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Items: 1 to 50 of 148

1.

Sibling-Implemented Script Fading to Promote Play-Based Statements of Children with Autism.

Akers JS, Higbee TS, Pollard JS, Reinert KS.

Behav Anal Pract. 2018 May 25;11(4):395-399. doi: 10.1007/s40617-018-0257-5. eCollection 2018 Dec 31.

2.

DREAM-Yara: an exact read mapper for very large databases with short update time.

Dadi TH, Siragusa E, Piro VC, Andrusch A, Seiler E, Renard BY, Reinert K.

Bioinformatics. 2018 Sep 1;34(17):i766-i772. doi: 10.1093/bioinformatics/bty567.

PMID:
30423080
3.

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

Rahn R, Budach S, Costanza P, Ehrhardt M, Hancox J, Reinert K.

Bioinformatics. 2018 Oct 15;34(20):3437-3445. doi: 10.1093/bioinformatics/bty380.

PMID:
29726911
4.

Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection.

Grzeskowiak L, Martínez-Vallespín B, Dadi TH, Radloff J, Amasheh S, Heinsen FA, Franke A, Reinert K, Vahjen W, Zentek J, Pieper R.

J Infect Dis. 2018 Apr 11;217(9):1442-1452. doi: 10.1093/infdis/jix567.

PMID:
29099941
5.

The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.

Reinert K, Dadi TH, Ehrhardt M, Hauswedell H, Mehringer S, Rahn R, Kim J, Pockrandt C, Winkler J, Siragusa E, Urgese G, Weese D.

J Biotechnol. 2017 Nov 10;261:157-168. doi: 10.1016/j.jbiotec.2017.07.017. Epub 2017 Sep 6.

6.

OpenMS - A platform for reproducible analysis of mass spectrometry data.

Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O.

J Biotechnol. 2017 Nov 10;261:142-148. doi: 10.1016/j.jbiotec.2017.05.016. Epub 2017 May 27. Review.

7.

Flexbar 3.0 - SIMD and multicore parallelization.

Roehr JT, Dieterich C, Reinert K.

Bioinformatics. 2017 Sep 15;33(18):2941-2942. doi: 10.1093/bioinformatics/btx330.

PMID:
28541403
8.

SLIMM: species level identification of microorganisms from metagenomes.

Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K.

PeerJ. 2017 Mar 28;5:e3138. doi: 10.7717/peerj.3138. eCollection 2017.

9.

Alternate-locus aware variant calling in whole genome sequencing.

Jäger M, Schubach M, Zemojtel T, Reinert K, Church DM, Robinson PN.

Genome Med. 2016 Dec 13;8(1):130.

10.

High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications.

Zühlke M, Riebe D, Beitz T, Löhmannsröben HG, Andreotti S, Reinert K, Zenichowski K, Diener M.

J Sep Sci. 2016 Dec;39(24):4756-4764. doi: 10.1002/jssc.201600749. Epub 2016 Nov 28.

PMID:
27805770
11.

Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis.

Vatansever B, Muñoz A, Klein CL, Reinert K.

Anal Bioanal Chem. 2017 Feb;409(4):989-997. doi: 10.1007/s00216-016-0013-z. Epub 2016 Oct 28.

PMID:
27796452
12.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
13.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624
14.

The Role of Religious Involvement in the Relationship Between Early Trauma and Health Outcomes Among Adult Survivors.

Reinert KG, Campbell JC, Bandeen-Roche K, Lee JW, Szanton S.

J Child Adolesc Trauma. 2016;9:231-241. Epub 2015 Nov 23.

15.

From the desktop to the grid: scalable bioinformatics via workflow conversion.

de la Garza L, Veit J, Szolek A, Röttig M, Aiche S, Gesing S, Reinert K, Kohlbacher O.

BMC Bioinformatics. 2016 Mar 12;17:127. doi: 10.1186/s12859-016-0978-9.

16.

CIDANE: comprehensive isoform discovery and abundance estimation.

Canzar S, Andreotti S, Weese D, Reinert K, Klau GW.

Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0.

17.

Gender and Race Variations in the Intersection of Religious Involvement, Early Trauma, and Adult Health.

Reinert KG, Campbell JC, Bandeen-Roche K, Sharps P, Lee J.

J Nurs Scholarsh. 2015 Jul;47(4):318-27. doi: 10.1111/jnu.12144. Epub 2015 Jun 15.

