Jan 15;13(1):9. doi: 10.1186/s13256-018-1919-1.


Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs.

Gupta S, Palmer C, Bik EM, Cardenas JP, Nuñez H, Kraal L, Bird SW, Bowers J, Smith A, Walton NA, Goddard AD, Almonacid DE, Zneimer S, Richman J, Apte ZS.

Front Public Health. 2018 Apr 9;6:77. doi: 10.3389/fpubh.2018.00077. eCollection 2018. Review.


Novel Insights for Inhibiting Mutant Heterodimer IDH1wt-R132H in Cancer: An In-Silico Approach.

Juritz EI, Bascur JP, Almonacid DE, González-Nilo FD.

Mol Diagn Ther. 2018 Jun;22(3):369-380. doi: 10.1007/s40291-018-0331-2.


16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Almonacid DE, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JP, Bik EM, Goddard AD, Richman J, Apte ZS.

PLoS One. 2017 May 3;12(5):e0176555. doi: 10.1371/journal.pone.0176555. eCollection 2017. Erratum in: PLoS One. 2019 Feb 12;14(2):e0212474.


Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers.

Márquez-Miranda V, Camarada MB, Araya-Durán I, Varas-Concha I, Almonacid DE, González-Nilo FD.

PLoS One. 2015 Sep 18;10(9):e0138392. doi: 10.1371/journal.pone.0138392. eCollection 2015.


A transient receptor potential ion channel in Chlamydomonas shares key features with sensory transduction-associated TRP channels in mammals.

Arias-Darraz L, Cabezas D, Colenso CK, Alegría-Arcos M, Bravo-Moraga F, Varas-Concha I, Almonacid DE, Madrid R, Brauchi S.

Plant Cell. 2015 Jan;27(1):177-88. doi: 10.1105/tpc.114.131862. Epub 2015 Jan 16.


Participation of the Salmonella OmpD porin in the infection of RAW264.7 macrophages and BALB/c mice.

Ipinza F, Collao B, Monsalva D, Bustamante VH, Luraschi R, Alegría-Arcos M, Almonacid DE, Aguayo D, Calderón IL, Gil F, Santiviago CA, Morales EH, Calva E, Saavedra CP.

PLoS One. 2014 Oct 31;9(10):e111062. doi: 10.1371/journal.pone.0111062. eCollection 2014.


The Structure-Function Linkage Database.

Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.


Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.

Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):E1196-202. doi: 10.1073/pnas.1300632110. Epub 2013 Mar 14.


MACiE: exploring the diversity of biochemical reactions.

Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3.


Toward mechanistic classification of enzyme functions.

Almonacid DE, Babbitt PC.

Curr Opin Chem Biol. 2011 Jun;15(3):435-42. doi: 10.1016/j.cbpa.2011.03.008. Epub 2011 Apr 12. Review.


Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000700. doi: 10.1371/journal.pcbi.1000700.


The chemistry of protein catalysis.

Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.

J Mol Biol. 2007 Oct 5;372(5):1261-77. Epub 2007 Aug 2.


Using reaction mechanism to measure enzyme similarity.

O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB.

J Mol Biol. 2007 May 18;368(5):1484-99. Epub 2007 Mar 2.


A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes.

Matamala AR, Almonacid DE, Figueroa MF, Martínez-Oyanedel J, Bunster MC.

J Comput Chem. 2007 May;28(7):1200-7.


MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D515-20. Epub 2006 Nov 1.


MACiE: a database of enzyme reaction mechanisms.

Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB.

Bioinformatics. 2005 Dec 1;21(23):4315-6. Epub 2005 Sep 27.

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