Raw Lab

Write without fear. Edit without mercy - Rogena Mitchell-Jones

Publications

69
White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

Publications

69
White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

68
White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

67
Buivydaitė Ž, Aryal L, Corrêa FB, Chen T, Langlois V, Elberg CL, Netherway T, Wang R, Zhao T, Acharya B, Emerson JB, Hillary L, Khadka RB, Mason-Jones K, Sapkota R, Sutela S, Trubl G, White III RA, Winding A, Carreira C. Meeting Report: The first soil viral workshop 2022. Virus Res. 2023, 199121. doi: 10.1016/j.virusres.2023.199121. PMID: 37086855.

66
Ford CT, Yasa S, Machado DJ, White III RA, Janies D. Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling. Front. Virol. 2023, 3:1172027. doi: 10.3389/fviro.2023.1172027.

65
Braley LE, Jewell JB, Figueroa III JL, Humann J, Main D, Mora-Romero GA, Moroz N, Woodhall JW, White III RA, Tanaka K. Nanopore sequencing with GraphMap for comprehensive pathogen detection in potato field soil. Plant Disease. 2023, doi: 10.1094/PDIS-01-23-0052-SR.

Publications

64
Starke R, Fiore-Donno AM, White III RA, Parente Fernandes ML, Martinović T, Bastida F, Delgado-Baquerizo M, Jehmlich N. Biomarker metaproteomics for relative taxa abundances across soil organisms. Soil Biology and Biochemistry. 2023, 175, 108861 doi: 10.1016/j.soilbio.2022.108861.

Publications

63
Jacob Machado D, White III RA, Kofsky J, Janies DA. Multiple'omics'-analysis reveals the role of prostaglandin E2 in Hirschsprung's disease. Antimicrob Stewardship Healthcare Epidemiol. 2021, 1(1), e60. https://doi: doi.org/10.1017/ash.2021.222.

62
Tang W, Chen M, Guo X, Zhou K, Wen Z, Liu F, Liu X, Mao X,He X, Hu W, Sun X, Tang J, Li H, White III RA, Lv W, Wang P, Hang B, Sun R, Wang X, Xia Y. Multiple'omics'-analysis reveals the role of prostaglandin E2 in Hirschsprung's disease. Free Radical Biology and Medicine. 2021, 164:390-398 doi: 10.1016freeradbiomed.2020.12.456.

61
Chen T, Qin Y, Chen M, Zhang Y, Wang X, Dong T, Chen G, Sun X, Lu T, White III RA, Ye P, Tun HM, Xia Y. Gestational diabetes mellitus is associated with the neonatal gut microbiota and metabolome. BMC Med. 2021, 19(1):120. doi: 10.1186/s12916-021-01991-w. PMID: 34039350; PMCID: PMC8157751.

60
Zayed AA, Lücking D, Mohssen M, Cronin D, Bolduc B, Gregory AC, Hargreaves KR, Piehowski PD, White III RA, Huang EL, Adkins JN, Roux S, Moraru C, Sullivan MB. efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics. 2021, 37(22):4202-4208. doi: 10.1093/bioinformatics/btab451. PMID: 34132786; PMCID: PMC9502166.

59
White III RA, Rosnow J, Piehowski PD, Brislawn CJ, Moran JJ. In situ non-destructive temporal measurements of the rhizosphere microbiome ‘hot-spots’ using metaproteomics Agronomy 2021, 11(11), 2248, doi: 10.3390/agronomy11112248

58
White III RA. The future of virology is synthetic. mSystems. 2021, 6(4):e0077021. doi: 10.1128/mSystems.00770-21. PMID: 34463577; PMCID: PMC8519122.

57
Blake II RC, Shively JE, Timkovich R, White III RA. Homogeneous cytochrome 579 Is an octamer that reacts too slowly with soluble iron to be the initial iron oxidase in the respiratory chain of Leptospirillum ferriphilum. Front Microbiol. 2021, 12:673066. doi: 10.3389/fmicb.2021.673066. PMID: 34012429; PMCID: PMC8126622.

56
White III RA, Visscher PT, Burns BP. Between a rock and a soft place: the role of viruses in lithification of modern microbial mats. Trends Microbiol. 2021, (3):204-213. doi: 10.1016/j.tim.2020.06.004. PMID: 32654857.

Publications

55
Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White III RA, Burns BP, Coolen MJL. Functional gene expression in Shark Bay hypersaline mMicrobial mats: adaptive responses. Front Microbiol. 2020, 11:560336. doi: 10.3389/fmicb.2020.560336. PMID: 33312167; PMCID: PMC7702295.

