PUB - Publikationen an der Universität Bielefeld

DADA2: High-resolution sample inference from Illumina amplicon data.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP., Nat. Methods 13(7), 2016
PMID: 27214047

Collaborative cloud-enabled tools allow rapid, reproducible biological insights.
Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG., ISME J 7(3), 2012
PMID: 23096404

Sequence-length requirements for phylogenetic methods
Moret BME, Roshan U, Warnow T., 2002

Conservation evaluation and phylogenetic diversity
Faith DP., 1992

UniFrac: an effective distance metric for microbial community comparison.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R., ISME J 5(2), 2010
PMID: 20827291

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.
Berger SA, Krompass D, Stamatakis A., Syst. Biol. 60(3), 2011
PMID: 21436105

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
Matsen FA, Kodner RB, Armbrust EV., BMC Bioinformatics 11(), 2010
PMID: 21034504

SEPP: SATe-enabled phylogenetic placement.
Mirarab S, Nguyen N, Warnow T., Pac Symp Biocomput (), 2012
PMID: 22174280

HMMER web server: interactive sequence similarity searching.
Finn RD, Clements J, Eddy SR., Nucleic Acids Res. 39(Web Server issue), 2011
PMID: 21593126

QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131

Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men.
Abrahamson M, Hooker E, Ajami NJ, Petrosino JF, Orwoll ES., Contemp Clin Trials Commun 7(), 2017
PMID: 29250605

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Katoh K, Standley DM., Mol. Biol. Evol. 30(4), 2013
PMID: 23329690

FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP., PLoS ONE 5(3), 2010
PMID: 20224823

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P., ISME J 6(3), 2011
PMID: 22134646

PyNAST: a flexible tool for aligning sequences to a template alignment.
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R., Bioinformatics 26(2), 2009
PMID: 19914921

Common beans and cowpeas as complementary foods to reduce environmental enteric dysfunction and stunting in Malawian children: study protocol for two randomized controlled trials.
Trehan I, Benzoni NS, Wang AZ, Bollinger LB, Ngoma TN, Chimimba UK, Stephenson KB, Agapova SE, Maleta KM, Manary MJ., Trials 16(), 2015
PMID: 26578308

A new method for non-parametric multivariate analysis of variance
Anderson MJ., 2001

Human gut microbiome viewed across age and geography.
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI., Nature 486(7402), 2012
PMID: 22699611

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.
Hamady M, Lozupone C, Knight R., ISME J 4(1), 2009
PMID: 19710709

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.
Lozupone CA, Hamady M, Kelley ST, Knight R., Appl. Environ. Microbiol. 73(5), 2007
PMID: 17220268

Comparison of phylogenetic trees
Robinson DF, Foulds LR., 1981

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG., PeerJ 2(), 2014
PMID: 25177538

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noe L, Touzet H., Bioinformatics 28(24), 2012
PMID: 23071270

Cohabiting family members share microbiota with one another and with their dogs.
Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R., Elife 2(), 2013
PMID: 23599893

The microbiome of uncontacted Amerindians.
Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcon O, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG., Sci Adv 1(3), 2015
PMID: 26229982

