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Pavlopoulos GA, Baltoumas FA, Liu s, Selvitopi O, Nayfach S, Azad A, Roux S, Call L, Antonio Pedro Camargo AP, Ivanova NN, Chen I-M, Paez-Espino D, Karatzas E, Novel Metagenome Protein Families Consortium (including Blanchard JL), Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge1 J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC (2022) Discovery, diversity and distribution of functional dark matter through global metagenomics. In Review

Lee B, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, RNA Virus Discovery Consortium (including Blanchard JL), Simmonds P, Kyrpides NC,  Gophna U, Dolj VV, Koonin EV (2022) A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes. Cell. 2023 Jan 21:S0092-8674(22)01582-3. doi: 10.1016/j.cell.2022.12.039. Also available on bioRxiv

Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen I-M, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D, RNA Virus Discovery Consortium (including Blanchard JL), Krupovic M,  Dolj VV, Kyrpides NC,  Koonin EV, Gophna U (2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 185:21(4023-4037) .e18.

Fremin BJ, Bhatt AM, Kyrpides NC, Global Phage Small Open Reading Frame (GP-SmORF) Consortium (including Blanchard JL) (2022) Thousands of small, novel genes predicted in global phage genomes. Cell Reports. 39:12.

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A; IMG/M Data Consortium (including members of our lab Blanchard JL, Alteio LV, Rodriguez-Reillo W)), Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA (2021) A genomic catalogue of Earth's microbiome Nat Biotechnology 39(4):499-509. doi: 10.1038/s41587-020-0718-6.

Roy Chowdhury P, Golas SM, Alteio LV, Stevens JTE, Billings AF, Blanchard JL, Melillo JM, DeAngelis KM. (2021) The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest Front Microbiol. 12:666558. doi: 10.3389/fmicb.2021.666558.

Pec GJ, van Diepen LTA, Knorr M, Grandy AS, Melillo JM, DeAngelis KM, Blanchard JL, Frey SD (2021) Fungal community response to long‐term soil warming with potential implications for soil carbon dynamics Ecosphere 12 (5), e03460

LaCroix R, Walpen N, Sander M, Tfaily MM, Blanchard JL, Keiluweit M (2021) Long-Term Warming Decreases Redox Capacity of Soil Organic Matter Environ. Sci. Technol. Lett. 2021, 8, 1, 92–97 doi: 10.1021/acs.estlett.0c00748

Haas KN and Blanchard JL (2020) Kineothrix. Bergey's Manual of Systematics of Archaea and Bacteria. doi: 10.1002/9781118960608.gbm01648

Andras JP, Rodriguez-Reillo WG, Truchon A, Blanchard JL, Pierce EA, Ballantine KA (2020) Rewilding the small stuff: The effect of ecological restoration on prokaryotic communities of peatland soils FEMS Microbiology Ecology Oct 2;96(10):fiaa144. doi: 10.1093/femsec/fiaa144.

Alteio L, Schulz F, Seshadri R, Varghese N, Rodriguez-Reillo W, Ryan E, Goudeau D, Eichorst S, Malmstrom R, Bowers R, Katz L, Blanchard J, Woyke T (2020) Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil. mSystems. doi: 10.1128/mSystems.00768-19.

Haas KN, Blanchard JL (2020) Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov., and Lacrimaspora gen. nov., including reclassification of fifteen taxa. Int J Syst Evol Microbiol. 2020 Jan;70(1):23-34. doi: 10.1099/ijsem.0.003698.

Zandvakili OR, Cole E, Etemadi F, Hashemi M, Blanchard JL, Xing B (2019) Investigating soil bacterial community composition and response to hardwood biochar amendment using quantitative PCR Applied Soil Ecology.

Schulz F, Alteio L, Goudeau D, Ryan E, Yu G, Malmstrom R, Blanchard J, Woyke T (2018) Hidden diversity of soil giant viruses Nature Communications Nov 19;9(1):4881. doi: 10.1038/s41467-018-07335-2.

Haas KH, Blanchard JL (2017) Kineothrix alysoides, gen. nov., sp. nov., a saccharolytic, butyrate-producer within the family Lachnospiraceae. IJSEM. Nov 8. doi: 10.1099/ijsem.0.001643

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE (2016) Tempo and mode of genome evolution in a 50,000-generation experiment. Nature. Aug 1. doi: 10.1038/nature18959.

G Pold, AF Billings, JL Blanchard, DB Burkhardt, SD Frey, JM Melillo, J Schnabel, LT van Diepen, KM DeAngelis (2016) Long-term warming alters carbohydrate degradation potential in temperate forest soils. Applied and Environmental Microbiology. 02012-16

Petit E, Coppi MV, Hayes JC, Tolonen A, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova, N, Lykidis A, Land M, Hauser L, Kripides N, Henrissat B, Lau J, Schnell D, Church G, Leschine SB, Blanchard JL (2015) Genome and transcriptome of Clostridium phytofermentans, catalyst for the direct conversion of plant feedstocks to fuels . PLoS ONE. 10(6): e0118285.

DeAngelis KM, Pold G, Topcuoglu BD, van Diepen LTA, Varney R, Blanchard JL, Melillo J, Frey SD (2015) Long-term forest soil warming alters microbial communities in temperate forest soils. Frontiers in Microbiology. 6:104.