54
Wong HL, MacLeod FI, White III RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome. 2020, 8(1):135. doi: 10.1186/s40168-020-00910-0. PMID: 32938503; PMCID: PMC7495880.

53
McClure RS, Lee JY, Chowdhury TR, Bottos EM, White III RA, Kim YM, Nicora CD, Metz TO, Hofmockel KS, Jansson JK, Song HS. Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Sci Rep. 2020, 10(1):10882. doi: 10.1038/s41598-020-67878-7. PMID: 32616808; PMCID: PMC7331712.

52
Gañán L, White III RA, Friesen ML, Peever TL, Amiri A. A genome resource for the apple powdery mildew pathogen Podosphaera leucotricha. Phytopathology. 2020, 110(11):1756-1758. doi: 10.1094/PHYTO-05-20-0158-A. PMID: 32515644.

51
White III RA, Soles SA, Brady AL, Southam G, Lim DSS, Slater GF. Biosignatures associated with freshwater microbialites. Life (Basel). 2020, 10(5):66. doi: 10.3390/life10050066. PMID: 32429118; PMCID: PMC7281397.

50
Petipas RH, Bowsher AW, Bekkering CS, Jack CN, McLachlan EE, White III RA, Younginger BS, Tiemann LK, Evans SE, Friesen ML. Evolution of Functional Traits in Plants (vol 181, pg 20, 2020). International journal of plant sciences. 181 (3), 386-386.

49
Blake II RC, White III RA. In situ absorbance measurements: a new means to study respiratory electron transfer in chemolithotrophic microorganisms. Adv Microb Physiol. 2020;76:81-127. doi: 10.1016/bs.ampbs.2020.01.003. Epub 2020 Feb 5. PMID: 32408948.

Publications

48
White III RA, Norman JS, Mclachlan EE, Dunham JP, Garoutte A, Friesen ML. Revealing the draft genome sequence of Bradyrhizobium sp. strain USDA 3458, an effective symbiotic diazotroph isolated from Cowpea (Vigna unguiculata) genotype IT82E-16. Microbiol Resour Announc. 2019, 8(38):e00813-19. doi: 10.1128/MRA.00813-19. PMID: 31537665; PMCID: PMC6753269.

47
Köberl M, Erschen S, Etemadi M, White III RA, El-Arabi TF, Berg G. Deciphering the microbiome shift during fermentation of medicinal plants. Sci Rep. 2019, 9(1):13461. doi: 10.1038/s41598-019-49799-2. PMID: 31530872; PMCID: PMC6748931.

46
Roy Chowdhury T, Lee JY, Bottos EM, Brislawn CJ, White III RA, Bramer LM, Brown J, Zucker JD, Kim YM, Jumpponen A, Rice CW, Fansler SJ, Metz TO, McCue LA, Callister SJ, Song HS, Jansson JK. Metaphenomic responses of a native prairie soil microbiome to moisture perturbations. mSystems. 2019, 4(4):e00061-19. doi: 10.1128/mSystems.00061-19. PMID: 31186334; PMCID: PMC6561317.

45
White III RA, Norman JS, Mclachlan EE, Dunham JP, Garoutte A, Friesen ML. Elucidation of the genome of Bradyrhizobium sp. strain USDA 3456, a historic agricultural diazotroph fom cowpea (Vigna unguiculata). Microbiol Resour Announc. 2019, 8(33):e00812-19. doi: 10.1128/MRA.00812-19. PMID: 31416877; PMCID: PMC6696652.

44
Adelshin RV, Sidorova EA, Bondaryuk AN, Trukhina AG, Sherbakov DY, White III RA, Andaev EI, Balakhonov SV. '886-84-like' tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics. Ticks Tick Borne Dis. 2019, 10(5):1168-1172. doi: 10.1016/j.ttbdis.2019.06.006. PMID: 31253516.

43
Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White III RA; IBDMDB Investigators; Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019, 569(7758):655-662. doi: 10.1038/s41586-019-1237-9. PMID: 31142855; PMCID: PMC6650278.

42
Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White III RA, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME, Blackwell M, Nicora CD, Kim YM, Reardon PN, Lipton MS, Adkins JN, Pett-Ridge J, Brodie EL. Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle. Nat Microbiol. 2019 May;4(5):864-875. doi: 10.1038/s41564-019-0384-y. Epub 2019 Mar 11. PMID: 30858574.

41
White III RA, Soles SA, Gavelis G, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The complete genome and physiological analysis of the eurythermal firmicute Exiguobacterium chiriqhucha strain RW2 isolated from a freshwater microbialite, widely adaptable to broad thermal, pH, and salinity ranges. Front Microbiol. 2019, 9:3189. doi: 10.3389/fmicb.2018.03189. PMID: 30671032; PMCID: PMC6331483.

