| 2024 |
| 119. Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. “DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum." Nucleic Acids Research preprint. 2024 Jul 5:gkae585. doi: 10.1093/nar/gkae585. (Supplement) |  |
| 2023 |
| 118. Singh MK, Bonnell VA, Da Silva IT, Santiago VF, Moraes MS, Adderley J, Doerig C, Palmisano G, Llinás M, Garcia CRS. “Plasmodium falciparum MORC protein modulates gene expression through interaction with heterochromatin." bioRxiv preprint. 2023 doi: https://doi.org/10.1101/2023.09.11.557196. (Also see THIS paper on PfMORC from the lab of Karine Le Roch) | |
| 117. Hagenah LM, Dhingra SK, Small-Saunders JL, Qahash T, Willems A, Schindler KA, Rangel GW, Gil-Iturbe E, Kim J, Akhundova E, Yeo T, Okombo J, Mancia F, Quick M, Roepe PD, Llinás M, Fidock DA. “Additional PfCRT mutations driven by selective pressure for improved fitness can result in the loss of piperaquine resistance and altered Plasmodium falciparum physiology." mBio. 2023 Dec 7:e0183223. doi: 10.1128/mbio.01832-23. (Supplement) | |
| 116. Nair SC, Munro JT, Mann A, Llinás M, Prigge ST. “The mitochondrion of Plasmodium falciparum is required for cellular acetyl-CoA metabolism and protein acetylation." PNAS. 2023 Apr 25;120(17):e2210929120. doi: 10.1073/pnas.2210929120. Epub 2023 Apr 17. (Supplement) | |
| 115. Butler JH, Painter HJ, Bremers EK, Krai P, Llinás M, Cassera MB. “Cripowellins Pause Plasmodium falciparum Intraerythrocytic Development at the Ring Stage." Molecules. 2023 Mar 13;28(6):2600. doi: 10.3390/molecules28062600. | |
| 114. Istvan ES, Guerra F, Abraham M, Huang KS, Rocamora F, Zhao H, Xu L, Pasaje C, Kumpornsin K, Luth MR, Cui H, Yang T, Palomo Diaz S, Gomez-Lorenzo MG, Qahash T, Mittal N, Ottilie S, Niles J, Lee MCS, Llinas M, Kato N, Okombo J, Fidock DA, Schimmel P, Gamo FJ, Goldberg DE, Winzeler EA. “Cytoplasmic isoleucyl tRNA synthetase as an attractive multistage antimalarial drug target.” Science Translational Medicine. 2023 Mar 8;15(686):eadc9249. doi: 10.1126/scitranslmed.adc9249. Epub 2023 Mar 8. (Supplement) | |
| 113. Komazin G, Rizk AA, Armbruster KM, Bonnell VA, Llinás M, Meredith TC. “A Copper-Responsive Two-Component System Governs Lipoprotein Remodeling in Listeria monocytogenes.” Journal of Bacteriology. 2023 Jan 26;205(1):e0039022. doi: 10.1128/jb.00390-22. Epub 2023 Jan 9. | |
| 2022 |
| 112. Okombo J, Mok S, Qahash T, Yeo T, Bath J, Orchard LM, Owens E, Koo I, Albert I, Llinás M, Fidock DA. “Piperaquine-resistant PfCRT mutations differentially impact drug transport, hemoglobin catabolism and parasite physiology in Plasmodium falciparum asexual blood stages.” PLoS Pathogens. 2022 Oct 28;18(10):e1010926. doi: 10.1371/journal.ppat.1010926. eCollection 2022 Oct. (Supplement) | |
| 111. Arendse LB, Murithi JM, Qahash T, Pasaje CFA, Godoy LC, Dey S, Gibhard L, Ghidelli-Disse S, Drewes G, Bantscheff M, Lafuente-Monasterio MJ, Fienberg S, Wambua L, Gachuhi S, Coertzen D, van der Watt M, Reader J, Aswat AS, Erlank E, Venter N, Mittal N, Luth MR, Ottilie S, Winzeler EA, Koekemoer LL, Birkholtz LM, Niles JC, Llinás M, Fidock DA, Chibale K. “ The anticancer human mTOR inhibitor sapanisertib potently inhibits multiple Plasmodium kinases and life cycle stages. ” Science Translational Medicine. 2022 Oct 19;14(667):eabo7219. doi: 10.1126/scitranslmed.abo7219. Epub 2022 Oct 19. (Supplement) (Read PSU Press Release Summary) | |
| 110. Russell TJ, De Silva EK, Crowley VM, Shaw-Saliba K, Dube N, Josling G, Pasaje CFA, Kouskoumvekaki I, Panagiotou G, Niles JC, Jacobs-Lorena M, Denise Okafor C, Gamo FJ, Llinás M. “Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites. ” PLoS Pathogens. 2022 Oct 12;18(10):e1010887. doi: 10.1371/journal.ppat.1010887. eCollection 2022 Oct. (Supplement) | |
| 109. de Vries LE, Jansen PAM, Barcelo C, Munro J, Verhoef JMJ, Pasaje CFA, Rubiano K, Striepen J, Abla N, Berning L, Bolscher JM, Demarta-Gatsi C, Henderson RWM, Huijs T, Koolen KMJ, Tumwebaze PK, Yeo T, Aguiar ACC, Angulo-Barturen I, Churchyard A, Baum J, Fernández BC, Fuchs A, Gamo FJ, Guido RVC, Jiménez-Diaz MB, Pereira DB, Rochford R, Roesch C, Sanz LM, Trevitt G, Witkowski B, Wittlin S, Cooper RA, Rosenthal PJ, Sauerwein RW, Schalkwijk J, Hermkens PHH, Bonnert RV, Campo B, Fidock DA, Llinás M, Niles JC, Kooij TWA, Dechering KJ. “Preclinical characterization and target validation of the antimalarial pantothenamide MMV693183. ” Nature Communications. 2022 Apr 20;13(1):2158. doi: 10.1038/s41467-022-29688-5. (Supplement) | |