Biddle AS, Leschine S, Huntemann M, Han J, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Schaumberg A, Pati A, Stamatis D, Reddy T, Lobos E, Goodwin L, Nordberg HP, Cantor MN, Hua SX, Woyke T, Blanchard JL (2014). The complete genome sequence of Clostridium indolis. Standards in Genome Sciences. Mar;9(3)

Sun Z, Blanchard JL (2014) Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PLOS ONE. 9(3):e88837

Blanchard J, Abdul-Rahman F (2014) Carboxysomes, Structure and Function. In: Gargaud M. (Ed.) Encyclopedia of Astrobiology: SpringerReference. Springer-Verlag Berlin Heidelberg

Mukherjee S, Thompson LK, Godin S, Schackwitz W, Lipzen A, Martin J, Blanchard, JL (2014) Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans. PLOS ONE. 9(1):e86731

Biddle AS, Black SJ, Blanchard JL (2013) An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLOS ONE. PLoS ONE 8(10): e77599

Abdul-Rahman F, Petit E, Blanchard JL (2013) The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly. J Phylogen Evolution Biol. 1:e118

Biddle AS, Stewart L, Blanchard JL, Leschine SB (2013) Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities. Diversity 5(3), 627-640

Andrew C. Tolonen, Elsa Petit, Jeffrey L. Blanchard, Tom Warnick, Susan B. Leschine (2013). "Technologies to Study Plant Biomass Fermentation using the Model Bacterium Clostridium phytofermentans." Chapt 7 (pp 114-139) in "Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems". Edited by Jianzhong Sun, Shi-You Ding and Joy Peterson. The Royal Society of Chemistry.

Petit E, Latouf W, Coppi M, Currie D, Rhomasko I, Desphande S, Haas K, Alvelo-Maurosa JG, Wardman C, Schnell D, Leschine L, Blanchard J (2013) Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS One. 8(1):e54337.

Damery D, Hayes J, Blanchard JL (2010). The potential for production of ethanol from woody biomass by the microbe Clostridium phytofermentans. Wood Structures and Properties '10. Edited by Kúdela and Lagaňa. Arbora Publishers. p21-25.

Hu J, Blanchard JL (2009) Environmental sequence data from the Sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus are not a harbinger for an escalation in genetic drift. Molecular Biology and Evolution. Jan;26(1):5-13.

Lu S, Becker KA, Hagen MJ, Yan H, Roberts AL, Mathews LA, Schneider SS, Siegelmann HT, Macbeth KJ, Tirrell SM, Blanchard JL, Jerry DJ. (2008) Transcriptional Responses to Estrogen and Progesterone in Mammary Gland Identify Networks Regulating p53 Activity. Endocrinology. 2008 Oct;149(10):4809-20. Epub 2008 Jun 12.

Blanchard JL, Chen W, Conlon EM, Pomposiello PJ. (2007) Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE. 2(11):e1186

Conlon EM, Alpargu G, Blanchard JL. (2006) Comparative genomics approaches for identifying genetic regulatory networks. Chance. 19:45-48.

Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, McLeod R, Roberts CW. (2006) Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot Cell. 5:1517-31.

Blanchard JL (2004) Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change. Field Crops Research. 90:117-131.

de Visser AJM, Hermisson J, Wagner, GP, Ancel LW, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, Whitlock MC (2003) Evolution and detection of genetic robustness. Evolution. 57:1959-1972.

Kuffner RM, Gonzales M, Steadman P, Wlodek DK, Jankowitz RJ, Boinoff JR, Montoya AL, Peterson TF, Bulmore DL, Blanchard JL (2002) PathDB. Nucleic Acids Research Database Issue.

Brinkman FSL, Blanchard JL, Greberg H, Wan I, De Koning A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling P, Hancock REW, Rose AM, SJM Jones (2002). Plant-like genes in Chlamydia species reflect Chlamydia's ancestral relationship with cyanobacteria and the chloroplast. Genome Research. 12:1159-67.

Blanchard JL, Lynch M (2000) Organelle Genes: why do organellar genes end up in the nucleus? Trends in Genetics. 16:315-320. de Visser AJM, Zeyl CW, Gerrish PJ,

Blanchard JL, Lenski RE (1999) Diminishing returns from mutation supply rate in asexual populations. Science. 283:404-406.

Lynch M, Blanchard JL, Houle D, Kibota T, Schultz S, Vassileva L, Willis J (1999) Spontaneous deleterious mutation. Evolution. 53:645–663.

Blanchard JL, Hicks JS (1999) The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. Journal of Eukaryotic Microbiology. 46:367-375.

Lynch M, Blanchard JL (1998) Deleterious mutation accumulation in organelle genomes. Genetica. 102/103:29-39.

Bruns BU, Blanchard JL, Schmidt GW (1998) On the modulation of thylakoid structure and function upon adaptation to prolonged nitrogen-deficiency. Pp. 3081-3086 in Photosynthesis: Mechanisms and Effects (IV), G. Garab (ed), Kluwer Acad. Publ., Dordrecht.

Blanchard JL, Schmidt GW (1996) Mitochondrial DNA migration events in yeast and mammals: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Molecular Biology and Evolution. 13:537-548.

Blanchard JL, Schmidt GW (1995) Pervasive migration of organellar DNA to the nucleus in plants. Journal of Molecular Evolution. 41:397-406.

Chen AB, Championsmith AA, Blanchard JL, Niepelt BA, Federici MM, Formento J, Sinicropi DV (1992) Quantitation of E. coli protein impurities in recombinant human interferon. Applied Biochemistry and Biotechnology. 36:137-152.

Weathers PJ, Blanchard JL (1990) Multiple fruiting of the edible mushroom, Coprinus cinereus, from explants of the stipe. Applied Microbiology and Biotechnology. 33:652-656.

Weathers PJ, Cheetham RD, Blanchard JL, Niedzielski J, Crusberg TC (1987) Biotraps for heavy metal removal and recovery from electroplating wastewater. Society for Industrial Microbiology (SIM) News 37:9-11.