Monte Carlo Club - Revision history

Wikiuser: /* Papers found by Hui */

2026-06-16T17:24:04Z

Papers found by Hui

← Older revision		Revision as of 17:24, 16 June 2026
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	* Abbas, M. N., Jmel, M. A., Mekki, I., Dijkgraaf, I., & Kotsyfakis, M. (2023). Recent Advances in Tick Antigen Discovery and Anti-Tick Vaccine Development. International journal of molecular sciences, 24(5), 4969. https://doi.org/10.3390/ijms24054969. I found this review article to be the most complete and well-rounded one. It summarizes recent progress in anti-tick vaccine development, especially antigen-based strategies that target tick feeding, reproduction, attachment, and pathogen transmission. The authors also explain how modern approaches such as genomics, transcriptomics, proteomics, and reverse vaccinology have helped identify new vaccine candidates from tick tissues including the salivary glands, midgut, eggs, Malpighian tubules, and cement. The review covers several major antigens and vaccine targets, including Bm86/Bm95, ferritin, aquaporins, subolesin, Salp15, metalloproteases, serpins, and the recent 19ISP mRNA vaccine targeting Ixodes scapularis salivary proteins.		* Abbas, M. N., Jmel, M. A., Mekki, I., Dijkgraaf, I., & Kotsyfakis, M. (2023). Recent Advances in Tick Antigen Discovery and Anti-Tick Vaccine Development. International journal of molecular sciences, 24(5), 4969. https://doi.org/10.3390/ijms24054969. I found this review article to be the most complete and well-rounded one. It summarizes recent progress in anti-tick vaccine development, especially antigen-based strategies that target tick feeding, reproduction, attachment, and pathogen transmission. The authors also explain how modern approaches such as genomics, transcriptomics, proteomics, and reverse vaccinology have helped identify new vaccine candidates from tick tissues including the salivary glands, midgut, eggs, Malpighian tubules, and cement. The review covers several major antigens and vaccine targets, including Bm86/Bm95, ferritin, aquaporins, subolesin, Salp15, metalloproteases, serpins, and the recent 19ISP mRNA vaccine targeting Ixodes scapularis salivary proteins.
	* Allen J.R., Humphreys S.J. Immunisation of guinea pigs and cattle against ticks. Nature. 1979;280:491–493. doi: 10.1038/280491a0. https://www-nature-com.proxy.wexler.hunter.cuny.edu/articles/280491a0. The first review article referred to this early study, so I thought it was important to include. This paper is an early proof-of-concept showing that hosts can be immunized against ticks using antigens extracted from the internal organs of partially fed ticks, especially the midgut and reproductive organs. It helped establish the idea that internal tick antigens, not only salivary proteins, could be useful vaccine targets.		* Allen J.R., Humphreys S.J. Immunisation of guinea pigs and cattle against ticks. Nature. 1979;280:491–493. doi: 10.1038/280491a0. https://www-nature-com.proxy.wexler.hunter.cuny.edu/articles/280491a0. The first review article referred to this early study, so I thought it was important to include. This paper is an early proof-of-concept showing that hosts can be immunized against ticks using antigens extracted from the internal organs of partially fed ticks, especially the midgut and reproductive organs. It helped establish the idea that internal tick antigens, not only salivary proteins, could be useful vaccine targets.
	* Hart, T. M., Cui, Y., Telford, S. R., Marín-López, A., Calloway, K., Dai, Y., Matias, J., DePonte, K., Jaycox, J., DeBlasio, M., Hoornstra, D., Belperron, A. A., Cibichakravarthy, B., Johnson, E. E., Alameh, M. G., Dwivedi, G., Hovius, J. W. R., Bockenstedt, L. K., Weissman, D., Ring, A. M., … Fikrig, E. (2025). Tick feeding or vaccination with tick antigens elicits immunity to the Ixodes scapularis exoproteome in guinea pigs and humans. Science translational medicine, 17(791), eads9207. https://doi.org/10.1126/scitranslmed.ads9207		* Hart, T. M., Cui, Y., Telford, S. R., Marín-López, A., Calloway, K., Dai, Y., Matias, J., DePonte, K., Jaycox, J., DeBlasio, M., Hoornstra, D., Belperron, A. A., Cibichakravarthy, B., Johnson, E. E., Alameh, M. G., Dwivedi, G., Hovius, J. W. R., Bockenstedt, L. K., Weissman, D., Ring, A. M., … Fikrig, E. (2025). Tick feeding or vaccination with tick antigens elicits immunity to the Ixodes scapularis exoproteome in guinea pigs and humans. Science translational medicine, 17(791), eads9207. https://doi.org/10.1126/scitranslmed.ads9207. This paper developed a high-throughput yeast display platform called IscREAM, which can screen antibody responses against more than 3,000 predicted extracellular proteins from Ixodes scapularis. Using vaccinated guinea pigs, Lyme disease patients, and a naturally tick-resistant individual, the authors identified 199 immunogenic tick antigens. They also showed that both salivary and cement proteins may contribute to acquired tick resistance.
	~~https://pmc.ncbi.nlm.nih.gov/articles/PMC12067475/~~. This paper developed a high-throughput yeast display platform called IscREAM, which can screen antibody responses against more than 3,000 predicted extracellular proteins from Ixodes scapularis. Using vaccinated guinea pigs, Lyme disease patients, and a naturally tick-resistant individual, the authors identified 199 immunogenic tick antigens. They also showed that both salivary and cement proteins may contribute to acquired tick resistance.
	* Narasimhan, Sukanya et al. “Immunity against Ixodes scapularis salivary proteins expressed within 24 hours of attachment thwarts tick feeding and impairs Borrelia transmission.” PloS one vol. 2,5 e451. 16 May. 2007, https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000451. This article focuses on early Ixodes scapularis salivary proteins that are important for tick feeding and Borrelia burgdorferi transmission. The authors show that the tick salivary gland transcriptome and proteome change during feeding, especially between the first 24 hours of attachment and later feeding stages. Importantly, they found that guinea pigs repeatedly exposed only to the first 24 hours of tick feeding developed acquired tick immunity, shown by inflammation at the bite site, rapid tick rejection, reduced engorgement, and impaired Borrelia transmission.		* Narasimhan, Sukanya et al. “Immunity against Ixodes scapularis salivary proteins expressed within 24 hours of attachment thwarts tick feeding and impairs Borrelia transmission.” PloS one vol. 2,5 e451. 16 May. 2007, https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000451. This article focuses on early Ixodes scapularis salivary proteins that are important for tick feeding and Borrelia burgdorferi transmission. The authors show that the tick salivary gland transcriptome and proteome change during feeding, especially between the first 24 hours of attachment and later feeding stages. Importantly, they found that guinea pigs repeatedly exposed only to the first 24 hours of tick feeding developed acquired tick immunity, shown by inflammation at the bite site, rapid tick rejection, reduced engorgement, and impaired Borrelia transmission.
	* Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.