| 108. Campelo Morillo RA, Tong X, Xie W, Abel S, Orchard LM, Daher W, Patel DJ, Llinás M, Le Roch KG, Kafsack BFC. “The transcriptional regulator HDP1 controls expansion of the inner membrane complex during early sexual differentiation of malaria parasites.” Nature Microbiology. 2022 Feb;7(2):289-299. doi: 10.1038/s41564-021-01045-0. Epub 2022 Jan 27. (See News & Views by Kim Williamson) | |
| 2021 |
| 107. Eya’ane Meva F, Prior TJ, Evans DJ, Shah S, Tamngwa CF, Belengue HGL, Mang RE, Munro J, Qahash T, Llinás M. “Anti-inflammation and antimalarial profile of 5-pyridin-2-yl-1H-[1,2,4]triazole-3-carboxylic acid ethyl ester as a low molecular intermediate for hybrid drug synthesis. ” Research on Chemical Intermediates. 2021 October 28. | |
| 106. Niemand J, van Biljon R, van der Watt M, van Heerden A, Reader J, van Wyk R, Orchard L, Chibale K, Llinás M, Birkholtz LM. “Chemogenomic Fingerprints Associated with Stage-Specific Gametocytocidal Compound Action against Human Malaria Parasites. ” ACS Infectious Diseases. 2021 Sep 27. doi: 10.1021/acsinfecdis.1c00373. (Supplement) | |
| 105. Tintó-Font E, Michel-Todó L, Russell TJ, Casas-Vila N, Conway DJ, Bozdech Z, Llinás M, Cortés A. “A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures. ” Nature Microbiology. 2021 Sep;6(9):1163-1174. doi: 10.1038/s41564-021-00940-w. Epub 2021 Aug 16. (See News & Views by Vandana Thathy and David Fidock) (Read PSU Press Release Summary) | |
| 104. Summers RL, Pasaje CFA, Pisco JP, Striepen J, Luth MR, Kumpornsin K, Carpenter EF, Munro JT, Lin D, Plater A, Punekar AS, Shepherd AM, Shepherd SM, Vanaerschot M, Murithi JM, Rubiano K, Akidil A, Ottilie S, Mittal N, Dilmore AH, Won M, Mandt REK, McGowen K, Owen E, Walpole C, Llinás M, Lee MCS, Winzeler EA, Fidock DA, Gilbert IH, Wirth DF, Niles JC, Baragaña B, Lukens AK. “Chemogenomics identifies acetyl-coenzyme A synthetase as a target for malaria treatment and prevention.” Cell Chemical Biology. 2021 Jul 28:S2451-9456(21)00350-0. doi: 10.1016/j.chembiol.2021.07.010. (Supplement) | |
| 103. Rangel GW, Llinás M. “Re-Envisioning Anti-Apicomplexan Parasite Drug Discovery Approaches.” Frontiers in Cellular and Infection Microbiology. 2021 Jun 11;11:691121. doi: 10.3389/fcimb.2021.691121. eCollection 2021. | |
| 102. Llinás M. “The Kringle of Life.” Protein Journal. 2021 Aug;40(4):454-456. doi: 10.1007/s10930-021-10009-6. Epub 2021 Jun 16. (Full Protein Journal issue dedicated to my late father - Miguel Llinás) | |
| 101. Connacher J, Josling GA, Orchard LM, Reader J, Llinás M, Birkholtz LM. “H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum.” Epigenetics & Chromatin. 2021 Apr 1;14(1):19. doi: 10.1186/s13072-021-00393-9. (Supplement) | |
| 100. Rocamora F, Gupta P, Istvan ES, Luth MR, Carpenter EF, Kümpornsin K, Sasaki E, Calla J, Mittal N, Carolino K, Owen E, Llinás M, Ottilie S, Goldberg DR, Lee MCS, Winzeler EW. “PfMFR3: A Multidrug-Resistant Modulator in Plasmodium falciparum.” ACS Infectious Diseases. 2021 Mar 14. doi: 10.1021/acsinfecdis.0c00676. | |
| 99. Yang T, Ottilie S, Istvan ES, Godinez-Macias KP, Lukens AK, Baragaña B, Campo B, Walpole C, Niles JC, Chibale K, Dechering KJ, Llinás M, Lee MCS, Kato N, Wyllie S, McNamara CW, Gamo FJ, Burrows J, Fidock DA, Goldberg DE, Gilbert IH, Wirth DF, Winzeler EA, Malaria Drug Accelerator Consortium. “MalDA, Accelerating Malaria Drug Discovery.” Trends in Parasitology. 2021 Feb 26;S1471-4922(21)00012-X. doi: 10.1016/j.pt.2021.01.009. | |
| 98. Singh S, Santos JM, Orchard LM, Yamada N, van Biljon R, Painter HJ, Mahony S, Llinás M. “The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation.” Molecular Microbiology. 2020 Dec 25. doi: 10.1111/mmi.14676. (Supplement) | |
| 97. Painter HJ, Morrisey JM, Mather MW, Orchard LM, Luck C, Smilkstein MJ, Riscoe MK, Vaidya AB, Llinás M. “Atypical Molecular Basis for Drug Resistance to Mitochondrial Function Inhibitors in Plasmodium falciparum.” Antimicrobial Agents Chemotherapy. 2021 Feb 17;65(3):e02143-20. doi: 10.1128/AAC.02143-20. (Supplement) | |