40
Shetty P, Boboescu IZ, Pap B, Wirth R, Kovács KL, Bíró T, Futó Z, White III RA, Maróti G. Exploitation of algal-bacterial consortia in combined biohydrogen generation and wastewater treatment. Frontiers in Energy Research. 2019, 7:52. doi: 10.3389/fenrg.2019.00052. PMID: 31139652; PMCID: PMC6528179.

Publications

39
Müller O, Bang-Andreasen T, White III RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol. 2018, 20(12):4328-4342. doi: 10.1111/1462-2920.14348. PMID: 29971895.

38
Wong HL, White III RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP. Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME J. 2018, 12(11):2619-2639. doi: 10.1038/s41396-018-0208-8. PMID: 29980796; PMCID: PMC6194083.

37
White III RA, Gavelis G, Soles SA, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The complete genome and physiological analysis of the microbialite-dwelling Agrococcus pavilionensis sp. nov; reveals genetic promiscuity and predicted adaptations to environmental stress. Front Microbiol. 2018, 9:2180. doi: 10.3389/fmicb.2018.02180. PMID: 30374333; PMCID: PMC6196244.

36
Callister SJ, McCue LA, Boaro AA, LaMarche B, White III RA, Brown JM, Ahring BK. Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor. PLoS One. 2018, 13(10):e0204831. doi: 10.1371/journal.pone.0204831. PMID: 30289885; PMCID: PMC6173382.

35
Callister SJ, Fillmore TL, Nicora CD, Shaw JB, Purvine SO, Orton DJ, White III RA, Moore RJ, Burnett MC, Nakayasu ES, Payne SH, Jansson JK, Paša-Tolić L. Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography. J Proteome Res. 2018, 17(8):2714-2725. doi: 10.1021/acs.jproteome.8b00222. PMID: 30004228.

34
Dong T, Chen T, White III RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H, Xia Y. Meconium microbiome associates with the development of neonatal jaundice. Clin Transl Gastroenterol. 2018, 9(9):182. doi: 10.1038/s41424-018-0048-x. PMID: 30237489; PMCID: PMC6147945.

33
Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White III RA, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. ISME J. 2018, 12(6):1605-1618. doi: 10.1038/s41396-018-0099-8. PMID: 29568113; PMCID: PMC5955906.

32
Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White III RA, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES. The MPLEx protocol for multi-omic analyses of soil samples. J Vis Exp. 2018, (135):57343. doi: 10.3791/57343. PMID: 29912205; PMCID: PMC6101435.

31
Braun J, Brislawn C, Casero D, Purvine S, Scott JJ, White III RA, Arze C, Lloyd-Price J, Vlamakis H, Xavier R, Huttenhower C, Graeber T, Jansson J. 1100-Dynamics of the microbial metaproteome in inflammatory bowel disease. Gastroenterology. 2018, 154 (6), S-217.

30
White III RA, Wong HL, Ruvindy R, Neilan BA, Burns BP. Viral communities of Shark Bay modern stromatolites. Front Microbiol. 2018, 9:1223. doi: 10.3389/fmicb.2018.01223. PMID: 29951046; PMCID: PMC6008428.

Publications

29
White III RA, Borkum MI, Rivas-Ubach A, Bilbao A, Wendler JP, Colby SM, Köberl M, Jansson C. From data to knowledge: The future of multi-omics data analysis for the rhizosphere. Rhizosphere. 2017 Dec 1;3:222-229. doi: 10.1016/j.rhisph.2017.08.003. PMID: 29552679.

28
White III RA, Rivas-Ubach A, Borkum MI, Köberl M, Bilbao A, Colby SM, Hoyt DW, Bingol K, Kim Y-M, Wendler JP, Hixson KK, Jansson C. The state of rhizospheric science in the era of multi-omics: a practical guide to omics technologies. Rhizosphere. 2017, 3:212-21. PMID: 29552661.

27
Ahkami AH, White III RA, Handakumbura PP, Jansson C. Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity. Rhizosphere. 2017, 3:233-43. doi: 10.1016/j.rhisph.2017.07.007. PMID: 30728845; PMCID: PMC6352235.

26
Wong HL, Visscher PT, White III RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep. 2017, 7:46160. doi: 10.1038/srep46160. PMID: 28397816; PMCID: PMC5387419.

Publications

25
Khadempour L, Burnum-Johnson KE, Baker ES, Nicora CD, Webb-Robertson BM, White III RA, Monroe ME, Huang EL, Smith RD, Currie CR. The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Mol Ecol. 2016, 25(22):5795-5805. doi: 10.1111/mec.13872. PMID: 27696597; PMCID: PMC5118115.