A communal catalogue reveals Earth's multiscale microbial diversity.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vazquez-Baeza Y, Gonzalez A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium, Rivera JLA, Al-Moosawi L, Alverdy J, Amato KR, Andras J, Angenent LT, Antonopoulos DA, Apprill A, Armitage D, Ballantine K, Barta J, Baum JK, Berry A, Bhatnagar A, Bhatnagar M, Biddle JF, Bittner L, Boldgiv B, Bottos E, Boyer DM, Braun J, Brazelton W, Brearley FQ, Campbell AH, Caporaso JG, Cardona C, Carroll J, Cary SC, Casper BB, Charles TC, Chu H, Claar DC, Clark RG, Clayton JB, Clemente JC, Cochran A, Coleman ML, Collins G, Colwell RR, Contreras M, Crary BB, Creer S, Cristol DA, Crump BC, Cui D, Daly SE, Davalos L, Dawson RD, Defazio J, Delsuc F, Dionisi HM, Dominguez-Bello MG, Dowell R, Dubinsky EA, Dunn PO, Ercolini D, Espinoza RE, Ezenwa V, Fenner N, Findlay HS, Fleming ID, Fogliano V, Forsman A, Freeman C, Friedman ES, Galindo G, Garcia L, Garcia-Amado MA, Garshelis D, Gasser RB, Gerdts G, Gibson MK, Gifford I, Gill RT, Giray T, Gittel A, Golyshin P, Gong D, Grossart HP, Guyton K, Haig SJ, Hale V, Hall RS, Hallam SJ, Handley KM, Hasan NA, Haydon SR, Hickman JE, Hidalgo G, Hofmockel KS, Hooker J, Hulth S, Hultman J, Hyde E, Ibanez-Alamo JD, Jastrow JD, Jex AR, Johnson LS, Johnston ER, Joseph S, Jurburg SD, Jurelevicius D, Karlsson A, Karlsson R, Kauppinen S, Kellogg CTE, Kennedy SJ, Kerkhof LJ, King GM, Kling GW, Koehler AV, Krezalek M, Kueneman J, Lamendella R, Landon EM, Lane-deGraaf K, LaRoche J, Larsen P, Laverock B, Lax S, Lentino M, Levin II, Liancourt P, Liang W, Linz AM, Lipson DA, Liu Y, Lladser ME, Lozada M, Spirito CM, MacCormack WP, MacRae-Crerar A, Magris M, Martin-Platero AM, Martin-Vivaldi M, Martinez LM, Martinez-Bueno M, Marzinelli EM, Mason OU, Mayer GD, McDevitt-Irwin JM, McDonald JE, McGuire KL, McMahon KD, McMinds R, Medina M, Mendelson JR, Metcalf JL, Meyer F, Michelangeli F, Miller K, Mills DA, Minich J, Mocali S, Moitinho-Silva L, Moore A, Morgan-Kiss RM, Munroe P, Myrold D, Neufeld JD, Ni Y, Nicol GW, Nielsen S, Nissimov JI, Niu K, Nolan MJ, Noyce K, O'Brien SL, Okamoto N, Orlando L, Castellano YO, Osuolale O, Oswald W, Parnell J, Peralta-Sanchez JM, Petraitis P, Pfister C, Pilon-Smits E, Piombino P, Pointing SB, Pollock FJ, Potter C, Prithiviraj B, Quince C, Rani A, Ranjan R, Rao S, Rees AP, Richardson M, Riebesell U, Robinson C, Rockne KJ, Rodriguezl SM, Rohwer F, Roundstone W, Safran RJ, Sangwan N, Sanz V, Schrenk M, Schrenzel MD, Scott NM, Seger RL, Seguin-Orlando A, Seldin L, Seyler LM, Shakhsheer B, Sheets GM, Shen C, Shi Y, Shin H, Shogan BD, Shutler D, Siegel J, Simmons S, Sjoling S, Smith DP, Soler JJ, Sperling M, Steinberg PD, Stephens B, Stevens MA, Taghavi S, Tai V, Tait K, Tan CL, Tas N, Taylor DL, Thomas T, Timling I, Turner BL, Urich T, Ursell LK, van der Lelie D, Van Treuren W, van Zwieten L, Vargas-Robles D, Thurber RV, Vitaglione P, Walker DA, Walters WA, Wang S, Wang T, Weaver T, Webster NS, Wehrle B, Weisenhorn P, Weiss S, Werner JJ, West K, Whitehead A, Whitehead SR, Whittingham LA, Willerslev E, Williams AE, Wood SA, Woodhams DC, Yang Y, Zaneveld J, Zarraonaindia I, Zhang Q, Zhao H., Nature 551(7681), 2017
PMID: 29088705

Improvements in multiprocessor system design
Rodgers DP., 1985