| 96. Mok S, Stokes BH, Gnädig NF, Ross LS, Yeo T, Amaratunga C, Allman E, Solyakov L, Bottrill AR, Tripathi J, Fairhurst RM, Llinás M, Bozdech Z, Tobin AB, Fidock DA. “Artemisinin-resistant K13 mutations rewire Plasmodium falciparum's intra-erythrocytic metabolic program to enhance survival.” Nature Communications. 2021 Jan 22;12(1):530. doi: 10.1038/s41467-020-20805-w. (Supplement) | |
| 95. Reader J, van der Watt ME, Taylor D, Le Manach C, Mittal N, Ottilie S, Theron A, Moyo P, Erlank E, Nardini L, Venter N, Lauterbach S, Bezuidenhout B, Horatscheck A, van Heerden A, Spillman NJ, Cowell AN, Connacher J, Opperman D, Orchard LM, Llinás M, Istvan ES, Goldberg DE, Boyle GA, Calvo D, Mancama D, Coetzer TL, Winzeler EA, Duffy J, Koekemoer LL, Basarab G, Chibale K, Birkholtz LM. “Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box.” Nature Communications. 2021 Jan 11;12(1):269. doi: 10.1038/s41467-020-20629-8. (Supplement) | |
| 2020 |
| 94. Andrade CM, Fleckenstein H, Thomson-Luque R, Doumbo S, Lima NF, Anderson C, Hibbert J, Hopp CS, Tran TM, Li S, Niangaly M, Cisse H, Doumtabe D, Skinner J, Sturdevant D, Ricklefs S, Virtaneva K, Asghar M, Homann MV, Turner L, Martins J, Allman EL, N'Dri ME, Winkler V, Llinás M, Lavazec C, Martens C, Färnert A, Kayentao K, Ongoiba A, Lavstsen T, Osório NS, Otto TD, Recker M, Traore B, Crompton PD, Portugal S. “Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season.” Nature Medicine. 2020 Oct 26. doi: 10.1038/s41591-020-1084-0. (See News & Views by Philip Bejon) (Read PSU Press Release Summary) (Read NY Times Article) | |
| 93. Shafik SH, Cobbold SA, Barkat K, Richards SN, Lancaster NS, Llinás M, Hogg SJ, Summers RL, McConville MJ, Martin RE. “The natural function of the malaria parasite's chloroquine resistance transporter.” Nature Communications. 2020 Aug 6;11(1):3922. doi: 10.1038/s41467-020-17781-6. (Supplement) | |
| 92. Chappell L, Ross P, Orchard L, Russell TJ, Otto TD, Berriman M, Rayner JC, Llinás M. “Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq.” BMC Genomics. 2020 Jun 8;21(1):395. doi: 10.1186/s12864-020-06787-5. (Supplement) (See News & Analysis by Johanna Hoshizaki and Marcus Lee) | |
| 91. Vanaerschot M, Murithi JM, et al. “Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity.” Cell Chemical Biology. 2020 Apr 16:S2451-9456(20)30115-X. doi: 10.1016/j.chembiol.2020.04.001. (Supplement) (Supplementary Table) | |
| 90. Ling L, Mulaka M, Munro J, Dass S, Mather MW, Riscoe MK, Llinás M, Zhou J, Ke H. “Genetic ablation of the mitoribosome in the malaria parasite Plasmodium falciparum sensitizes it to antimalarials that target mitochondrial functions.” Journal of Biological Chemistry. 2020 May 22;295(21):7235-7248. doi: 10.1074/jbc.RA120.012646. Epub 2020 Apr 9. (Supplement) | |
| 89. Josling GA, Russell TJ, Venezia J, Orchard L, van Biljon R, Painter HJ, Llinás M. “Dissecting the role of PfAP2-G in malaria gametocytogenesis.” Nature Communications. 2020 Mar 20;11(1):1503. doi: 10.1038/s41467-020-15026-0. (Supplement) | |
| 88. Akkaya M, Bansal A, Sheehan PW, Pena M, Molina-Cruz A, Orchard LM, Cimperman CK, Qi CF, Ross P, Yazew T, Sturdevant D, Anzick SL, Thiruvengadam G, Otto TD, Billker O, Llinás M, Miller LH, Pierce SK. “A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity.” Science Advances. 2020 Feb 5;6(6):eaaw6957. doi: 10.1126/sciadv.aaw6957. (Supplement) | |
| 2019 |
| 87. Murithi JM, Owen ES, Istvan ES, Lee MCS, Ottilie S, Chibale K, Goldberg DE, Winzeler EA, Llinás M, Fidock DA, Vanaerschot M. “Combining Stage Specificity and Metabolomic Profiling to Advance Antimalarial Drug Discovery.” Cell Chemical Biology. 2019 Nov 29. pii: S2451-9456(19)30391-5. doi: 10.1016/j.chembiol.2019.11.009. (Supplement) (Metabolomics data Excel.xls) | |
| 86. van Biljon R, van Wyk R, Painter HJ, Orchard L, Reader J, Niemand J, Llinás M, Birkholtz LM. “Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation.” BMC Genomics. 2019 Dec 3;20(1):920. doi: 10.1186/s12864-019-6322-9. (Supplement) | |
| 85. Clements RL, Streva V, Dumoulin P, Huang W, Owens E, Raj DK, Burleigh B, Llinás M, Winzeler EA, Zhang Q, Dvorin JD. “A novel antiparasitic compound kills ring-stage Plasmodium falciparum and retains activity against artemisinin-resistant parasites.” Journal of Infectious Diseases. 2019 Oct 16. pii: jiz534. doi: 10.1093/infdis/jiz534. (Supplement) | |
| 84. Ngwa CJ, Kiesow MJ, Orchard LM, Farrukh A, Llinás M, Pradel G. “The G9a Histone Methyltransferase Inhibitor BIX-01294 Modulates Gene Expression during Plasmodium falciparum Gametocyte Development and Transmission.” International Journal of Molecular Sciences. 2019 Oct 14;20(20). pii: E5087. doi: 10.3390/ijms20205087. | |
