Papers

One of our group's primary ways of disseminating our research is through peer reviewed publications. To make our data and finings as open and easy to access as possible, we have provided links to the PDFs of the manuscripts, the associated code used in the studies, and the raw data when applicable. Please feel free to reach out to talk about our work. We are always interested in building upon what we have done to tackle new and exciting scientific questions.
  • PDF version of published paper
  • Preprint version of manuscript
  • GitHub repository for paper
  • Raw data used in manuscript
  1. Hall B, Levy S, Dufault-Thompson K, Arp G, Zhong A, Ndjite GM, Weiss A, Braccia D, Jenkins C, Yang Y, Arp G, Abeysinghe S, Jermain M, Wu CH, Jiang X. 2024. BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. Nature Microbiology. 9: 173-184. DOI: 10.1038/s41564-023-01549-x.
  2. Zhong A, Jiang X, Hickman AB, Klier K, Teodoro GIC, Dyda F, Laub TM, Storz S. 2023. Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins. Proceedings of the National Academy of Sciences. 120: e2307382120. DOI: 10.1073/pnas.2307382120.
  3. Yang Y, Jiang X. 2023. Evolink: A Phylogenetic Approach for Rapid Identification of Genotype-Phenotype Associations in Large-scale Microbial Multi-Species Data. Bioinformatics. DOI: 10.1093/bioinformatics/btad215.
  4. Fontenele RS, Yang Y, Driver EM, Magge A, Kraberger S, Custer JM, Dufault-Thompson K, Cox E, Newell ME, Varsani A, Halden RU, Scotch M, Jiang X. 2023. Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Sci Total Environ.. 877: 162862. DOI: 10.1016/j.scitotenv.2023.162862.
  5. Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A M, Cui Y, Jiang X, Peng S, Li S, Tong Y. 2022. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR genomics and bioinformatics. 4: lqac057. DOI: 10.1093/nargab/lqac057.
  6. Yang Y, Dufault-Thompson K, Fontenele RS, Jiang X. 2022. Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants. mSystem. DOI: 10.1128/msystems.00179-22.
  7. Yan W, Hall AB, Jiang X. 2022. Bacteroidales Species in the Human Gut Are a Reservoir of Antibiotic Resistance Genes Regulated by Invertible Promoters. Npj Biofilms and Microbiomes. 8: 1. DOI: 10.1038/s41522-021-00260-1.
  8. Olejniczak M, Jiang X, Basczok MM, Storz G. 2022. KH Domain Proteins: Another Family of Bacterial RNA Matchmakers. Molecular Microbiology. 117: 10-19. DOI: 10.1111/mmi.14842.
  9. Dufault-Thompson K, Jiang X. 2022. Applications of de Bruijn Graphs in Microbiome Research. iMeta. 1: e4. DOI: 10.1002/imt2.4.
  10. Dufault-Thompson K, Hall AB, Jiang X. 2022. Taxonomic Distribution and Evolutionary Analysis of the Equol Biosynthesis Gene Cluster. BMC Genomics. 23: 1. DOI: 10.1186/s12864-022-08426-7.
  11. Braccia D J, Ndjite G M, Weiss A, Levy S, Abeysinghe S, Jiang X, Pop M, Hall B. 2022. Gut microbiome-wide search for bacterial azoreductases reveals potentially uncharacterized azoreductases encoded in the human gut microbiome. Drug Metabolism and Disposition. DOI: 10.1124/dmd.122.000898.
  12. Yang Y, Yan W, Hall AB, Jiang X. 2021. Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination. Molecular Biology and Evolution. 38: 1241-1248. DOI: 10.1093/molbev/msaa281.
  13. Mou Z, Yang Y, Hall AB, Jiang X. 2021. The Taxonomic Distribution of Histamine-Secreting Bacteria in the Human Gut Microbiome. BMC Genomics. 22: 695. DOI: 10.1186/s12864-021-08004-3.
  14. Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA 2nd, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. 2021. High-Throughput Sequencing of SARS-CoV-2 in Wastewater Provides Insights into Circulating Variants. Water Research. 205: 117710. DOI: 10.1016/j.watres.2021.117710.
  15. Braccia DJ, Jiang X, Pop M, Hall AB. 2021. The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome. Frontiers in Microbiology. 12: 705583. DOI: 10.3389/fmicb.2021.705583.
  16. Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. 2019. Analysis of 1135 Gut Metagenomes Identifies Sex-Specific Resistome Profiles. Gut Microbes. 10: 358-366. DOI: 10.1080/19490976.2018.1528822.
  17. Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, Livny J, Vlamakis H, Clish C, Bullock K, Deik A, Scott J, Pierce KA, Xavier RJ, Alm EJ. 2019. A Library of Human Gut Bacterial Isolates Paired with Longitudinal Multiomics Data Enables Mechanistic Microbiome Research. Nature Medicine. 25: 1442-1452. DOI: 10.1038/s41591-019-0559-3.
  18. Jiang X, Hall AB, Xavier RJ, Alm EJ. 2019. Comprehensive Analysis of Chromosomal Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools. Plos One. 14: e0223680. DOI: 10.1371/journal.pone.0223680.
  19. Jiang X*, Hall AB*, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. 2019. Invertible Promoters Mediate Bacterial Phase Variation, Antibiotic Resistance, and Host Adaptation in the Gut. Science. 363: 181-187. DOI: 10.1126/science.aau5238.