24
White III RA, Callister SJ, Moore RJ, Baker ES, Jansson JK. The past, present and future of microbiome analyses. Nature Protocols 11 (11), 2049-2053.

23
White III RA, Bottos EM, Roy Chowdhury T, Zucker JD, Brislawn CJ, Nicora CD, Fansler SJ, Glaesemann KR, Glass K, Jansson JK. Moleculo long-read sequencing facilitates assembly and genomic binning from complex soil metagenomes. mSystems. 2016, 1(3):e00045-16. doi: 10.1128/mSystems.00045-16. PMID: 27822530; PMCID: PMC5069762.

22
Oxford KL, Wendler JP, McDermott JE, White III RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. The landscape of viral proteomics and its potential to impact human health. Expert Rev Proteomics. 2016, 13(6):579-91. doi: 10.1080/14789450.2016.1184091. PMID: 27133506.

21
White III RA, Chan AM, Gavelis GS, Leander BS, Brady AL, Slater GF, Lim DS, Suttle CA. Metagenomic analysis suggests modern freshwater microbialites harbor a distinct core microbial community. Front Microbiol. 2016, 6:1531. doi: 10.3389/fmicb.2015.01531. PMID: 26903951; PMCID: PMC4729913.

20
Ruvindy R, White III RA, Neilan BA, Burns BP. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics. ISME J. 2016, 10(1):183-96. doi: 10.1038/ismej.2015.87. PMID: 26023869; PMCID: PMC4681862.

Publications

19
Gavelis GS, White III RA, Suttle CA, Keeling PJ, Leander BS. Single-cell transcriptomics using spliced leader PCR: evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates. BMC Genomics. 2015, 16(1):528. doi: 10.1186/s12864-015-1636-8. PMID: 26183220; PMCID: PMC4504456.

18
White III RA, Power IM, Dipple GM, Southam G, Suttle CA. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential. Front Microbiol. 2015, 6:966. doi: 10.3389/fmicb.2015.00966. PMID: 26441900; PMCID: PMC4585152.

17
Köberl M, White III RA, Erschen S, Spanberger N, El-Arabi TF, Jansson JK, Berg G. Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis. Genome Announc. 2015, 3(4):e00862-15. doi: 10.1128/genomeA.00862-15. PMID: 26272562; PMCID: PMC4536673.

16
Köberl M, White III RA, Erschen S, El-Arabi TF, Jansson JK, Berg G. Draft genome sequence of Streptomyces sp. strain Wb2n-11, a desert isolate with broad-spectrum antagonism against soilborne phytopathogens. Genome Announc. 2015, 3(4):e00860-15. doi: 10.1128/genomeA.00860-15. PMID: 26251492; PMCID: PMC4541278.

15
Köberl M, White III RA, Erschen S, El-Arabi TF, Jansson JK, Berg G. Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla. Genome Announc. 2015, 3(4):e00861-15. doi: 10.1128/genomeA.00861-15. PMID: 26251493; PMCID: PMC4541268.

14
Gavelis GS, Hayakawa S, White III RA, Gojobori T, Suttle CA, Keeling PJ, Leander BS. Eye-like ocelloids are built from different endosymbiotically acquired components. Nature. 2015, 523(7559):204-7. doi: 10.1038/nature14593. PMID: 26131935.

13
Chow CE, Winget DM, White III RA, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Front Microbiol. 2015, 6:265. doi: 10.3389/fmicb.2015.00265. PMID: 25914678; PMCID: PMC4392320.

Publications

12
Zheng Q, Zhang R, Xu Y, White III RA, Wang Y, Luo T, Jiao N. A marine inducible prophage vB_CibM-P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354. Sci Rep. 2014, 4:7118. doi: 10.1038/srep07118. PMID: 25406510; PMCID: PMC4236739.

Publications

11
White III RA, Grassa CJ, Suttle CA. First draft genome sequence from a member of the genus Agrococcus, isolated from modern microbialites. Genome Announc. 2013, 1(4):e00391-13. doi: 10.1128/genomeA.00391-13. PMID: 23814108; PMCID: PMC3695436.

10
White III RA, Suttle CA. The draft genome sequence of Sphingomonas paucimobilis strain HER1398 (Proteobacteria), host to the giant PAU phage, indicates that it is a member of the genus Sphingobacterium (Bacteroidetes). Genome Announc. 2013, 1(4):e00598-13. doi: 10.1128/genomeA.00598-13. PMID: 23929486; PMCID: PMC3738902.

9
Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White III RA, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife. 2013, ;2:e00569. doi: 10.7554/eLife.00569. PMID: 23840927; PMCID: PMC3699833.