| 83. Schalkwijk J, Allman EL, Jansen PAM, de Vries LE, et al., Sauerwein RW, Llinás M, Hermkens PHH, Dechering KJ. “Antimalarial pantothenamide metabolites target acetyl-coenzyme A biosynthesis in Plasmodium falciparum. ” Science Translational Medicine. 2019 Sep 18;11(510). pii: eaas9917. doi: 10.1126/scitranslmed.aas9917. (Supplement) (Read PSU Press Release Summary) (Nijmegen Press Release) | |
| 82. Lee MCS, Lindner SE, Lopez-Rubio JJ, Llinás M. “Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium.” Briefings in Functional Genomics. 2019 Jul 29. pii: elz012. doi: 10.1093/bfgp/elz012. | |
| 81. Josling GA, Llinás M. “Commitment Isn’t for Everyone. ” Trends in Parasitology. 2019 Apr 30. pii: S1471-4922(19)30065-0. doi: 10.1016/j.pt.2019.03.012. | |
| 80. Istvan ES, Das S, Bhatnagar S, Beck JR, Owen E, Llinas M, Ganesan SM, Niles JC, Winzeler E, Vaidya AB, Goldberg DE. “Plasmodium Niemann-Pick type C1-related protein is a druggable target required for parasite membrane homeostasis. ” Elife. 2019 Mar 19;8. pii: e40529. doi: 10.7554/eLife.40529. (Supplement) | |
| 2018 |
| 79. Leopold SJ, Ghose A, Allman EL, Kingston HWF, Hossain A, Dutta AK, Plewes K, Chotivanich K, Day NPJ, Tarning J, Winterberg M, White NJ, Llinás M, Dondorp AM. “Identifying the components of acidosis in patients with severe P. falciparum malaria using metabolomics. ” The Journal of Infectious Diseases. 2018 Dec 19. doi: 10.1093/infdis/jiy727. (Supplement) | |
| 78. Antonova-Koch Y, et al. “Open-source discovery of chemical leads for next-generation chemoprotective antimalarials.” Science. 2018 December 07 dos: 10.1126/science.aat9446. (Supplement) (Read Summary in Science) (Read Perspective in Science) (Read PSU Press Release Summary) | |
| 77. van Biljon R, Niemand J, van Wyk R, Clark K, Verlinden B, Abrie C, von Grüning H, Smidt W, Smit A, Reader J, Painter H, Llinás M, Doerig C, Birkholtz LM. “Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites. ” Scientific Reports. 2018 Nov 8;8(1):16581. doi: 10.1038/s41598-018-34964-w. (Supplement) | |
| 76. Aronson MR, Simonson AW, Orchard LM, Llinás M, Medina SH. “Lipopeptisomes: Anticancer peptide-assembled particles for fusolytic oncotherapy.” Acta Biomaterialia. 2018 October 15;80:269-277. doi: 10.1016/j.actbio.2018.09.025. Epub 2018 Sep 19. | |
| 75. Shukla A, Olszewski KL, Llinás M, Rommereim LM, Fox BA, Bzik DJ, Xia D, Wastling J, Beiting D, Roos DS, Shanmugam D. “Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii.” International Journal of Parasitology. 2018 Aug 31. pii: S0020-7519(18)30190-5. (Supplement) | |
| 74. Lee AH, Dhingra SK, Lewis IA, Singh MK, Siriwardana A, Dalal S, Rubiano K, Klein MS, Baska KS, Krishna S, Klemba M, Roepe PD, Llinás M, Garcia CRS, Fidock DA. “Evidence for Regulation of Hemoglobin Metabolism and Intracellular Ionic Flux by the Plasmodium falciparum Chloroquine Resistance Transporter.” Scientific Reports. 2018 Sep 11;8(1):13578. (Supplement) | |
| 73. Bennink S, von Bohl A, Ngwa CJ, Henschel L, Kuehn A, Pilch N, Weißbach T, Rosinski AN, Scheuermayer M, Repnik U, Przyborski JM, Minns AM, Orchard LM, Griffiths G, Lindner SE, Llinás M, Pradel G. “A seven-helix protein constitutes stress granules crucial for regulating translation during human-to-mosquito transmission of Plasmodium falciparum.” PLoS Pathogens. 2018 8 Aug 22;14(8):e1007249. (Supplement) | |
| 72. Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. “Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development.” Nature Communications. 2018 Jul 9;9(1):2656. (Supplement) (Read Nature Behind the Paper blog Summary) | |
| 71. Josling GA, Williamson KC, Llinás M. “Regulation of Sexual Commitment and Gametocytogenesis in Malaria Parasites.” Annual Review of Microbiology. 2018 Sep 8;72:501-519. | |
| 70. Cowell AN, et al. “Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics.” Science. 2018 January 12. doi: 10.1126/science.aan4472. (Supplement) (Summary Perspective from Science) (Read PSU Press Release Summary) | |
| 69. Gisselberg JE, Herrera Z, Orchard LM, Llinás M, Yeh E. “Specific Inhibition of the Bifunctional Farnesyl/Geranylgeranyl Diphosphate Synthase in Malaria Parasites via a New Small-Molecule Binding Site.” Cell Chemical Biology. 2018 Feb 15;25(2):185-193.e5.(Supplement) | |
