1. Lamendella, R., Oerther, D.B., Iker, B., and Santo Domingo, J.W. (2013). Probing the molecular diversity of fecal and environmental Bacteroidales populations uncovers host-specific targets for fecal source tracking.. Applied and Environmental Microbiology. 79 816.
2. Bagchi S., Tellez B.G., Rao, H.A., Lamendella, R., and P. E. Saikaly (2015). Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time.  Appl Microbiol Biotechnol. 99  2361
3. Buonaccorsi, V, Peterson, MP, Aguilar, A; Grove, D; Hunt, A; Lamendella, R; Newman, J; Praul, C; Tobin, T; Trun, N; Roberts, W; Roney, J. (2014). Vision and Change through the Genome Consortium for Active Teaching Using Next-Generation Sequencing (GCAT-SEEK)..  CBE-Life Science Education. 13  1.
4. Grant, C.J., Weimer, A.B., Marks, N.K., Perow, E.S., Oster, J.M., Brubaker, K., Trexler, R.V., Solomon, C.M., and Lamendella, R. (2014). Marcellus and mercury: assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania.  Journal of Environmental and Health Science. 50 (5). DOI: 10.1080/10934529.2015.992670
5. Lamendella, R., Borglin, S., Chakraborty, R., Strutt, S. Tas, N. Mason, O.U., Hultman, H., Prestat, E., Hazen, T.C., and J. K. Jansson. (2014). Multi-omics assessment of Deepwater Horizon oil spill on Gulf coast microbial communities.  Frontiers in Microbiology.
6. Prestat, E., David, M., Hultman, J., Taş, N., Lamendella, R., Dvornik, J., Mackelprang, R.; Myrold, D., Jumpponen, A., Tringe, S., Holman, E. Mavromatis, K., and Jansson, J. (2014). FOAM: Functional Ontology Assignments for Metagenomes: a Hidden Markov Model (HMM) database with environmental focus..  Nucleic Acids Research.  doi: 10.1093/nar/gku702
7. Stropko SJ*, Pipes SE*, and Newman JD. (2014). Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus..  Int J Syst Evol Microbiol. 64  3804.
8. Trexler R*, Solomon C*, Brislawn CJ*, Wright JR*, Rosenberger A*, McClure EE*, Grube AM*, Peterson MP, Keddache M, Mason OU, Hazen TC, Grant CJ and Lamendella R (2014). Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania.  Front. Microbiol. 5 (522) doi: 10.3389/fmicb.2014.00522
9. Peterson, MP; Malloy, JT; Buonaccorsi, VP; Marden, JH (2015). Teaching RNAseq at undergraduate institutions: A tutorial and R package from the Genome Consortium for Active Teaching. CourseSource. 2
10. Bagchi S, Lamendella R, Strutt S, Van Loosdrecht MC, Saikaly PE (2016). Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor.. Scientific Reports. 6  28327. DOI: 10.1038
11. Bergeron, N., Williams, P.T., Lamendella, R., Faghihnia, N., Grube, A., Li, X., Wang Z., Knight, R., Jansson, J.K., Hazen, S.L., and Krauss, R.M (2016). Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk.  British Journal of Nutrition. 20  1.
12. Daniel R. Dries, Yi Zhu, Mieu M. Brooks, Diego A. Forero, Megumi Adachi, Basar Cenik, James M. West, Jennifer Arbella, YuHong Han, Cong Yu, Annelie Nordin, Rolf Adolfsson, Jurgen Del-Favero, Q. Richard Lu, Patrick Callaerts, Shari G. Birnbaum, Gang Yu (2016). Loss of Nicastrin from oligodendrocytes results in hypomyelination and schizophrenia with compulsive behavior. Journal of Biological Chemistry. 291  11647.
13. Fower BL, Buonaccorsi VP (2016). Genomic characterization of sex-identification markers in Sebastes carnatus and S. chrysomelas rockfishes..  Molecular Ecology. 25  2165.
14. Podany, A.B., Wright, J.*, Lamendella, R., Soybel, D.I. and S.L. Kelleher (2016). ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice..  Cellular and Molecular Gastroenterology and Hepatology. 2  369.
15. Sangster, W., Hegarty, J.P., Schieffer, K.M., Wright, J.R. *, Hackman, J. *, Toole, D.R. *, Lamendella, R., Stewart, D.B. Sr. (2016). Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study..  Front. Microbiol.. 7  789.
16. Ulrich, N.*, Rosenberger, A.*, Brislawn, C.*, Wright, J.*, Kessler, C.*, Toole, D.*, Solomon, C.*, Strutt, S*, McClure, E.*, and R. Lamendella (2016). Aquatic bacterial community structure is remodeled by hydric dynamics associated with Superstorm Sandy.  Applied and Environmental Microbiology. 82  3525.
17. Bettina, A.M., Doing, G., O’Brien, K., Perron, G.G. and Jude, B.A (2018). Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed..  Genome Announcements. 6 (3),  e01426
18. Buonaccorsi VP, Hamlin D*, Fowler B*, Wisyanski C*, Sickler A*. (2017). An introduction to Eukaryotic Genome Analysis in non-model species for undergrads: A tutorial from the Genome Consortium for Active Teaching..  CourseSource
19. Buonaccorsi VP, Malloy J*, Peterson M, Brubaker K, Grant C (2017). Population genomic analysis of brook trout Salvelinus fontinalis in Pennsylvania’s Appalachian region..  Trans. Am. Fish. Soc.