	===Tick genomics===		===Tick genomics===

Wikiuser: /* Papers found by Hui */

2026-06-16T17:15:44Z

Papers found by Hui

← Older revision		Revision as of 17:15, 16 June 2026
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	==Tick genomics & native immunity==		==Tick genomics & native immunity==
	===Papers found by Hui===		===Papers found by Hui===
	* Abbas, M. N., Jmel, M. A., Mekki, I., Dijkgraaf, I., & Kotsyfakis, M. (2023). Recent Advances in Tick Antigen Discovery and Anti-Tick Vaccine Development. International journal of molecular sciences, 24(5), 4969. https://doi.org/10.3390/ijms24054969		* Abbas, M. N., Jmel, M. A., Mekki, I., Dijkgraaf, I., & Kotsyfakis, M. (2023). Recent Advances in Tick Antigen Discovery and Anti-Tick Vaccine Development. International journal of molecular sciences, 24(5), 4969. https://doi.org/10.3390/ijms24054969. I found this review article to be the most complete and well-rounded one. It summarizes recent progress in anti-tick vaccine development, especially antigen-based strategies that target tick feeding, reproduction, attachment, and pathogen transmission. The authors also explain how modern approaches such as genomics, transcriptomics, proteomics, and reverse vaccinology have helped identify new vaccine candidates from tick tissues including the salivary glands, midgut, eggs, Malpighian tubules, and cement. The review covers several major antigens and vaccine targets, including Bm86/Bm95, ferritin, aquaporins, subolesin, Salp15, metalloproteases, serpins, and the recent 19ISP mRNA vaccine targeting Ixodes scapularis salivary proteins.
	~~https://pmc.ncbi.nlm.nih.gov/articles/PMC10003026/~~. I found this review article to be the most complete and well-rounded one. It summarizes recent progress in anti-tick vaccine development, especially antigen-based strategies that target tick feeding, reproduction, attachment, and pathogen transmission. The authors also explain how modern approaches such as genomics, transcriptomics, proteomics, and reverse vaccinology have helped identify new vaccine candidates from tick tissues including the salivary glands, midgut, eggs, Malpighian tubules, and cement. The review covers several major antigens and vaccine targets, including Bm86/Bm95, ferritin, aquaporins, subolesin, Salp15, metalloproteases, serpins, and the recent 19ISP mRNA vaccine targeting Ixodes scapularis salivary proteins.		* Allen J.R., Humphreys S.J. Immunisation of guinea pigs and cattle against ticks. Nature. 1979;280:491–493. doi: 10.1038/280491a0. https://www-nature-com.proxy.wexler.hunter.cuny.edu/articles/280491a0. The first review article referred to this early study, so I thought it was important to include. This paper is an early proof-of-concept showing that hosts can be immunized against ticks using antigens extracted from the internal organs of partially fed ticks, especially the midgut and reproductive organs. It helped establish the idea that internal tick antigens, not only salivary proteins, could be useful vaccine targets.
	* Allen J.R., Humphreys S.J. Immunisation of guinea pigs and cattle against ticks. Nature. 1979;280:491–493. doi: 10.1038/280491a0.
	https://www-nature-com.proxy.wexler.hunter.cuny.edu/articles/280491a0. The first review article referred to this early study, so I thought it was important to include. This paper is an early proof-of-concept showing that hosts can be immunized against ticks using antigens extracted from the internal organs of partially fed ticks, especially the midgut and reproductive organs. It helped establish the idea that internal tick antigens, not only salivary proteins, could be useful vaccine targets.