Publications

8
White III RA, Quake SR, Curr K. Digital PCR provides absolute quantitation of viral load for an occult RNA virus. J Virol Methods. 2012 179(1):45-50. doi: 10.1016/j.jviromet.2011.09.017. PMID: 21983150.

Publications

7
Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White III RA, Loomer P, Armitage GC, Relman DA. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012, 6(5):915-26. doi: 10.1038/ismej.2011.169. PMID: 22158393; PMCID: PMC3329113.

6
Jiang N, Weinstein JA, Penland L, White III RA, Fisher DS, Quake SR. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc Natl Acad Sci U S A. 2011, 108(13):5348-53. doi: 10.1073/pnas.1014277108. PMID: 21393572; PMCID: PMC3069157.

Publications

5
White III RA, Quake SR, Fan CHM, Blainey P. Digital PCR calibration for high throughput sequencing. US Patent App. 12/541,722.

Publications

4
Weinstein JA, Jiang N, White III RA, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science. 2009, 324(5928):807-10. doi: 10.1126/science.1170020. PMID: 19423829; PMCID: PMC3086368.

3
White III RA, Curr K. GBV-C acute infected cells reveal IL-16 cell mediated downregulation of critical hosts proteins involved in HIV-1 replication. Retrovirology. 2009, 6:2. doi: 10.1186/1742-4690-6-2. PMID: 19152648; PMCID: PMC2654897.

2
White III RA, Blainey PC, Fan HC, Quake SR. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics. 2009 Mar 19;10:116. doi: 10.1186/1471-2164-10-116. Erratum in: BMC Genomics. 2009;10:541. PMID: 19298667; PMCID: PMC2667538.

Publications

1
Waldrop MP, White III RA, Douglas TA. Isolation and identification of cold-adapted fungi in the Fox Permafrost Tunnel, Alaska. University of Alaska, Fairbanks.

Preprint Publications

8
White III RA, Garoutte A, McLachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. Preprints. 2023, 2023030168. doi: 10.20944/preprints202303.0168.v1.

7
Ford CT, Yasa S, Machado DJ, White III RA, Janies D. Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling. bioRxiv. 2023, 2023.02. doi: 10.1094/PDIS-01-23-0052-SR.

6
Figueroa III JL, Panyala A, Colby S, Friesen ML, Tiemann L, White III RA. MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data. bioRxiv, 2022, doi: 10.1101/2022.11.22.51756

5
Zhalnina K, White III RA, de Raad M, Deng K, Nicora CD, Karaoz U, Pett-Ridge J, Firestone M, Lipton MS, Northen T, Brodie EL. Metabolic traits and the niche of bulk soil bacteria in a Mediterranean rassland. bioRxiv, 2022.06. doi: 21.497019

4
White III RA, Norman JS, McLachlan EE, Dunham JP, Garoutte A, Friesen ML. Elucidation of the draft genome sequence of Ideonella azotifigens DSMZ21438 a novel aerobic diazotroph of the betaproteobacteria isolated from grass rhizosphere soil. Preprints. 2019, 2019100250. doi: 10.20944/preprints201910.0250.v1.

3
White III RA, McLachlan EE, Dunham JP, Garoutte A, Friesen ML. Unraveling the draft genome sequence of Paenibacillus sp.. tmac-D7 a non-rhizobial endophyte from Trifolium macraei located in Bodega Bay, California. Preprints. 2020, 2020010263. doi: 10.20944/preprints202001.0263.v1.

2
White III RA, Brown J, Colby S, Overall CC, J, Lee J, Zucker J, Glaesemann KR, Jansson C, Jansson JK. ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data. PeerJ Preprints. 2017;5:e2843v1.

1
White III RA, Panyala A, Glass K, Colby S, Glaesemann KR, Jansson C, Jansson JK. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data. PeerJ Preprints 5, e2825v1.

Patent Publications

1
White III RA, Quake SR, Fan CHM, Blainey P. Digital PCR calibration for high throughput sequencing. US Patent App. 12/541,722.

Theses Publications

1
White III RA. Metagenomic and genomic analyses of modern freshwater microbialites: unmasking a community of complex metabolic potential. University of British Columbia.

Book Chapters Publications

3
Visscher PT, Gallagher KL, Bouton A, Vennin E, Thomazo C, White III RA, Burns BP. Treatise Online No. 163: Part B, Volume 1, Chapter 3: Microbial Mats. In: Klimley AP, Orr RT, editors. The Treatise on Invertebrate Paleontology, Geobiology. Lawrence, Kansas: The University of Kansas Paleontological Institute; 2022. p. B1-B20. doi: 10.17161/to.v163.b.1.3.

