Google Scholar profile available here
Peer-Reviewed Publications
* denotes co-first authors
Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, and Lewis CM (2023). Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. American Journal of Biological Anthropology, 1-15 [PDF].
Haffner JJ, Katemauswa M, Kagone TS, Hossain E, Jacobson D, Flores K, Parab AR, Obregon-Tito AJ, Tito RY, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Meda N, Carabin H, Honap TP, Sankaranarayanan K, Lewis CM, and McCall LI (2022). Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions. Msystems. e00710-22.
Austin RM, Zuckerman M, Honap TP, Lee H, Ward GK, Warinner C, Sankaranarayanan K, and Hofman CA (2022). Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection. Communications Biology, 5(1), pp.1-10 [PDF].
Vågene ÅJ*, Honap TP*, Harkins KM, Rosenberg MS, Giffin K, Cárdenas-Arroyo F, Leguizamón LP, Arnett J, Buikstra JE, Herbig A, Krause J, Stone AC, and Bos KI (2022). Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nature Communications 13 (1): 1-12 [PDF].
Jacobson DK, Moore KN, Gunderson CC, Rowland MR, Austin RM, Honap TP, Xu J, Warinner C, Sankaranarayanan K, and Lewis CM (2021). Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer. PeerJ 9:e11574 [PDF].
Jacobson DK, Honap TP, Ozga AT, Meda N, Kagone T, Carabin H, Spicer PG, Tito RY, Obregon-Tito A, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Sankaranarayanan K, and Lewis CM (2021). Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. Scientific Reports 11: 1724 [PDF].
Jacobson DK, Honap TP, Monroe C, Lund J, Houk B, Novotny A, Robin C, Marini E, and Lewis CM (2020). Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philosophical Transactions of the Royal Society B 375: 20190586 [PDF]
Borry M, Cordova B, Perri A, Wibowo M, Honap TP, Ko J, Yu J, Britton K, Flink LG, Power RC, Stuijts I, Garcia SD, Hofman CA, Hagan RW, Kagone TS, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis CM, Kostic A, Jeong C, Herbig A, Hubner A, and Warinner C (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 8:e9001. [PDF]
Honap TP*, Sankaranarayanan K*, Schnorr SL, Ozga AT, Warinner C, and Lewis CM Jr. (2020). Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS ONE 15(1): e0226930. [PDF]
Schnorr SL, Hofman CA, Netshifhefhe SR, Duncan FD, Honap TP, Lesnik J, and Lewis CM (2019). Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa. BMC Microbiology 19 (164) [PDF]
Honap TP, Pfister L-A, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, and Stone AC (2018). Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Neglected Tropical Diseases 12(1): e0006190 [PDF]
Benjak A*, Honap TP*, Avanzi C, Becerril-Villanueva L, García I, Rojas-Espinosa O, Stone AC, and Cole ST (2017). Insights from the genome sequence of Mycobacterium lepraemurium: massive gene decay and reductive evolution. mBio 8:e01283-17 [PDF]
Ozga AT, Nieves-Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, and Warinner C (2016). Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology. 160: 220–228. doi:10.1002/ajpa.22960 [PDF]
Alagarasu K, Honap T, Damle IM, Mulay AP, Shah PS, and Cecilia D (2013). Polymorphisms in the Oligoadenylate Synthetase Gene Cluster and its Association with Clinical Outcomes of Dengue Virus Infection. Infection, Genetics, and Evolution 14:390-395 [PDF]
Alagarasu K*, Honap T*, Mulay AP, Bachal RV, Shah PS, and Cecilia D (2012). Association of vitamin D receptor gene polymorphisms with clinical outcomes of Dengue virus infection. Human Immunology 73(11):1194-1199 [PDF]
Press
The Atlantic: Tuberculosis got to South America through... seals? By Sarah Zhang, March 2022.
Science: The archaeological record is full of dog poop. By David Grimm, April 2020.
Vice: Does this 7,000 year old poop belong to a human or dog? By Becky Ferreira, April 2020.