	* Hart, T. M., Cui, Y., Telford, S. R., Marín-López, A., Calloway, K., Dai, Y., Matias, J., DePonte, K., Jaycox, J., DeBlasio, M., Hoornstra, D., Belperron, A. A., Cibichakravarthy, B., Johnson, E. E., Alameh, M. G., Dwivedi, G., Hovius, J. W. R., Bockenstedt, L. K., Weissman, D., Ring, A. M., … Fikrig, E. (2025). Tick feeding or vaccination with tick antigens elicits immunity to the Ixodes scapularis exoproteome in guinea pigs and humans. Science translational medicine, 17(791), eads9207. https://doi.org/10.1126/scitranslmed.ads9207		* Hart, T. M., Cui, Y., Telford, S. R., Marín-López, A., Calloway, K., Dai, Y., Matias, J., DePonte, K., Jaycox, J., DeBlasio, M., Hoornstra, D., Belperron, A. A., Cibichakravarthy, B., Johnson, E. E., Alameh, M. G., Dwivedi, G., Hovius, J. W. R., Bockenstedt, L. K., Weissman, D., Ring, A. M., … Fikrig, E. (2025). Tick feeding or vaccination with tick antigens elicits immunity to the Ixodes scapularis exoproteome in guinea pigs and humans. Science translational medicine, 17(791), eads9207. https://doi.org/10.1126/scitranslmed.ads9207
	https://pmc.ncbi.nlm.nih.gov/articles/PMC12067475/. This paper developed a high-throughput yeast display platform called IscREAM, which can screen antibody responses against more than 3,000 predicted extracellular proteins from Ixodes scapularis. Using vaccinated guinea pigs, Lyme disease patients, and a naturally tick-resistant individual, the authors identified 199 immunogenic tick antigens. They also showed that both salivary and cement proteins may contribute to acquired tick resistance.		https://pmc.ncbi.nlm.nih.gov/articles/PMC12067475/. This paper developed a high-throughput yeast display platform called IscREAM, which can screen antibody responses against more than 3,000 predicted extracellular proteins from Ixodes scapularis. Using vaccinated guinea pigs, Lyme disease patients, and a naturally tick-resistant individual, the authors identified 199 immunogenic tick antigens. They also showed that both salivary and cement proteins may contribute to acquired tick resistance.
	* Narasimhan, Sukanya et al. “Immunity against Ixodes scapularis salivary proteins expressed within 24 hours of attachment thwarts tick feeding and impairs Borrelia transmission.” PloS one vol. 2,5 e451. 16 May. 2007, ~~doi:10.1371/journal.pone.0000451~~		* Narasimhan, Sukanya et al. “Immunity against Ixodes scapularis salivary proteins expressed within 24 hours of attachment thwarts tick feeding and impairs Borrelia transmission.” PloS one vol. 2,5 e451. 16 May. 2007, https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000451. This article focuses on early Ixodes scapularis salivary proteins that are important for tick feeding and Borrelia burgdorferi transmission. The authors show that the tick salivary gland transcriptome and proteome change during feeding, especially between the first 24 hours of attachment and later feeding stages. Importantly, they found that guinea pigs repeatedly exposed only to the first 24 hours of tick feeding developed acquired tick immunity, shown by inflammation at the bite site, rapid tick rejection, reduced engorgement, and impaired Borrelia transmission.
	https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000451. This article focuses on early Ixodes scapularis salivary proteins that are important for tick feeding and Borrelia burgdorferi transmission. The authors show that the tick salivary gland transcriptome and proteome change during feeding, especially between the first 24 hours of attachment and later feeding stages. Importantly, they found that guinea pigs repeatedly exposed only to the first 24 hours of tick feeding developed acquired tick immunity, shown by inflammation at the bite site, rapid tick rejection, reduced engorgement, and impaired Borrelia transmission.
	* Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.		* Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.