2
White III RA. The global distribution of modern microbialites: not so uncommon after all. Astrobiology and Cuatro Ciénegas basin as an analog of Early Earth, 107-134.

1
White III RA, Cardenas JNB, Hayden RT. Virology: the next generation from digital PCR to single virion genomics. Methods in Microbiology 42, 555-567.

Write without fear. Edit without mercy - Rogena Mitchell-Jones

Publications

White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

Publications

White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

White III RA, A Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. 2023. Agronomy 13 (5), 1294.

Ford CT, Yasa S, Machado DJ, White III RA, Janies D. Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling. Front. Virol. 2023, 3:1172027. doi: 10.3389/fviro.2023.1172027.

Braley LE, Jewell JB, Figueroa III JL, Humann J, Main D, Mora-Romero GA, Moroz N, Woodhall JW, White III RA, Tanaka K. Nanopore sequencing with GraphMap for comprehensive pathogen detection in potato field soil. Plant Disease. 2023, doi: 10.1094/PDIS-01-23-0052-SR.

Publications

Starke R, Fiore-Donno AM, White III RA, Parente Fernandes ML, Martinović T, Bastida F, Delgado-Baquerizo M, Jehmlich N. Biomarker metaproteomics for relative taxa abundances across soil organisms. Soil Biology and Biochemistry. 2023, 175, 108861 doi: 10.1016/j.soilbio.2022.108861.

Publications

Jacob Machado D, White III RA, Kofsky J, Janies DA. Multiple'omics'-analysis reveals the role of prostaglandin E2 in Hirschsprung's disease. Antimicrob Stewardship Healthcare Epidemiol. 2021, 1(1), e60. https://doi: doi.org/10.1017/ash.2021.222.

Chen T, Qin Y, Chen M, Zhang Y, Wang X, Dong T, Chen G, Sun X, Lu T, White III RA, Ye P, Tun HM, Xia Y. Gestational diabetes mellitus is associated with the neonatal gut microbiota and metabolome. BMC Med. 2021, 19(1):120. doi: 10.1186/s12916-021-01991-w. PMID: 34039350; PMCID: PMC8157751.

White III RA, Rosnow J, Piehowski PD, Brislawn CJ, Moran JJ. In situ non-destructive temporal measurements of the rhizosphere microbiome ‘hot-spots’ using metaproteomics Agronomy 2021, 11(11), 2248, doi: 10.3390/agronomy11112248

White III RA. The future of virology is synthetic. mSystems. 2021, 6(4):e0077021. doi: 10.1128/mSystems.00770-21. PMID: 34463577; PMCID: PMC8519122.

White III RA, Visscher PT, Burns BP. Between a rock and a soft place: the role of viruses in lithification of modern microbial mats. Trends Microbiol. 2021, (3):204-213. doi: 10.1016/j.tim.2020.06.004. PMID: 32654857.

Publications

Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White III RA, Burns BP, Coolen MJL. Functional gene expression in Shark Bay hypersaline mMicrobial mats: adaptive responses. Front Microbiol. 2020, 11:560336. doi: 10.3389/fmicb.2020.560336. PMID: 33312167; PMCID: PMC7702295.

Wong HL, MacLeod FI, White III RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome. 2020, 8(1):135. doi: 10.1186/s40168-020-00910-0. PMID: 32938503; PMCID: PMC7495880.

Gañán L, White III RA, Friesen ML, Peever TL, Amiri A. A genome resource for the apple powdery mildew pathogen Podosphaera leucotricha. Phytopathology. 2020, 110(11):1756-1758. doi: 10.1094/PHYTO-05-20-0158-A. PMID: 32515644.

White III RA, Soles SA, Brady AL, Southam G, Lim DSS, Slater GF. Biosignatures associated with freshwater microbialites. Life (Basel). 2020, 10(5):66. doi: 10.3390/life10050066. PMID: 32429118; PMCID: PMC7281397.

Petipas RH, Bowsher AW, Bekkering CS, Jack CN, McLachlan EE, White III RA, Younginger BS, Tiemann LK, Evans SE, Friesen ML. Evolution of Functional Traits in Plants (vol 181, pg 20, 2020). International journal of plant sciences. 181 (3), 386-386.

Blake II RC, White III RA. In situ absorbance measurements: a new means to study respiratory electron transfer in chemolithotrophic microorganisms. Adv Microb Physiol. 2020;76:81-127. doi: 10.1016/bs.ampbs.2020.01.003. Epub 2020 Feb 5. PMID: 32408948.

Publications

Köberl M, Erschen S, Etemadi M, White III RA, El-Arabi TF, Berg G. Deciphering the microbiome shift during fermentation of medicinal plants. Sci Rep. 2019, 9(1):13461. doi: 10.1038/s41598-019-49799-2. PMID: 31530872; PMCID: PMC6748931.