18.

Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models.

Schultz L, Zurich MG, Culot M, da Costa A, Landry C, Bellwon P, Kristl T, Hörmann K, Ruzek S, Aiche S, Reinert K, Bielow C, Gosselet F, Cecchelli R, Huber CG, Schroeder OH, Gramowski-Voss A, Weiss DG, Bal-Price A.

Toxicol In Vitro. 2015 Dec 25;30(1 Pt A):138-65. doi: 10.1016/j.tiv.2015.05.016. Epub 2015 May 27.

19.

IMSEQ--a fast and error aware approach to immunogenetic sequence analysis.

Kuchenbecker L, Nienen M, Hecht J, Neumann AU, Babel N, Reinert K, Robinson PN.

Bioinformatics. 2015 Sep 15;31(18):2963-71. doi: 10.1093/bioinformatics/btv309. Epub 2015 May 18.

PMID:
25987567
20.

Alignment of Next-Generation Sequencing Reads.

Reinert K, Langmead B, Weese D, Evers DJ.

Annu Rev Genomics Hum Genet. 2015;16:133-51. doi: 10.1146/annurev-genom-090413-025358. Epub 2015 May 4. Review.

PMID:
25939052
21.

Methods for the detection and assembly of novel sequence in high-throughput sequencing data.

Holtgrewe M, Kuchenbecker L, Reinert K.

Bioinformatics. 2015 Jun 15;31(12):1904-12. doi: 10.1093/bioinformatics/btv051. Epub 2015 Feb 2.

PMID:
25649620
22.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber CG, Berthold MR, Reinert K, Kohlbacher O.

Proteomics. 2015 Apr;15(8):1443-7. doi: 10.1002/pmic.201400391. Epub 2015 Feb 14.

24.

LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks.

Hu J, Reinert K.

Bioinformatics. 2015 Feb 1;31(3):363-72. doi: 10.1093/bioinformatics/btu652. Epub 2014 Oct 4.

PMID:
25282642
25.

Fiona: a parallel and automatic strategy for read error correction.

Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H.

Bioinformatics. 2014 Sep 1;30(17):i356-63. doi: 10.1093/bioinformatics/btu440.

26.

Lambda: the local aligner for massive biological data.

Hauswedell H, Singer J, Reinert K.

Bioinformatics. 2014 Sep 1;30(17):i349-55. doi: 10.1093/bioinformatics/btu439.

27.

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.

Trappe K, Emde AK, Ehrlich HC, Reinert K.

Bioinformatics. 2014 Dec 15;30(24):3484-90. doi: 10.1093/bioinformatics/btu431. Epub 2014 Jul 14.

PMID:
25028727
28.

Journaled string tree-a scalable data structure for analyzing thousands of similar genomes on your laptop.

Rahn R, Weese D, Reinert K.

Bioinformatics. 2014 Dec 15;30(24):3499-505. doi: 10.1093/bioinformatics/btu438. Epub 2014 Jul 15.

PMID:
25028723
29.

Genome alignment with graph data structures: a comparison.

Kehr B, Trappe K, Holtgrewe M, Reinert K.

BMC Bioinformatics. 2014 Apr 9;15:99. doi: 10.1186/1471-2105-15-99.

30.

Short-term effects of an endotoxin on substantia nigra dopamine neurons.

Reinert KR, Umphlet CD, Quattlebaum A, Boger HA.

Brain Res. 2014 Apr 4;1557:164-70. doi: 10.1016/j.brainres.2014.02.005. Epub 2014 Feb 8.

31.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

Hu J, Kehr B, Reinert K.

Bioinformatics. 2014 Feb 15;30(4):540-8. doi: 10.1093/bioinformatics/btt715. Epub 2013 Dec 13.

PMID:
24336806
32.

The duplication-loss small phylogeny problem: from cherries to trees.

Andreotti S, Reinert K, Canzar S.

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.

33.

Re-examining definitions of spirituality in nursing research.

Reinert KG, Koenig HG.

J Adv Nurs. 2013 Dec;69(12):2622-34. doi: 10.1111/jan.12152. Epub 2013 Apr 18.

34.

The relationship between executive function and obesity in children and adolescents: a systematic literature review.

Reinert KR, Po'e EK, Barkin SL.

