Publications

owl

Publications

books
2017
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)
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)
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.
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 and 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. Pubmed
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.
Protein Folding, Stability & 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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