Stefan Janssen

stefan.janssen@uni-bielefeld.de
ORCID logo https://orcid.org/0000-0003-0955-0589

PEVZ-ID
10656617

26 Publikationen

Alle markieren

  • [26]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934274
    Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D (2019)
    Assessing taxonomic metagenome profilers with OPAL.
    Genome biology 20(1): 51.
    PUB | DOI | WoS | PubMed | Europe PMC | Preprint
     
  • [25]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941280
    Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao J-Y, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li W-J, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R (2019)
    Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
    Nature Communications 10(1): 5477.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [24]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941281
    Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim J-N, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC (2019)
    The impact of skin care products on skin chemistry and microbiome dynamics.
    BMC Biology 17(1): 47.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [23]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934328
    Iszatt N, Janssen S, Lenters V, Dahl C, Stigum H, Knight R, Mandal S, Peddada S, González A, Midtvedt T, Eggesbø M (2019)
    Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.
    Microbiome 7(1): 34.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [22]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921267
    McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R, Mann AE, Amir A, Frazier A, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Lovelace E, Pierce E, TerAvest E, Bolyen E, Bushman FD, Wu GD, Church GM, Saxe G, Holscher HD, Ugrina I, German JB, Caporaso JG, Wozniak JM, Kerr J, Ravel J, Lewis JD, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Raes J, Chase JH, Eisen JA, Monk J, Clemente JC, Petrosino J, Goodrich J, Gauglitz J, Jacobs J, Zengler K, Swanson KS, Lewis K, Mayer K, Bittinger K, Dillon L, Zaramela LS, Schriml LM, Dominguez-Bello MG, Jankowska MM, Blaser M, Pirrung M, Minson M, Kurisu M, Ajami N, Gottel NR, Chia N, Fierer N, White O, Cani PD, Gajer P, Strandwitz P, Kashyap P, Dutton R, Park RS, Xavier RJ, Mills RH, Krajmalnik-Brown R, Ley R, Owens SM, Klemmer S, Matamoros S, Mirarab S, Moorman S, Holmes S, Schwartz T, Eshoo-Anton TW, Vigers T, Pandey V, Treuren WV, Fang X, Zech Xu Z, Jarmusch A, Geier J, Reeve N, Silva R, Kopylova E, Nguyen D, Sanders K, Salido Benitez RA, Heale AC, Abramson M, Waldispühl J, Butyaev A, Drogaris C, Nazarova E, Ball M, Gunderson B (2018)
    American Gut: an Open Platform for Citizen Science Microbiome Research.
    mSystems 3(3): e00031-18.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [21]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921270
    Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R (2018)
    KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.
    mSystems 3(3): e00218-17.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [20]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921268
    Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R (2018)
    Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.
    mSystems 3(3): e00021-18.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [19]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921273
    Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC (2018)
    Creating a 3D microbial and chemical snapshot of a human habitat.
    Scientific Reports 8(1): 3669.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    2018 | Preprint | Veröffentlicht | PUB-ID: 2931839
    Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope E, Da Silva R, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley G, Janssen S, Jarmusch AK, Jiang L, Kaehler B, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin B, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton J, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson, II MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Knight R, Caporaso JG (2018)
    QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science.
    PeerJ.
    PUB | DOI
     
  • [17]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2931438
    Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R (2018)
    Qiita: rapid, web-enabled microbiome meta-analysis.
    Nature Methods 15(10): 796-798.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [16]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914868
    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, Vázquez-Baeza Y, González 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, Rivera JLA, Al-Moosawi L, Alverdy J, Amato KR, Andras J, Angenent LT, Antonopoulos DA, Apprill A, Armitage D, Ballantine K, Bárta 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 JL, 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 H-P, Guyton K, Haig S-J, 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, Ibáñez-Álamo 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, Martín-Platero AM, Martín-Vivaldi M, Martínez LM, Martínez-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-Sánchez 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, Sjöling 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 (2017)
    A communal catalogue reveals Earth’s multiscale microbial diversity.
    Nature 551(7681): 457-463.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [15]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
    Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu Y-W, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin H-H, Liao Y-C, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk H-P, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC (2017)
    Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software.
    Nature Methods 14(11): 1063-1071.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [14]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907305
    Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet M-F, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK (2016)
    Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease.
    Cell 167(6): 1469-1480.e12.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [13]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764888 OA
    Janssen S, Giegerich R (2015)
    Ambivalent covariance models.
    BMC Bioinformatics 16(1): 178.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [12]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2700599
    Janssen S, Giegerich R (2014)
    The RNA shapes studio.
    Bioinformatics 31(3): 423-425.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [11]
    2014 | Bielefelder E-Dissertation | PUB-ID: 2682131 OA
    Janssen S (2014)
    Kisses, ambivalent models and more: Contributions to the analysis of RNA secondary structure.
    Bielefeld: Universitätsbibliothek.
    PUB | PDF
     
  • [10]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2551798
    Sauthoff G, Mohl M, Janssen S, Giegerich R (2013)
    Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis.
    Bioinformatics 29(5): 551-560.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [9]
    2012 | Sammelwerksbeitrag | PUB-ID: 2439665
    Janssen S, Giegerich R (2012)
    Abstract Shape Analysis of RNA.
    In: RNA Bioinformatics t.b.a. Gorodkin J, Weinberg Z (Eds); 1-35.
    PUB
     
  • [8]
    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410526 OA
    Janssen S, Schudoma C, Steger G, Giegerich R (2011)
    Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
    BMC Bioinformatics 12(1): 429.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [7]
    2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310489
    Sauthoff G, Janssen S, Giegerich R (2011)
    Bellman's GAP: a declarative language for dynamic programming.
    In: Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming. New York, NY, USA: ACM: 29-40.
    PUB | DOI | Download (ext.)
     
  • [6]
    2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785497 OA
    Schlüter J-P, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jaenicke S, Becker JD, Giegerich R, Becker A (2010)
    A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
    BMC Genomics 11(1): 245.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [5]
    2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893988 OA
    Grond F, Janssen S, Schirmer S, Hermann T (2010)
    Browsing RNA Structures by Interactive Sonification.
    In: Proceedings of the 3rd Interactive Sonification Workshop. Bresin R, Hermann T, Hunt A (Eds); KTH, Stockholm, Sweden: KTH School of Computer Science and Communication (CSC): 11-16.
    PUB | Datei | Download (ext.)
     
  • [4]
    2010 | Datenpublikation | PUB-ID: 2698354 OA
    Grond F, Janssen S, Schirmer S, Hermann T (2010)
    Supplementary Material for "Browsing RNA Structures by Interactive Sonification".
    Bielefeld University.
    PUB | Dateien verfügbar | DOI
     
  • [3]
    2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1894008 OA
    Theis C, Janssen S, Giegerich R (2010)
    Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs.
    In: Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Moulton V, Singh M (Eds); Lecture Notes in Bioinformatics, 6293. Berlin: Springer: 52-64.
    PUB | Datei | DOI
     
  • [2]
    2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893946 OA
    Janssen S, Giegerich R (2010)
    Faster computation of exact RNA shape probabilities.
    Bioinformatics 26(5): 632-639.
    PUB | Datei | DOI | WoS | PubMed | Europe PMC
     
  • [1]
    2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893917 OA
    Janssen S, Reeder J, Giegerich R (2008)
    Shape based indexing for faster search of RNA family databases.
    BMC Bioinformatics 9(1): 131.
    PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
     
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