| 2017 |
| 68. Llinás M. “Less Lipid, More Commitment.” Cell. 2017 Dec 14;171(7):1474-1476. | |
| 67. Malaria Eradication Research Agenda (malERA) Refresh Consultative Panel on Basic Science and Enabling Technologies. “malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication.” PLoS Medicine. 2017 Nov 30;14(11):e1002451.(Link to the full collection malERA reports) (Read PSU Press Release Summary) | |
| 66. Turnbull LB, Siwo GH, Button-Simons KA, Tan A, Checkley LA, Painter HJ, Llinás M, Ferdig MT. “Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite.” PLoS One. 2017 Nov 7;12(11):e0187595.(Supplement) | |
| 65. Ngwa CJ, Kiesow MJ, Papst O, Orchard LM, Filarsky M, Rosinski AN, Voss TS, Llinás M, Pradel G. “Transcriptional profiling defines histone acetylation as a regulator of gene expression during human-to-mosquito transmission of the malaria parasite Plasmodium falciparum.” Frontiers in Cellular and Infection Microbiology. 2017 July 24; doi:10.3389/fcimb.2017.00320. (Supplement) | |
| 64. Mancio-Silva L, Slavic K, Ruivo MTG, Grosso AR, Modrzynska KK, Vera IM, Sales-Dias J, Gomes AR, McPherson CR, Crozet P, Adamo M, Baena-Gonzalez E, Tewari R, Llinás M, Billker O, Mota MM. “Nutrient sensing modulates malaria parasite virulence.” Nature. 2017 July 05;doi:10.1038/nature23009. (Supplement) (Spotlight in Trends in Parasitology) (Read PSU Press Release Summary) | |
| 63. Santos JM, Josling G, Ross P, Joshi P, Orchard L, Campbell T, Schieler A, Cristea IM, Llinás M. “Red blood cell invasion by the malaria parasite is coordinated by the PfAP2-I transcription factor.” Cell Host and Microbe. 2017 Jun 14;21(6):731-741.e10. doi: 10.1016/j.chom.2017.05.006. (Supplement) (Read PSU Press Release Summary) (Read Summary from Voice of America) | |
| 62. Painter HJ, Carrasquilla M, Llinás M. “Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum.” Genome Research. 2017 Apr 17. doi: 10.1101/gr.217356.116. (Supplement) | |
| 61. Coetzee N, Sidoli S, van Biljon R, Painter H, Llinás M, Garcia BA, Birkholtz LM. “Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites.” Scientific Reports. 2017 April 04;7(1):607. (Supplement) | |
| 2016 |
| 60. Gabryszewski SJ, Dhingra SK, Combrinck JM, Lewis IA, Callaghan PS, Hassett MR, Siriwardana A, Henrich PP, Lee AH, Gnädig NF, Musset L, Llinás M, Egan TJ, Roepe PD, Fidock DA. “Evolution of Fitness Cost-Neutral Mutant PfCRT Conferring P. falciparum 4-Aminoquinoline Drug Resistance Is Accompanied by Altered Parasite Metabolism and Digestive Vacuole Physiology.” PLos Pathogens. 2016 Nov 10;12(11):e1005976. doi: 10.1371/journal.ppat.1005976.(Supplement) | |
| 59. Allman EL, Painter HJ, Samra J, Carrasquilla M, Llinás M. “Metabolomic Profiling of the Malaria Box Reveals Antimalarial Target Pathways.” Antimicrobial Agents and Chemotherapy. 2016 Aug 29; pii: AAC.01224-16. (Supplement) (Published back-to-back with THIS paper from Darren Creek and Malcolm McConville) | |
| 58. Van Voorhies WC et al. “Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.” PLoS Pathogens. 2016 Jul 28; 12(7):e1005763. (Supplement) | |
| 57. Shears MJ, MacRae JI, Mollard V, Goodman CD, Sturm A, Orchard LM, Llinás M, McConville MJ, Botté CY, McFadden GI. “Characterization of the Plasmodium falciparum and P. berghei glycerol 3-phosphate acyltransferase involved in FASII fatty acid utilization in the malaria parasite apicoplast.” Cellular Microbiology. 2016 Jun 20;doi: 10.1111/cmi.12633. (Supplement) | |
| 56. Cobbold SA, Santos JM, Ochoa A, Perlman DH, Llinás M. “Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite.” Scientific Reports. 2016 Jan 27;6:19722. (Supplement) | |
| 2015 |
| 55. Adjalley SH, Scanfeld D, Kozlowski E, Llinás M, Fidock DA. “Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1.” BMC Genomics. 2015 Dec 21;16(1):1090. | |
| 54. Cobbold SA, Llinás M, Kirk K. “Sequestration and metabolism of host cell arginine by the intraerythrocytic malaria parasite Plasmodium falciparum.” Cellular Microbiology. 2015 Dec 3;doi: 10.1111/cmi.12552. | |
| 53. Ochoa A, Storey JD, Llinás M, Singh M. “Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.” PLoS Computational Biology. 2015 Nov 17;11(11):e1004509. | |