	===Tick genomics===		===Tick genomics===
	* Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.		* Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.

Wikiuser: /* Tick genomics & native immunity */

2026-06-16T17:13:40Z

Tick genomics & native immunity

@@ Line 21: / Line 21: @@
 ==Tick genomics & native immunity==
 * Mini-review: [https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2018.00176/full Kitsou & Pal (2018).] Ixodes immune responses against Lyme disease pathogens. Font Cell Infect Microb.
 * The IMD pathway: [https://journals.asm.org/doi/10.1128/mbio.00703-22 Sidak-Loftis et al (2022)]; mBio

Wikiuser: /* Simulations: artificial immune systems (AIS) */

2026-06-04T21:15:56Z

Simulations: artificial immune systems (AIS)

← Older revision		Revision as of 21:15, 4 June 2026
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	* Prey-predator enrichment		* Prey-predator enrichment
	==Simulations: artificial immune systems (AIS)==		==Simulations: artificial immune systems (AIS)==
			* r-contiguous symbols rule for antigen recognition: https://www.pnas.org/doi/10.1073/pnas.90.5.1691
	* Negative selection: weed out self-antigens, http://dpnm.postech.ac.kr/ANM/resources/papers/09_Nature/hofmeyr_forrest.pdf		* Negative selection: weed out self-antigens, http://dpnm.postech.ac.kr/ANM/resources/papers/09_Nature/hofmeyr_forrest.pdf
	* Clonal selection algorithm for learning: https://ieeexplore.ieee.org/abstract/document/1011539		* Clonal selection algorithm for learning: https://ieeexplore.ieee.org/abstract/document/1011539

Wikiuser: /* Simulations: Non-adaptive selection */

2026-06-04T21:12:48Z

Simulations: Non-adaptive selection

← Older revision		Revision as of 21:12, 4 June 2026
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	* May threshold: Ecological stability		* May threshold: Ecological stability
	* Prey-predator enrichment		* Prey-predator enrichment
			==Simulations: artificial immune systems (AIS)==
			* Negative selection: weed out self-antigens, http://dpnm.postech.ac.kr/ANM/resources/papers/09_Nature/hofmeyr_forrest.pdf
			* Clonal selection algorithm for learning: https://ieeexplore.ieee.org/abstract/document/1011539

	==Pan-genome graphs: an efficient computational representation of whole-genomic variations==		==Pan-genome graphs: an efficient computational representation of whole-genomic variations==
	* A summary (including data standards & libraries): https://pangenome.github.io/		* A summary (including data standards & libraries): https://pangenome.github.io/

Wikiuser: /* Readings on Microbiome & Evolution of Complexity: the Holobionts/Gia hypothesis vs Non-adaptive selection */

2026-06-04T02:05:52Z

Readings on Microbiome & Evolution of Complexity: the Holobionts/Gia hypothesis vs Non-adaptive selection

← Older revision		Revision as of 02:05, 4 June 2026
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	* Tcik genome resource:		* Tcik genome resource:

	==~~Readings on~~ Microbiome & Evolution of Complexity: the Holobionts/Gia hypothesis vs Non-adaptive selection==		==Microbiome & Evolution of Complexity: the Holobionts/Gia hypothesis vs Non-adaptive selection==
	* [https://press.uchicago.edu/ucp/books/book/chicago/N/bo244157692.html Non-adaptive Selection], by John Damuth & Lev Ginzburg		* [https://press.uchicago.edu/ucp/books/book/chicago/N/bo244157692.html Non-adaptive Selection], by John Damuth & Lev Ginzburg
	* C.H. Lean, W.F. Doolittle, & J.P. Bielawski, Community-level evolutionary processes: Linking community genetics with '''replicator-interactor theory''', Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2202538119, https://doi.org/10.1073/pnas.2202538119 (2022).		* C.H. Lean, W.F. Doolittle, & J.P. Bielawski, Community-level evolutionary processes: Linking community genetics with '''replicator-interactor theory''', Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2202538119, https://doi.org/10.1073/pnas.2202538119 (2022).

Wikiuser: /* Pan-genome graphs: an efficient computational representation of whole-genomic variations */

2026-06-04T02:05:29Z

Pan-genome graphs: an efficient computational representation of whole-genomic variations

← Older revision		Revision as of 02:05, 4 June 2026
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	__FORCETOC__		__FORCETOC__
	=Mcirobiome & tick pop gen: Ecology & Evolution perspectives (Spring & Summer 2026)=		=Mcirobiome & tick pop gen: Ecology & Evolution perspectives (Spring & Summer 2026)=
			==Simulations: Non-adaptive selection==
			* Heterosis: maintenance of genomic diversity by heterozygote advantages
			* Stability of the food web
			* May threshold: Ecological stability
			* Prey-predator enrichment
	==Pan-genome graphs: an efficient computational representation of whole-genomic variations==		==Pan-genome graphs: an efficient computational representation of whole-genomic variations==
	* A summary (including data standards & libraries): https://pangenome.github.io/		* A summary (including data standards & libraries): https://pangenome.github.io/

Wikiuser: /* Pan-genome graphs: an efficient computational representation of whole-genomic variations */

2026-06-02T21:10:23Z

Pan-genome graphs: an efficient computational representation of whole-genomic variations

← Older revision		Revision as of 21:10, 2 June 2026
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	* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI		* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI
	* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4		* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4
	* Phylogenetic compression of bacterial genome data: https://www.nature.com/articles/s41579-026-01303-0		* Phylogenetic compression of bacterial genome data: MiniPhy & PanMan algorithms; https://www.nature.com/articles/s41579-026-01303-0

	==Tick genomics & native immunity==		==Tick genomics & native immunity==

Wikiuser: /* Pan-genome graphs: an efficient computational representation of whole-genomic variations */

2026-06-02T21:07:51Z

Pan-genome graphs: an efficient computational representation of whole-genomic variations

← Older revision		Revision as of 21:07, 2 June 2026
Line 8:		Line 8:
	* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI		* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI
	* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4		* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4
			* Phylogenetic compression of bacterial genome data: https://www.nature.com/articles/s41579-026-01303-0

	==Tick genomics & native immunity==		==Tick genomics & native immunity==

Wikiuser: /* Pan-genome graphs: an efficient computational representation of whole-genomic variations */

2026-06-02T18:39:59Z

Pan-genome graphs: an efficient computational representation of whole-genomic variations

← Older revision		Revision as of 18:39, 2 June 2026
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	* A review paper: https://www.nature.com/articles/s41588-024-02029-6		* A review paper: https://www.nature.com/articles/s41588-024-02029-6
	* A paper (Huamn & Drosophila models): https://www.nature.com/articles/s41587-023-01793-w		* A paper (Huamn & Drosophila models): https://www.nature.com/articles/s41587-023-01793-w
	* SARS-CoV-2 application: whole-genome alignment with Twilight & compression by panMAN: https://www.amd.com/en/developer/resources/technical-articles/2026/ucsd-researchers-use-amd-gpus-to-build-the-worlds-large.html		* SARS-CoV-2 application: whole-genome alignment with Twilight & compression by [https://github.com/TurakhiaLab/panman panMAN]: https://www.amd.com/en/developer/resources/technical-articles/2026/ucsd-researchers-use-amd-gpus-to-build-the-worlds-large.html
	* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI		* An application: PHI, for pangenome-based genotyping: https://github.com/at-cg/PHI
	* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4		* Build bacterial pangenome with Panaroo: https://link.springer.com/article/10.1186/s13059-020-02090-4