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Best matches for Schönhuth A[au]:

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Patterson M et al. J Comput Biol. (2015)

Genotyping inversions and tandem duplications. Ebler J et al. Bioinformatics. (2017)

De novo assembly of viral quasispecies using overlap graphs. Baaijens JA et al. Genome Res. (2017)

Search results

Items: 34

1.

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.

Yin B, Balvert M, van der Spek RAA, Dutilh BE, Bohté S, Veldink J, Schönhuth A.

Bioinformatics. 2019 Jul 15;35(14):i538-i547. doi: 10.1093/bioinformatics/btz369.

2.

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants.

Denti L, Previtali M, Bernardini G, Schönhuth A, Bonizzoni P.

iScience. 2019 Aug 30;18:20-27. doi: 10.1016/j.isci.2019.07.011. Epub 2019 Jul 12.

3.

Full-length de novo viral quasispecies assembly through variation graph construction.

Baaijens JA, Van der Roest B, Köster J, Stougie L, Schönhuth A.

Bioinformatics. 2019 May 30. pii: btz443. doi: 10.1093/bioinformatics/btz443. [Epub ahead of print]

PMID:
31147688
4.

Overlap graph-based generation of haplotigs for diploids and polyploids.

Baaijens JA, Schönhuth A.

Bioinformatics. 2019 Apr 17. pii: btz255. doi: 10.1093/bioinformatics/btz255. [Epub ahead of print]

PMID:
30994902
5.

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.

6.

De novo assembly of viral quasispecies using overlap graphs.

Baaijens JA, Aabidine AZE, Rivals E, Schönhuth A.

Genome Res. 2017 May;27(5):835-848. doi: 10.1101/gr.215038.116. Epub 2017 Apr 10.

7.

Genotyping inversions and tandem duplications.

Ebler J, Schönhuth A, Marschall T.

Bioinformatics. 2017 Dec 15;33(24):4015-4023. doi: 10.1093/bioinformatics/btx020.

PMID:
28169394
8.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V.

Nat Commun. 2016 Oct 6;7:12989. doi: 10.1038/ncomms12989.

9.

Snowball: strain aware gene assembly of metagenomes.

Gregor I, Schönhuth A, McHardy AC.

Bioinformatics. 2016 Sep 1;32(17):i649-i657. doi: 10.1093/bioinformatics/btw426.

PMID:
27587685
10.

Repeat- and error-aware comparison of deletions.

Wittler R, Marschall T, Schönhuth A, Mäkinen V.

Bioinformatics. 2015 Sep 15;31(18):2947-54. doi: 10.1093/bioinformatics/btv304. Epub 2015 May 15.

PMID:
25979471
11.

SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.

Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A, Maoz Moss TY.

BMC Genomics. 2015 Mar 25;16:238. doi: 10.1186/s12864-015-1376-9.

12.

Characteristics of de novo structural changes in the human genome.

Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC; Genome of Netherlands Consortium, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V.

Genome Res. 2015 Jun;25(6):792-801. doi: 10.1101/gr.185041.114. Epub 2015 Apr 16.

13.

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.

J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157. Epub 2015 Feb 6.

14.

Viral quasispecies assembly via maximal clique enumeration.

Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar.

15.

Mapping proteins in the presence of paralogs using units of coevolution.

El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW.

BMC Bioinformatics. 2013;14 Suppl 15:S18. doi: 10.1186/1471-2105-14-S15-S18. Epub 2013 Oct 15.

16.

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Marschall T, Hajirasouliha I, Schönhuth A.

Bioinformatics. 2013 Dec 15;29(24):3143-50. doi: 10.1093/bioinformatics/btt556. Epub 2013 Sep 25.

17.

Discovering motifs that induce sequencing errors.

Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T.

BMC Bioinformatics. 2013;14 Suppl 5:S1. doi: 10.1186/1471-2105-14-S5-S1. Epub 2013 Apr 10.

18.

CLEVER: clique-enumerating variant finder.

Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A.

Bioinformatics. 2012 Nov 15;28(22):2875-82. doi: 10.1093/bioinformatics/bts566. Epub 2012 Oct 11.

PMID:
23060616
19.

Mirroring co-evolving trees in the light of their topologies.

Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC.

Bioinformatics. 2012 May 1;28(9):1202-8. doi: 10.1093/bioinformatics/bts109. Epub 2012 Mar 6.

PMID:
22399677
20.

Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.

Hafemeister C, Costa IG, Schönhuth A, Schliep A.

Bioinformatics. 2011 Apr 1;27(7):946-52. doi: 10.1093/bioinformatics/btr037. Epub 2011 Jan 25.

PMID:
21266444
21.

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

Singer M, Engström A, Schönhuth A, Pachter L.

Stat Appl Genet Mol Biol. 2011 Sep 23;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1677/1544-6115.1677.xml. doi: 10.2202/1544-6115.1677.

PMID:
23089814
22.

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

Colak R, Moser F, Chu JS, Schönhuth A, Chen N, Ester M.

PLoS One. 2010 Oct 25;5(10):e13348. doi: 10.1371/journal.pone.0013348. Erratum in: PLoS One. 2010;5(12) doi: 10.1371/annotation/ab9e87d9-f59c-4dab-aea5-a3c1116d3d85.

23.

MetMap enables genome-scale Methyltyping for determining methylation states in populations.

Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L.

PLoS Comput Biol. 2010 Aug 19;6(8):e1000888. doi: 10.1371/journal.pcbi.1000888.

24.

Inferring cancer subnetwork markers using density-constrained biclustering.

Dao P, Colak R, Salari R, Moser F, Davicioni E, Schönhuth A, Ester M.

Bioinformatics. 2010 Sep 15;26(18):i625-31. doi: 10.1093/bioinformatics/btq393.

25.

Towards improved assessment of functional similarity in large-scale screens: a study on indel length.

Schönhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC.

J Comput Biol. 2010 Jan;17(1):1-20. doi: 10.1089/cmb.2009.0031.

PMID:
20078394
26.

Constrained mixture estimation for analysis and robust classification of clinical time series.

Costa IG, Schönhuth A, Hafemeister C, Schliep A.

Bioinformatics. 2009 Jun 15;25(12):i6-14. doi: 10.1093/bioinformatics/btp222.

27.

Dense graphlet statistics of protein interaction and random networks.

Colak R, Hormozdiari F, Moser F, Schönhuth A, Holman J, Ester M, Sahinalp SC.

Pac Symp Biocomput. 2009:178-89.

28.

The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study.

Hormozdiari F, Salari R, Hsing M, Schönhuth A, Chan SK, Sahinalp SC, Cherkasov A.

J Comput Biol. 2009 Feb;16(2):159-67. doi: 10.1089/cmb.2008.03TT.

PMID:
19193143
29.

Analyzing gene expression time-courses.

Schliep A, Costa IG, Steinhoff C, Schönhuth A.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):179-93.

PMID:
17044182
30.

A fractional programming approach to efficient DNA melting temperature calculation.

Leber M, Kaderali L, Schönhuth A, Schrader R.

Bioinformatics. 2005 May 15;21(10):2375-82. Epub 2005 Mar 15.

PMID:
15769839
31.

The Graphical Query Language: a tool for analysis of gene expression time-courses.

Costa IG, Schönhuth A, Schliep A.

Bioinformatics. 2005 May 15;21(10):2544-5. Epub 2005 Feb 8.

PMID:
15701683
32.

Robust inference of groups in gene expression time-courses using mixtures of HMMs.

Schliep A, Steinhoff C, Schönhuth A.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i283-9.

PMID:
15262810
33.

Using hidden Markov models to analyze gene expression time course data.

Schliep A, Schönhuth A, Steinhoff C.

Bioinformatics. 2003;19 Suppl 1:i255-63.

PMID:
12855468
34.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002

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