| 52. Pulcini S, Staines HM, Lee AH, Shafik SH, Bouyer G, Moore CM, Daley DA, Hoke MJ, Altenhofen LM, Painter HJ, Mu J, Ferguson DJ, Llinás M, Martin RE, Fidock DA, Cooper RA, Krishna S. “Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, enlarge the parasite’s food vacuole and alter drug sensitivities.” Scientific Reports. 2015 Sep 30;5:14552. doi: 10.1038/srep14552. (Supplement) | |
| 51. Josling GA, Llinás M. “Sexual development in Plasmodium parasites: knowing when it’s time to commit.” Nature Reviews Microbiology 2015 Aug 14;13(9):573-87. | |
| 50. Ke H, Lewis IA, Morrisey JM, McLean KJ, Ganesan SM, Painter HJ, Mather MW, Jacobs-Lorena M, Llinás M, Vaidya AB. “Genetic investigation of tricarboxylic acid metabolism during the Plasmodium falciparum life cycle.” Cell Reports. 2015 Apr 7;11(1):164-74. doi: 10.1016/j.celrep.2015.03.011. Epub 2015 Apr 2.(Supplement) | |
| 49. Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R.”PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs.” Molecular Microbiology. 2015 Jun;96(6):1283-97. doi: 10.1111/mmi.13007. Epub 2015 Apr 16. (Supplement) | |
| 2014 |
| 48. Lisewski AM, Quiros JP, Ng CL, Adikesavan AK, Miura K, Putluri N, Eastman RT, Scanfeld D, Regenbogen SJ, Altenhofen L, Llinás M, Sreekumar A, Long C, Fidock DA, Lichtarge O.”Supergenomic Network Compression and the Discovery of EXP1 as a Glutathione Transferase Inhibited by Artesunate.” Cell. 2014 Aug 14;158(4):916-28. doi: 10.1016/j.cell.2014.07.011. | |
| 47. Coleman BI, Skillman KM, Jiang RH, Childs LM, Altenhofen LM, Ganter M, Leung Y, Goldowitz I, Kafsack BF, Marti M, Llinás M, Buckee CO, Duraisingh MT. “A Plasmodium falciparum Histone Deacetylase Regulates Antigenic Variation and Gametocyte Conversion.” Cell Host & Microbe. 2014 Aug 13;16(2):177-86. doi: 10.1016/j.chom.2014.06.014. (Read Highlight Summary from Cell Host & Microbe) | |
| 46. Oberstaller J, Pumpalova Y, Schieler A, Llinás M, Kissinger JC. “The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems.” Nucleic Acids Research. 2014 June 23. pii: gku500. | |
| 45. O’Hara JK, Kerwin LJ, Cobbold SA, Tai J, Bedell TA, Reider PJ, Llinás M. “Targeting NAD+ metabolism in the human nalaria parasite Plasmodium falciparum.” PLoS ONE. 2014 April; 9(4):e94061. (Supplement) | |
| 44. Kafsack BFC, Rovira-Graells N, Clark TG, Bancells C, Crowley VM, Campino SG, Williams AE, Drought LG, Kwiatkowski DP, Baker DA, Cortés A, Llinás M. “A transcriptional switch underlies commitment to sexual development in malaria parasites.” Nature. 2014 Mar 13;507(7491):248-52. (Supplement) (Read Highlight Summary in Current Biology) (Read Highlight Summary in Nature Reviews Microbiology) (Read Review on Sexual Commitment by Pietro Alano) (Read PSU Press Release Summary) | |
| 43. Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R, Kafsack BFC, Williams AE, Llinás M, Berriman M, Billker O, Waters AP. “A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium.” Nature. 2014 Mar 13;507 (7491):253-7. (Supplement) | |
| 42. Lewis IA, Wacker M, Olszewski KL, Cobbold SA, Baska KS, Tan A, Ferdig MT, Llinás M. “Metabolic QTL Analysis Links Chloroquine Resistance in Plasmodium falciparum to Impaired Hemoglobin Catabolism.” PLoS Genetics. 2014 Jan;10(1):e1004085. (Supplement) | |
| 41. Klein EY, Graham AL, Llinás M, Levin S. “Cross-reactive immune responses as primary drivers of malaria chronicity”. Infection & Immunity. 2014 Jan;82(1): 140-51. (Supplement) | |
| 2013 |
| 40. Cobbold SA, Vaughan AM, Lewis IA, Painter HJ, Camargo N, Perlman DH, Fishbaugher M, Healer J, Cowman AF, Kappe SH, Llinás M. “Kinetic Flux Profiling Elucidates Two Independent Acetyl-CoA Biosynthetic Pathways in Plasmodium falciparum”. J Biol Chem. 2013 Dec 20; 288(51): 36338-50. (Supplement) | |
| 39. Caudy AA, Guan Y, et al. “A new system for comparative functional genomics of Saccharomyces yeasts.” Genetics. 2013 Sep; 195(1): 275-87. | |
| 38. Mira-Martínez S, Rovira-Graells N, Crowley VM, Altenhofen LM, Llinás M, Cortés A. “Epigenetic switches in clag3 genes mediate blasticidin S resistance in malaria parasites”. Cellular Microbiology. 2013 Nov;15(11): 1913-23. | |
| 37. Carter LM, Kafsack B, Llinás M, Pollitt L, Reece S “Stress and Sex in Malaria Parasites: Why Does Commitment Vary?” Evolution, Medicine, and Public Health. 2013 June 4; 135-147. | |
| 36. Radke JB, Lucas O, De Silva EK, Ma Y, Sullivan WJ Jr, Weiss LM, Llinás M, White MW. “ApiAP2 transcription factor restricts development of the Toxoplasma tissue cyst.” PNAS 2013 April 09. | |
