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Items: 1 to 50 of 141

1.

Differential transcriptome and development of human peripheral plasma cell subsets.

Garimilla S, Nguyen DC, Halliley JL, Tipton C, Rosenberg AF, Fucile CF, Saney CL, Kyu S, Kaminski D, Qian Y, Scheuermann RH, Gibson G, Sanz I, Lee FE.

JCI Insight. 2019 May 2;4(9). pii: 126732. doi: 10.1172/jci.insight.126732. eCollection 2019 May 2.

2.

Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).

Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH.

Virology. 2019 Mar;529:29-42. doi: 10.1016/j.virol.2019.01.005. Epub 2019 Jan 6.

3.

Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR).

Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH.

Methods Mol Biol. 2019;1911:47-69. doi: 10.1007/978-1-4939-8976-8_3.

PMID:
30593617
4.

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.

Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B.

PLoS One. 2018 Dec 26;13(12):e0209648. doi: 10.1371/journal.pone.0209648. eCollection 2018.

5.

Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells.

Brown DM, Hixon AM, Oldfield LM, Zhang Y, Novotny M, Wang W, Das SR, Shabman RS, Tyler KL, Scheuermann RH.

MBio. 2018 Oct 16;9(5). pii: e01954-18. doi: 10.1128/mBio.01954-18.

6.

Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant.

Wang W, Huang H, Halagan M, Vierra-Green C, Heuer M, Brelsford JE, Haagenson M, Scheuermann RH, Telenti A, Biggs W, Pearson NM, Udell J, Spellman S, Maiers M, Kennedy CJ.

Blood Adv. 2018 Oct 9;2(19):2419-2429. doi: 10.1182/bloodadvances.2018019513.

7.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G.

Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27.

8.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG.

Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018.

9.

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

10.

DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.

Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y.

Cytometry A. 2018 Jun;93(6):597-610. doi: 10.1002/cyto.a.23371. Epub 2018 Apr 17.

11.

Cell type discovery using single-cell transcriptomics: implications for ontological representation.

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH.

Hum Mol Genet. 2018 May 1;27(R1):R40-R47. doi: 10.1093/hmg/ddy100.

12.

Cell type discovery and representation in the era of high-content single cell phenotyping.

Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH.

BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):559. doi: 10.1186/s12859-017-1977-1.

13.

Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration.

Scheuermann RH, Bui J, Wang HY, Qian Y.

Clin Lab Med. 2017 Dec;37(4):931-944. doi: 10.1016/j.cll.2017.07.011. Review.

14.

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG.

BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z.

15.

Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.

Pedersen NW, Chandran PA, Qian Y, Rebhahn J, Petersen NV, Hoff MD, White S, Lee AJ, Stanton R, Halgreen C, Jakobsen K, Mosmann T, Gouttefangeas C, Chan C, Scheuermann RH, Hadrup SR.

Front Immunol. 2017 Jul 26;8:858. doi: 10.3389/fimmu.2017.00858. eCollection 2017.

16.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.

Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064. doi: 10.1073/pnas.1707945114. Epub 2017 Jul 3.

17.

Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses.

Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE.

PLoS One. 2017 May 31;12(5):e0178199. doi: 10.1371/journal.pone.0178199. eCollection 2017.

18.

Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak.

Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH.

Virus Evol. 2016 Jun 15;2(1):vew015. doi: 10.1093/ve/vew015. eCollection 2016 Jan.

19.

Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells.

Schulten V, Tripple V, Seumois G, Qian Y, Scheuermann RH, Fu Z, Locci M, Rosales S, Vijayanand P, Sette A, Alam R, Crotty S, Peters B.

J Allergy Clin Immunol. 2018 Feb;141(2):775-777.e6. doi: 10.1016/j.jaci.2017.04.032. Epub 2017 May 12. No abstract available.

20.

A bioinformatics roadmap for the human vaccines project.

Scheuermann RH, Sinkovits RS, Schenkelberg T, Koff WC.

Expert Rev Vaccines. 2017 Jun;16(6):535-544. doi: 10.1080/14760584.2017.1322752. Epub 2017 May 9. Review.

PMID:
28434256
21.

Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus.

Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann RH.

PLoS One. 2017 Jan 26;12(1):e0170462. doi: 10.1371/journal.pone.0170462. eCollection 2017.

22.

An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.

Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann RH, Sette A, Peters B.

J Immunol. 2017 Feb 15;198(4):1748-1758. doi: 10.4049/jimmunol.1601750. Epub 2017 Jan 9.