Publications

Wong HL, White III RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP. Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME J. 2018, 12(11):2619-2639. doi: 10.1038/s41396-018-0208-8. PMID: 29980796; PMCID: PMC6194083.

Dong T, Chen T, White III RA, Wang X, Hu W, Liang Y, Zhang Y, Lu C, Chen M, Aase H, Xia Y. Meconium microbiome associates with the development of neonatal jaundice. Clin Transl Gastroenterol. 2018, 9(9):182. doi: 10.1038/s41424-018-0048-x. PMID: 30237489; PMCID: PMC6147945.

Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White III RA, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES. The MPLEx protocol for multi-omic analyses of soil samples. J Vis Exp. 2018, (135):57343. doi: 10.3791/57343. PMID: 29912205; PMCID: PMC6101435.

Braun J, Brislawn C, Casero D, Purvine S, Scott JJ, White III RA, Arze C, Lloyd-Price J, Vlamakis H, Xavier R, Huttenhower C, Graeber T, Jansson J. 1100-Dynamics of the microbial metaproteome in inflammatory bowel disease. Gastroenterology. 2018, 154 (6), S-217.

White III RA, Wong HL, Ruvindy R, Neilan BA, Burns BP. Viral communities of Shark Bay modern stromatolites. Front Microbiol. 2018, 9:1223. doi: 10.3389/fmicb.2018.01223. PMID: 29951046; PMCID: PMC6008428.

Publications

White III RA, Borkum MI, Rivas-Ubach A, Bilbao A, Wendler JP, Colby SM, Köberl M, Jansson C. From data to knowledge: The future of multi-omics data analysis for the rhizosphere. Rhizosphere. 2017 Dec 1;3:222-229. doi: 10.1016/j.rhisph.2017.08.003. PMID: 29552679.

White III RA, Rivas-Ubach A, Borkum MI, Köberl M, Bilbao A, Colby SM, Hoyt DW, Bingol K, Kim Y-M, Wendler JP, Hixson KK, Jansson C. The state of rhizospheric science in the era of multi-omics: a practical guide to omics technologies. Rhizosphere. 2017, 3:212-21. PMID: 29552661.

Ahkami AH, White III RA, Handakumbura PP, Jansson C. Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity. Rhizosphere. 2017, 3:233-43. doi: 10.1016/j.rhisph.2017.07.007. PMID: 30728845; PMCID: PMC6352235.

Wong HL, Visscher PT, White III RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep. 2017, 7:46160. doi: 10.1038/srep46160. PMID: 28397816; PMCID: PMC5387419.

Publications

White III RA, Callister SJ, Moore RJ, Baker ES, Jansson JK. The past, present and future of microbiome analyses. Nature Protocols 11 (11), 2049-2053.

Oxford KL, Wendler JP, McDermott JE, White III RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. The landscape of viral proteomics and its potential to impact human health. Expert Rev Proteomics. 2016, 13(6):579-91. doi: 10.1080/14789450.2016.1184091. PMID: 27133506.

White III RA, Chan AM, Gavelis GS, Leander BS, Brady AL, Slater GF, Lim DS, Suttle CA. Metagenomic analysis suggests modern freshwater microbialites harbor a distinct core microbial community. Front Microbiol. 2016, 6:1531. doi: 10.3389/fmicb.2015.01531. PMID: 26903951; PMCID: PMC4729913.

Ruvindy R, White III RA, Neilan BA, Burns BP. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics. ISME J. 2016, 10(1):183-96. doi: 10.1038/ismej.2015.87. PMID: 26023869; PMCID: PMC4681862.

Publications

Gavelis GS, White III RA, Suttle CA, Keeling PJ, Leander BS. Single-cell transcriptomics using spliced leader PCR: evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates. BMC Genomics. 2015, 16(1):528. doi: 10.1186/s12864-015-1636-8. PMID: 26183220; PMCID: PMC4504456.

White III RA, Power IM, Dipple GM, Southam G, Suttle CA. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential. Front Microbiol. 2015, 6:966. doi: 10.3389/fmicb.2015.00966. PMID: 26441900; PMCID: PMC4585152.

Köberl M, White III RA, Erschen S, El-Arabi TF, Jansson JK, Berg G. Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla. Genome Announc. 2015, 3(4):e00861-15. doi: 10.1128/genomeA.00861-15. PMID: 26251493; PMCID: PMC4541268.

Gavelis GS, Hayakawa S, White III RA, Gojobori T, Suttle CA, Keeling PJ, Leander BS. Eye-like ocelloids are built from different endosymbiotically acquired components. Nature. 2015, 523(7559):204-7. doi: 10.1038/nature14593. PMID: 26131935.