| 2012 |
| 35. Pino P, Sebastian S, Kim EA, Bush E, Brochet M, Volkmann K, Kozlowski E, Llinás M, Billker O, Soldati-Favre D. “A tetracycline-repressible transactivator system to study essential genes in malaria parasites.” Cell Host & Microbe 2012 Dec 13;12(6):824-34.(Supplement) | |
| 34. Babbitt SE, Altenhofen L, Cobbold SA, Istvan ES, Fennell C, Doerig C, Llinás M, Goldberg DE. “Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state.” PNAS 2012 Nov 20;109(47):E3278-87. | |
| 33. Painter HJ, Altenhofen LM, Kafsack BF, Llinás M. “Whole-Genome Analysis of Plasmodium spp. Utilizing a New Agilent Technologies DNA Microarray Platform.” Methods Mol Biol. 2012 923:213-9. | |
| 32. Olszewski KL, Llinás M. “Extraction of Hydrophilic Metabolites from Plasmodium falciparum-Infected Erythrocytes for Metabolomic Analysis.” Methods Mol Biol. 2012 923:259-66. | |
| 31. Straimer J, Lee MC, Lee AH, Zeitler B, Williams AE, Pearl JR, Zhang L, Rebar EJ, Gregory PD, Llinás M, Urnov FD, Fidock DA. “Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases.” Nature Methods. 2012 Aug 2. | |
| 30. Kafsack BF, Painter HJ, Llinás M. “New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community.” Malaria Journal. 2012 Jun 8;11(1):187. | |
| 29. Painter HJ, Llinás M. “Comment on “emerging functions of transcription factors in malaria parasite.” J Biomed Biotechnol. 2012 Epub 2012 May 20. | |
| 28. Klein EY, Lewis IA, Jung C, Llinás M, Levin SA. “Relationship between treatment-seeking behaviour and artemisinin drug quality in Ghana.” Malaria Journal. 2012 Apr 6;11:110. | |
| 2011 |
| 27. Lindner SE, Llinás M, Keck JL, Kappe SH. “The primase domain of PfPrex is a proteolytically matured, essential enzyme of the apicoplast.” Molecular and Biochemical Parasitology. 2011 Dec;180(2):69-75. | |
| 26. Storm J, Aparicio I, Patzewitz EM, Olszewski K, Llinás M, Engel PC, Muller S. “Plasmodium falciparum glutamate dehydrogenase a is dispensable and not a drug target during erythrocytic development.” Malaria Journal. 2011 July 14; 10 (1): 193. | |
| 25. Ochoa A, Llinás M and Singh M. “Using context to improve protein domain identification.” BMC Bioninformatics. 2011 March 31; 12 (1): 90. | |
| 2010 |
| 24. Painter HJ, Campbell TL, and Llinás M. “The Apicomplexan AP2 family: Integral factors regulating Plasmodium development.” Molecular and Biochemical Parasitology. 2011 March; 176 (1) Epub Nov 2010. | |
| 23. Campbell TL, De Silva EK, Olszewski KL, Elemento O, Llinás M. “Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite.” PLoS Pathogens. 2010 October 28; 6 (10). (Supplementary text and figures file) | |
| 22. Helm S, Lehmann C, Nagel A, Stanway RR, Horstmann S, Llinás M, Heussler VT. “Identification and characterization of a liver stage-specific promoter region of the malaria parasite Plasmodium.” PLoS One. 2010 October 27; 5 (10). | |
| 21. Olszewski KL and Llinás M. “Central carbon metabolism of malaria parasites.” Molecular and Biochemical Parasitology. 2010 September 14. | |
| 20. Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D. “Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.” Molecular Systems Biology. 2010 September 07; 6 (408). | |
| 19. MANUSCRIPT RETRACTED Olszewski KL, Mather MW, Morrisey JM, Garcia BA, Vaidya AB, Rabinowitz JD, Llinás M. “Branched Tricarboxylic Acid Metabolism in Plasmodium falciparum.” Nature. 2010 August 05; 466 (7307), pp. 774-8. (See 2010 News & Views by Hagai Ginsburg) (2010 Corrigendum) | |
| 18. Dowling DP, Ilies M, Olszewski KL, Portugal S, Mota MM, Llinás M, Christianson DW. “Crystal structure of arginase from Plasmodium falciparum and implications for L-arginine depletion in malarial infection.” Biochemistry 2010, July 6;49 (26), pp. 5600-8. | |
| 17. Otto DT, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C, Llinás M. “New insights into the blood stage transcriptome of Plasmodium falciparum using RNA-Seq.” Molecular Microbiology 2010, April;67 (1), pp. 12-24. | |
| 16. Kafsack BF, Llinás M. “Eating at the Table of Another: Metabolomics of Host-Parasite Interactions.” Cell Host & Microbe. 2010, Feb 18; 7 (2) pp. 90-99. | |
| 15. Lindner SE, De Silva EK, Keck JL, Llinás M. “Structural Determinants of DNA Binding by a P. falciparum ApiAP2 Transcriptional Regulator.” Journal of Molecular Biology 2010, Feb 04;395 (3), pp. 558-67. | |