J Obes. 2013;2013:820956. doi: 10.1155/2013/820956. Epub 2013 Feb 21. Review.

35.

Optimal precursor ion selection for LC-MALDI MS/MS.

Zerck A, Nordhoff E, Lehrach H, Reinert K.

BMC Bioinformatics. 2013 Feb 18;14:56. doi: 10.1186/1471-2105-14-56.

36.

Rapid and comprehensive impurity profiling of synthetic thyroxine by ultrahigh-performance liquid chromatography-high-resolution mass spectrometry.

Neu V, Bielow C, Gostomski I, Wintringer R, Braun R, Reinert K, Schneider P, Stuppner H, Huber CG.

Anal Chem. 2013 Mar 19;85(6):3309-17. doi: 10.1021/ac303722j. Epub 2013 Feb 28.

PMID:
23394260
37.

Fast and accurate read mapping with approximate seeds and multiple backtracking.

Siragusa E, Weese D, Reinert K.

Nucleic Acids Res. 2013 Apr;41(7):e78. doi: 10.1093/nar/gkt005. Epub 2013 Jan 28.

38.
39.

Tools for label-free peptide quantification.

Nahnsen S, Bielow C, Reinert K, Kohlbacher O.

Mol Cell Proteomics. 2013 Mar;12(3):549-56. doi: 10.1074/mcp.R112.025163. Epub 2012 Dec 17. Review.

40.

RazerS 3: faster, fully sensitive read mapping.

Weese D, Holtgrewe M, Reinert K.

Bioinformatics. 2012 Oct 15;28(20):2592-9. doi: 10.1093/bioinformatics/bts505. Epub 2012 Aug 24.

PMID:
22923295
41.

Inferring proteolytic processes from mass spectrometry time series data using degradation graphs.

Aiche S, Reinert K, Schütte C, Hildebrand D, Schlüter H, Conrad TO.

PLoS One. 2012;7(7):e40656. doi: 10.1371/journal.pone.0040656. Epub 2012 Jul 17.

42.

Analysis of C. elegans NR2E nuclear receptors defines three conserved clades and ligand-independent functions.

Weber KP, Alvaro CG, Baer GM, Reinert K, Cheng G, Clever S, Wightman B.

BMC Evol Biol. 2012 Jun 12;12:81. doi: 10.1186/1471-2148-12-81.

43.

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.

J Proteome Res. 2012 Jul 6;11(7):3914-20. doi: 10.1021/pr300187f. Epub 2012 May 24.

PMID:
22583024
44.

PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios.

Bauer C, Kleinjung F, Rutishauser D, Panse C, Chadt A, Dreja T, Al-Hasani H, Reinert K, Schlapbach R, Schuchhardt J.

BMC Bioinformatics. 2012 Feb 16;13:34. doi: 10.1186/1471-2105-13-34.

45.

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K.

Bioinformatics. 2012 Mar 1;28(5):619-27. doi: 10.1093/bioinformatics/bts019. Epub 2012 Jan 11.

PMID:
22238266
46.

STELLAR: fast and exact local alignments.

Kehr B, Weese D, Reinert K.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S15. doi: 10.1186/1471-2105-12-S9-S15.

47.

A novel and well-defined benchmarking method for second generation read mapping.

Holtgrewe M, Emde AK, Weese D, Reinert K.

BMC Bioinformatics. 2011 May 26;12:210. doi: 10.1186/1471-2105-12-210.

48.

Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset.

Bauer C, Kleinjung F, Smith CJ, Towers MW, Tiss A, Chadt A, Dreja T, Beule D, Al-Hasani H, Reinert K, Schuchhardt J, Cramer R.

BMC Bioinformatics. 2011 May 9;12:140. doi: 10.1186/1471-2105-12-140.

49.

MSSimulator: Simulation of mass spectrometry data.

Bielow C, Aiche S, Andreotti S, Reinert K.

J Proteome Res. 2011 Jul 1;10(7):2922-9. doi: 10.1021/pr200155f. Epub 2011 Apr 28.

PMID:
21526843
50.

Cellular and metabolic origins of flavoprotein autofluorescence in the cerebellar cortex in vivo.

Reinert KC, Gao W, Chen G, Wang X, Peng YP, Ebner TJ.

Cerebellum. 2011 Sep;10(3):585-99. doi: 10.1007/s12311-011-0278-x.

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