Chow CE, Winget DM, White III RA, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Front Microbiol. 2015, 6:265. doi: 10.3389/fmicb.2015.00265. PMID: 25914678; PMCID: PMC4392320.

Publications

Zheng Q, Zhang R, Xu Y, White III RA, Wang Y, Luo T, Jiao N. A marine inducible prophage vB_CibM-P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354. Sci Rep. 2014, 4:7118. doi: 10.1038/srep07118. PMID: 25406510; PMCID: PMC4236739.

Publications

White III RA, Grassa CJ, Suttle CA. First draft genome sequence from a member of the genus Agrococcus, isolated from modern microbialites. Genome Announc. 2013, 1(4):e00391-13. doi: 10.1128/genomeA.00391-13. PMID: 23814108; PMCID: PMC3695436.

Publications

White III RA, Quake SR, Curr K. Digital PCR provides absolute quantitation of viral load for an occult RNA virus. J Virol Methods. 2012 179(1):45-50. doi: 10.1016/j.jviromet.2011.09.017. PMID: 21983150.

Publications

Jiang N, Weinstein JA, Penland L, White III RA, Fisher DS, Quake SR. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc Natl Acad Sci U S A. 2011, 108(13):5348-53. doi: 10.1073/pnas.1014277108. PMID: 21393572; PMCID: PMC3069157.

Publications

White III RA, Quake SR, Fan CHM, Blainey P. Digital PCR calibration for high throughput sequencing. US Patent App. 12/541,722.

Publications

Weinstein JA, Jiang N, White III RA, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science. 2009, 324(5928):807-10. doi: 10.1126/science.1170020. PMID: 19423829; PMCID: PMC3086368.

White III RA, Curr K. GBV-C acute infected cells reveal IL-16 cell mediated downregulation of critical hosts proteins involved in HIV-1 replication. Retrovirology. 2009, 6:2. doi: 10.1186/1742-4690-6-2. PMID: 19152648; PMCID: PMC2654897.

White III RA, Blainey PC, Fan HC, Quake SR. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics. 2009 Mar 19;10:116. doi: 10.1186/1471-2164-10-116. Erratum in: BMC Genomics. 2009;10:541. PMID: 19298667; PMCID: PMC2667538.

Publications

Waldrop MP, White III RA, Douglas TA. Isolation and identification of cold-adapted fungi in the Fox Permafrost Tunnel, Alaska. University of Alaska, Fairbanks.

Preprint Publications

White III RA, Garoutte A, McLachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-resolved metagenomics of nitrogen transformations in the switchgrass rhizosphere microbiome on marginal lands. Preprints. 2023, 2023030168. doi: 10.20944/preprints202303.0168.v1.

Ford CT, Yasa S, Machado DJ, White III RA, Janies D. Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling. bioRxiv. 2023, 2023.02. doi: 10.1094/PDIS-01-23-0052-SR.

Figueroa III JL, Panyala A, Colby S, Friesen ML, Tiemann L, White III RA. MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data. bioRxiv, 2022, doi: 10.1101/2022.11.22.51756

Zhalnina K, White III RA, de Raad M, Deng K, Nicora CD, Karaoz U, Pett-Ridge J, Firestone M, Lipton MS, Northen T, Brodie EL. Metabolic traits and the niche of bulk soil bacteria in a Mediterranean rassland. bioRxiv, 2022.06. doi: 21.497019

White III RA, McLachlan EE, Dunham JP, Garoutte A, Friesen ML. Unraveling the draft genome sequence of Paenibacillus sp.. tmac-D7 a non-rhizobial endophyte from Trifolium macraei located in Bodega Bay, California. Preprints. 2020, 2020010263. doi: 10.20944/preprints202001.0263.v1.

White III RA, Panyala A, Glass K, Colby S, Glaesemann KR, Jansson C, Jansson JK. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data. PeerJ Preprints 5, e2825v1.

Patent Publications

White III RA, Quake SR, Fan CHM, Blainey P. Digital PCR calibration for high throughput sequencing. US Patent App. 12/541,722.

Theses Publications

White III RA. Metagenomic and genomic analyses of modern freshwater microbialites: unmasking a community of complex metabolic potential. University of British Columbia.

Book Chapters Publications

White III RA. The global distribution of modern microbialites: not so uncommon after all. Astrobiology and Cuatro Ciénegas basin as an analog of Early Earth, 107-134.

White III RA, Cardenas JNB, Hayden RT. Virology: the next generation from digital PCR to single virion genomics. Methods in Microbiology 42, 555-567.