National Geographic: Tooth Plaque May Hold Clues About Ancient Life. By Anna Nowogrodzki, March 2016
* denotes co-first authors
Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, and Lewis CM (2023). Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. American Journal of Biological Anthropology, 1-15 [PDF].
Haffner JJ, Katemauswa M, Kagone TS, Hossain E, Jacobson D, Flores K, Parab AR, Obregon-Tito AJ, Tito RY, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Meda N, Carabin H, Honap TP, Sankaranarayanan K, Lewis CM, and McCall LI (2022). Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions. Msystems. e00710-22.
Austin RM, Zuckerman M, Honap TP, Lee H, Ward GK, Warinner C, Sankaranarayanan K, and Hofman CA (2022). Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection. Communications Biology, 5(1), pp.1-10 [PDF].
Vågene ÅJ*, Honap TP*, Harkins KM, Rosenberg MS, Giffin K, Cárdenas-Arroyo F, Leguizamón LP, Arnett J, Buikstra JE, Herbig A, Krause J, Stone AC, and Bos KI (2022). Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nature Communications 13 (1): 1-12 [PDF].
Jacobson DK, Moore KN, Gunderson CC, Rowland MR, Austin RM, Honap TP, Xu J, Warinner C, Sankaranarayanan K, and Lewis CM (2021). Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer. PeerJ 9:e11574 [PDF].
Jacobson DK, Honap TP, Ozga AT, Meda N, Kagone T, Carabin H, Spicer PG, Tito RY, Obregon-Tito A, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Sankaranarayanan K, and Lewis CM (2021). Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. Scientific Reports 11: 1724 [PDF].
Jacobson DK, Honap TP, Monroe C, Lund J, Houk B, Novotny A, Robin C, Marini E, and Lewis CM (2020). Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philosophical Transactions of the Royal Society B 375: 20190586 [PDF]
Borry M, Cordova B, Perri A, Wibowo M, Honap TP, Ko J, Yu J, Britton K, Flink LG, Power RC, Stuijts I, Garcia SD, Hofman CA, Hagan RW, Kagone TS, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis CM, Kostic A, Jeong C, Herbig A, Hubner A, and Warinner C (2020). CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 8:e9001. [PDF]
Honap TP*, Sankaranarayanan K*, Schnorr SL, Ozga AT, Warinner C, and Lewis CM Jr. (2020). Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS ONE 15(1): e0226930. [PDF]
Schnorr SL, Hofman CA, Netshifhefhe SR, Duncan FD, Honap TP, Lesnik J, and Lewis CM (2019). Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa. BMC Microbiology 19 (164) [PDF]
Honap TP, Pfister L-A, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, and Stone AC (2018). Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Neglected Tropical Diseases 12(1): e0006190 [PDF]
Benjak A*, Honap TP*, Avanzi C, Becerril-Villanueva L, García I, Rojas-Espinosa O, Stone AC, and Cole ST (2017). Insights from the genome sequence of Mycobacterium lepraemurium: massive gene decay and reductive evolution. mBio 8:e01283-17 [PDF]
Ozga AT, Nieves-Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, and Warinner C (2016). Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology. 160: 220–228. doi:10.1002/ajpa.22960 [PDF]
Alagarasu K, Honap T, Damle IM, Mulay AP, Shah PS, and Cecilia D (2013). Polymorphisms in the Oligoadenylate Synthetase Gene Cluster and its Association with Clinical Outcomes of Dengue Virus Infection. Infection, Genetics, and Evolution 14:390-395 [PDF]
Alagarasu K*, Honap T*, Mulay AP, Bachal RV, Shah PS, and Cecilia D (2012). Association of vitamin D receptor gene polymorphisms with clinical outcomes of Dengue virus infection. Human Immunology 73(11):1194-1199 [PDF]
Press
The Atlantic: Tuberculosis got to South America through... seals? By Sarah Zhang, March 2022.
Science: The archaeological record is full of dog poop. By David Grimm, April 2020.
Vice: Does this 7,000 year old poop belong to a human or dog? By Becky Ferreira, April 2020.
National Geographic: Tooth Plaque May Hold Clues About Ancient Life. By Anna Nowogrodzki, March 2016