20. Doing, G., Perron, G.G. and Jude, B.A (2018). Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed..  Genome Announcements. 6 (1),  e01428.
21. Halfvarson, J., Brislawn, C*., Lamendella, R., Vazquez-Baeza, Y., Walters, W., Bramer, L., D'Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., McClure, E*., Dunklebarger, M*., Knight, R., and Jansson, J.K. (2017). Dynamics of the human gut microbiome in Inflammatory Bowel Disease. Nature Microbiology. 2  17004.
22. O’Brien, K., Perron, G.G. and Jude, B.A. (2018). Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed..  Genome Announcements. 6 (1),  e01429.
23. Wang YW*, Chandler CH (2016). Candidate pathogenicity islands in the genome of 'Candidatus Rickettsiella isopodorum', an intracellular bacterium infecting terrestrial isopod crustaceans..  PeerJ. 4  e2806.
24. Wright, J.*, Kirchner, V.*, Bernard, W.*, Ulrich, N.*, McLimans, C.*, Campa, M.F., Hazen, T.C., Macbeth, T., Marabello, D., McDermott, J., Mackelprang, R. Roth, K., and Lamendella, R. (2017). Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation..  Frontiers in Microbiology. 8  2300.
25. Lamendella R, Jude BA. Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania. Microbiol Resour Announc. 2018;7(12):e01196-18. Published 2018 Sep 27. doi:10.1128/MRA.01196-18
26. Chan JP, Wright JR, Wong HT, et al. Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans. Sci Rep. 2019;9(1):5545. Published 2019 Apr 3. doi:10.1038/s41598-019-41452-2
27. Dahan D, Jude BA, Lamendella R, Keesing F, Perron GG. Exposure to Arsenic Alters the Microbiome of Larval Zebrafish. Front Microbiol. 2018;9:1323. Published 2018 Jun 21. doi:10.3389/fmicb.2018.01323
28. Lamendella, R., Wright, J.R., Hackman, J., McLimans, C., Toole, D.R., Rubio, W.B., Drucker, R., Wong, H.T., Sabey, K., Hegarty, J.P. and Stewart, D.B., 2018. Antibiotic treatments for Clostridium difficile infection are associated with distinct bacterial and fungal community structures. mSphere, 3(1), pp.e00572-17.
29. Ulrich N, Kirchner V, Drucker R, et al. Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study. Sci Rep. 2018;8(1):5683. Published 2018 Apr 9. doi:10.1038/s41598-018-23679-7
30. Tobin, T. 'A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class’ was published in FEMS Microbiology Letters. FEMS Microbiology Letters, Volume 365, Issue 10, May 2018, fny104, https://doi.org/10.1093/femsle/fny104
31. Azzouz-Olden, F., Hunt, A. G., and DeGrandi-Hoffman, G. (2018) Transcriptional response of honey bee (Apis mellifera) to differential nutritional status and Nosema infection. BMC Genomics 19, 628.
32. Pascar J* and Chandler CH. 2018. A bioinformatics approach to identifying Wolbachia infections in arthropods. PeerJ 6:e5486.
33. Bortniak VB, Pelletier DA, Newman JD (2019) Chryseobacterium populi sp. nov., isolated from the endosphere ofPopulus deltoides. Int. J. Syst. Evol. Microbiol. 69:356–362. https://doi.org/10.1099/ijsem.0.003140
34. Matu A, Lum Nde A, Oosthuizen L, Hitzeroth A, Badenhorst M, Duba L, Gidaga M, Klinck J, Kriek I-M, Lekoma PJ, Nel L, dos Ramos SM, Rossouw J, Salomane N, Segone N, Serobe S, Tiyani T, Hugo CJ, Newman JD. (2019) Draft Genome Sequences of Seven Chryseobacterium Type Strains. Microbiol Resource Announc 8:e01518-18. https://doi.org/10.1128/mra.01518-18
35. Miller, R. K., Kirkham, R. M., & Kleinschmit, A. J. (2018). Bioinformatics Analysis of Microbial Abundance and Diversity in Acid Mine Drainage from the Solomon Mine Near Creede, Colorado. Fine Focus, 4(1), 41-65.
36. Schieffer, K.M., Sabey, K., Wright, J.R., Toole, D.R., Drucker, R., Tokarev, V., Harris, L.R., Deiling, S., Eshelman, M.A., Hegarty, J.P. and Yochum, G.S., 2017. The microbial ecosystem distinguishes chronically diseased tissue from adjacent tissue in the sigmoid colon of chronic, recurrent diverticulitis patients. Scientific reports, 7(1), p.8467.
37. Toole, D.R., Cannon, G.H., Brislawn, C.J., Graves, J.M., Lamendella, R., Muth, T.R. and Muth, N.Z., 2018. Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness. Biological invasions, 20(4), pp.891-904.