23.

A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.

Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL.

mSphere. 2016 Dec 14;1(6). pii: e00275-16. eCollection 2016 Nov-Dec.

24.

PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.

Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH.

Pac Symp Biocomput. 2017;22:564-575. doi: 10.1142/9789813207813_0052.

25.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333.

26.

Influenza Research Database: An integrated bioinformatics resource for influenza virus research.

Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D466-D474. doi: 10.1093/nar/gkw857. Epub 2016 Sep 26.

27.

The Ontology for Biomedical Investigations.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

28.

Zika virus: designate standardized names.

Scheuermann RH.

Nature. 2016 Mar 10;531(7593):173. doi: 10.1038/531173a. No abstract available.

PMID:
26961650
29.

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.

Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS.

Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18.

30.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.

Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP.

Sci Rep. 2016 Feb 10;6:20686. doi: 10.1038/srep20686.

31.

Automated analysis of flow cytometry data comes of age.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2016 Jan;89(1):13-5. doi: 10.1002/cyto.a.22810. No abstract available.

32.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

33.

Molecular Profile of Mitochondrial Dysfunction in Kidney Transplant Biopsies Is Associated With Poor Allograft Outcome.

Zepeda-Orozco D, Kong M, Scheuermann RH.

Transplant Proc. 2015 Jul-Aug;47(6):1675-82. doi: 10.1016/j.transproceed.2015.04.086.

PMID:
26293032
34.

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann RH.

Cytometry A. 2016 Jan;89(1):71-88. doi: 10.1002/cyto.a.22735. Epub 2015 Aug 14.

35.

State-of-the-Art in the Computational Analysis of Cytometry Data.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2015 Jul;87(7):591-3. doi: 10.1002/cyto.a.22707. No abstract available.

36.

Thinking outside the gate: single-cell assessments in multiple dimensions.

Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM.

Immunity. 2015 Apr 21;42(4):591-2. doi: 10.1016/j.immuni.2015.04.006. No abstract available.

37.

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA.

Evol Bioinform Online. 2015 Mar 16;11:43-8. doi: 10.4137/EBO.S21501. eCollection 2015. Review.

38.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH.

J Virol. 2015 May;89(10):5427-40. doi: 10.1128/JVI.03636-14. Epub 2015 Mar 4.

39.

flowCL: ontology-based cell population labelling in flow cytometry.

Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.

Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6.

40.

Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

Squires RB, Pickett BE, Das S, Scheuermann RH.

Infect Genet Evol. 2014 Dec;28:351-7. doi: 10.1016/j.meegid.2014.07.015. Epub 2014 Jul 24.

41.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

42.

Response of human skin to esthetic scarification.

Gabriel VA, McClellan EA, Scheuermann RH.

Burns. 2014 Nov;40(7):1338-44. doi: 10.1016/j.burns.2014.01.005. Epub 2014 Feb 28.

43.

A comprehensive collection of systems biology data characterizing the host response to viral infection.

Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A 3rd, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH.

Sci Data. 2014 Oct 14;1:140033. doi: 10.1038/sdata.2014.33. eCollection 2014.

44.

Extracting actionable findings of appendicitis from radiology reports using natural language processing.

Rink B, Roberts K, Harabagiu S, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:221. eCollection 2013.

45.

Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes.

Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH.

Virology. 2013 Dec;447(1-2):45-51. doi: 10.1016/j.virol.2013.08.021. Epub 2013 Sep 14.

46.

GenePattern flow cytometry suite.

Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR.

Source Code Biol Med. 2013 Jul 3;8(1):14. doi: 10.1186/1751-0473-8-14.

47.

Critical assessment of automated flow cytometry data analysis techniques.

Aghaeepour N, Finak G; FlowCAP Consortium; DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.

Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. Erratum in: Nat Methods. 2013 May;10(5):445.

48.

A machine learning approach for identifying anatomical locations of actionable findings in radiology reports.

Roberts K, Rink B, Harabagiu SM, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R.

AMIA Annu Symp Proc. 2012;2012:779-88. Epub 2012 Nov 3.

49.

Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.

Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH.

Viruses. 2012 Nov 19;4(11):3209-26. doi: 10.3390/v4113209.

50.

FCSTrans: an open source software system for FCS file conversion and data transformation.

Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann RH.

Cytometry A. 2012 May;81(5):353-356. doi: 10.1002/cyto.a.22037. Epub 2012 Mar 19. No abstract available.

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