| 2009 |
| 14. Howitt CA, Wilinski D, Llinás M, Templeton TJ, Dzikowski R, Deitsch KW. “Clonally variant gene families in P. falciparum share a common activation factor.” Molecular Microbiology 2009, Sept; 73 (6), pp. 1171-85. | |
| 13. Zawada RJ, Kwan P, Olszewski KL, Llinás M, Huang SG. “Quantitative determination of urea concentrations in cell culture medium.” Biochem Cell Biol. 2009 Jun;87(3):541-4. | |
| 12. Olszewski KL, Morrisey JM, Wilinski D, Burns JM, Vaidya AB, Rabinowitz JD, Llinás M. “Host-Parasite Interactions Revealed by Plasmodium falciparum Metabolomics” Cell Host Microbe. 2009 Feb 19; 5(2), pp. 191-199. (Featured on the journal cover) | |
| 11. van Brummelen AC, Olszewski KL, Wilinski D, Llinás M, Louw AI, Birkholtz LM. “Co-inhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome and metabolome analyses.” J Biol Chem. 2009 Feb 13;284(7), pp. 4635-46. | |
| 2008 |
| 10. Llinás M., Deitsch KW., Voss TS. “Plasmodium gene regulation: far more to factor in.” Trends Parasitol. 2008 Dec;24(12), pp. 551-6. | |
| 9. Tamez PA., Bhattacharjee S., van Ooij C., Hiller NL., Llinás M., Balu B., Adams JH., Haldar K. “An erythrocyte vesicle protein exported by the malaria parasite promotes tubovesicular lipid import from the host cell surface” PLoS Pathog. 2008 Aug 8;4(8):e1000118. | |
| 8. De Silva EK., Gehrke AR., Olszewski K., León I, Chahal JS., Bulyk ML., Llinás M. “Specific DNA-binding by Apicomplexan AP2 transcription factors”. Proc Natl Acad Sci USA. 2008 Jun 17;105(24), pp. 8393-8.(See feature in Nature Reviews Microbiology) | |
| 7. Birkholtz L., van Brummelen AC., Clark K., Niemand J., Marechal E., Llinás M., Louw AI. “Exploring functional genomics for drug target and therapeutics discovery in Plasmodia” Acta Trop. 2008 Feb;105(2), pp. 113-23. | |
| 2007 |
| 6. Hu G., Llinás M., Li J., Preiser PR., Bozdech Z. “Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy” BMC Bioinformatics. 2007 Sep 19;8:350. | |
| 5. Deitsch K., Duraisingh M., Dzikowski R., Gunasekera A., Khan S., Le Roch K., Llinás M., Mair G., McGovern V., Roos D., Shock J., Sims J., Wiegand R., Winzeler E. “Mechanisms of Gene Regulation in Plasmodium” Am J Trop Med Hyg. 2007 Aug;77(2), pp. 201-8. | |
| 2006 |
| 4. Llinás M., Bozdech Z., Wong ED., Adai, AT., DeRisi JL. “Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains” Nucleic Acids Res. 2006 Feb 21;34(4), pp. 1166-73. | |
| 2005 |
| 3. Llinás, M. and del Portillo HA. “Mining the malaria transcriptome” Trends Parasitol. 2005 Aug;21(8), pp. 350-2. | |
| 2004 |
| 2. Llinás, M. and DeRisi JL. “Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis” Curr Opin Microbiol. 2004 Aug;7(4), pp. 382-7. | |
| 2003 |
| 1. Llinás M. and Bozdech Z., Pulliam BL., Wong ED., Zhu J., DeRisi JL. “The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum” PLoS Biol. 2003 Dec;3(12):e426. (2018 Nature Microbiology Feature onOpen Access) (Listen HERE) | |
| Protein Folding, Stability and Structure |
| 5. Cellitti J., Llinás M., Echols N., Shank E. A. Gillespie B., Kwon E., Crowder S. M., Dahlquist F. W., Alber T., Marqusee S. “Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment” Protein Sci. 2007 May;16(5):842-51. Epub 2007 Mar 30. | |
| 4. Llinás M., Gillespie B., Dahlquist FW., Marqusee S. “The energetics of T4 lysozyme reveal a hierarchy of conformations” Nat Struct Biol. 1999 Nov;6(11):1072-8. | |
| 3. Liu H., Farr-Jones S., Ulyanov NB., Llinás M., Marqusee S., Groth D., Cohen FE., Prusiner SB., James TL. “Solution structure of Syrian hamster prion protein rPrP (90-231)” Biochemistry. 1999 Apr 27;38(17):5362-77. | |
| 2. Llinás M. and Marqusee S. “Subdomain interactions as a determinant in the folding and stability of T4 lysozyme” Protein Sci. 1998 Jan;7(1):96-104. | |
| 1. Kohnert U., Wozny M., Llinás M., Roos A., Fischer S. “Active site labeling with dansyl-glutamyl-glycyl-arginyl chloromethyl ketone demonstrates the full activity of the refolded and purified tissue-type plasminogen activator variant BM 06.022” Appl Biochem Biotechnol. 1995 Nov;55(2):157-66. | |
| Other |
| Galgoczy DJ., Cassidy-Stone A., Llinás M., O’Rourke SM., Herskowitz I., DeRisi JL., Johnson AD. “Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae” Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18069-74. | |
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