  20. Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. 2018. Gut Microbiota Composition and Functional Changes in Inflammatory Bowel Disease and Irritable Bowel Syndrome. Science Translational Medicine. 10: eaap8914. DOI: 10.1126/scitranslmed.aap8914.
  21. Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. 2018. Predictability and Persistence of Prebiotic Dietary Supplementation in a Healthy Human Cohort. Scientific Reports. 8: 12699. DOI: 10.1038/s41598-018-30783-1.
  22. Prasad TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. 2017. Integrating Transcriptomic and Proteomic Data for Accurate Assembly and Annotation of Genomes. Genome Research. 27: 133-144. DOI: 10.1101/gr.201368.115.
  23. Jiang X, Hall AB, Biedler JK, Tu Z. 2017. Single Molecule RNA Sequencing Uncovers Trans -Splicing and Improves Annotations in Anopheles Stephensi: SMRT Sequencing Uncovers Trans-Splicing. Insect Molecular Biology. 26: 298-307. DOI: 10.1111/imb.12294.
  24. Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. 2017. A Novel Ruminococcus Gnavus Clade Enriched in Inflammatory Bowel Disease Patients. Genome Medicine. 9: 103. DOI: 10.1186/s13073-017-0490-5.
  25. Artemov GN, Peery AN, Jiang X, Tu Z, Stegniy VN, Sharakhova MV, Sharakhov IV. 2017. The Physical Genome Mapping of Anopheles Albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles. G3 Genes|Genomes|Genetics. 7: 155-164. DOI: 10.1534/g3.116.034959.
  26. Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. 2016. Radical Remodeling of the Y Chromosome in a Recent Radiation of Malaria Mosquitoes. Proceedings of the National Academy of Sciences. 113: E2114-23. DOI: 10.1073/pnas.1525164113.
  27. Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. 2015. Highly Evolvable Malaria Vectors: The Genomes of 16 Anopheles Mosquitoes. Science. 347: 1258522. DOI: 10.1126/science.1258522.
  28. Jiang X, Biedler JK, Qi Y, Hall AB, Tu Z. 2015. Complete Dosage Compensation in Anopheles Stephensi and the Evolution of Sex-Biased Genes in Mosquitoes. Genome Biology and Evolution. 7: 1914-24. DOI: 10.1093/gbe/evv115.
  29. Hall AB, Basu S, Jiang X, Qi Y, Timoshevskiy VA, Biedler JK, Sharakhova MV, Elahi R, Anderson MA, Chen XG, Sharakhov IV, Adelman ZN, Tu Z. 2015. A Male-Determining Factor in the Mosquito Aedes Aegypti. Science. 348: 1268-70. DOI: 10.1126/science.aaa2850.
  30. Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. 2015. Extensive Introgression in a Malaria Vector Species Complex Revealed by Phylogenomics. Science. 347: 1258524. DOI: 10.1126/science.1258524.
  31. Chen XG, Jiang X, Gu J, Xu M, Wu Y, Deng Y, Zhang C, Bonizzoni M, Dermauw W, Vontas J, Armbruster P, Huang X, Yang Y, Zhang H, He W, Peng H, Liu Y, Wu K, Chen J, Lirakis M, Topalis P, Van Leeuwen T, Hall AB, Jiang X, Thorpe C, Mueller RL, Sun C, Waterhouse RM, Yan G, Tu ZJ, Fang X, James AA. 2015. Genome Sequence of the Asian Tiger Mosquito, Aedes Albopictus, Reveals Insights into Its Biology, Genetics, and Evolution. Proceedings of the National Academy of Sciences. 112: E5907-15. DOI: 10.1073/pnas.1516410112.
  32. Marinotti O, Ngo T, Kojin BB, Chou SP, Nguyen B, Juhn J, Carballar-Lejarazú R, Marinotti PN, Jiang X, Walter MF, Tu Z, Gershon PD, James AA. 2014. Integrated Proteomic and Transcriptomic Analysis of the Aedes Aegypti Eggshell. BMC Developmental Biology. 14: 15. DOI: 10.1186/1471-213X-14-15.
  33. Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z. 2014. Genome Analysis of a Major Urban Malaria Vector Mosquito, Anopheles Stephensi. Genome Biology. 15: 459. DOI: 10.1186/s13059-014-0459-2.
  34. Hall AB, Timoshevskiy VA, Sharakhova MV, Jiang X, Basu S, Anderson MA, Hu W, Sharakhov IV, Adelman ZN, Tu Z. 2014. Insights into the Preservation of the Homomorphic Sex-Determining Chromosome of Aedes Aegypti from the Discovery of a Male-Biased Gene Tightly Linked to the M-Locus. Genome Biology and Evolution. 6: 179-91. DOI: 10.1093/gbe/evu002.
  35. Jiang X, Jiang H, Li C, Wang S, Mi Z, An X, Chen J, Tong Y. 2011. Sequence Characteristics of T4-like Bacteriophage IME08 Genome Termini Revealed by High Throughput Sequencing. Virology Journal. 8: 194. DOI: 10.1186/1743-422X-8-194.
  36. Jiang H, Jiang X, Wang S, Li C, Chen B, An X, Mi Z, Chen J, Tong Y. 2011. The Complete Genome Sequence of a Novel T4-like Bacteriophage, IME08. Archives of Virology. 156: 1489-92. DOI: 10.1007/s00705-011-1033-9.