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Items: 1 to 50 of 134

1.

RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification.

Arslan M, Devisetty UK, Porsch M, Große I, Müller JA, Michalski SG.

BMC Genomics. 2019 Jun 13;20(1):489. doi: 10.1186/s12864-019-5886-8.

2.

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model.

Schutkowski A, König B, Kluge H, Hirche F, Henze A, Schwerdtle T, Lorkowski S, Dawczynski C, Gabel A, Große I, Stangl GI.

J Nutr Biochem. 2019 May;67:149-160. doi: 10.1016/j.jnutbio.2019.02.004. Epub 2019 Mar 3.

PMID:
30925412
3.

Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.

Cavalli M, Baltzer N, Umer HM, Grau J, Lemnian I, Pan G, Wallerman O, Spalinskas R, Sahlén P, Grosse I, Komorowski J, Wadelius C.

Sci Rep. 2019 Feb 25;9(1):2695. doi: 10.1038/s41598-019-39633-0.

4.

Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact.

Porsch M, Özdemir E, Wisniewski M, Graf S, Bull F, Hoffmann K, Ignatov A, Haybaeck J, Grosse I, Kalinski T, Nass N.

RNA Biol. 2019 May;16(5):661-674. doi: 10.1080/15476286.2019.1581597. Epub 2019 Mar 5.

PMID:
30760083
5.

Comparison of the oral microbiome of patients with generalized aggressive periodontitis and periodontitis-free subjects.

Schulz S, Porsch M, Grosse I, Hoffmann K, Schaller HG, Reichert S.

Arch Oral Biol. 2019 Mar;99:169-176. doi: 10.1016/j.archoralbio.2019.01.015. Epub 2019 Jan 28.

PMID:
30710838
6.

Feeding Biomechanics in Billfishes: Investigating the Role of the Rostrum through Finite Element Analysis.

Habegger L, Motta P, Huber D, Pulaski D, Grosse I, Dumont E.

Anat Rec (Hoboken). 2019 Jan 8. doi: 10.1002/ar.24059. [Epub ahead of print]

PMID:
30623594
7.

WebHERV: A Web Server for the Computational Investigation of Gene Expression Associated With Endogenous Retrovirus-Like Sequences.

Kruse K, Nettling M, Wappler N, Emmer A, Kornhuber M, Staege MS, Grosse I.

Front Microbiol. 2018 Nov 5;9:2384. doi: 10.3389/fmicb.2018.02384. eCollection 2018.

8.

EFFECTOR OF TRANSCRIPTION factors are novel plant-specific regulators associated with genomic DNA methylation in Arabidopsis.

Tedeschi F, Rizzo P, Huong BTM, Czihal A, Rutten T, Altschmied L, Scharfenberg S, Grosse I, Becker C, Weigel D, Bäumlein H, Kuhlmann M.

New Phytol. 2019 Jan;221(1):261-278. doi: 10.1111/nph.15439. Epub 2018 Sep 25.

PMID:
30252137
9.

Age- and Diabetes-Related Changes in the Free Fatty Acid Composition of the Human Stratum Corneum.

Wohlrab J, Gabel A, Wolfram M, Grosse I, Neubert RHH, Steinbach SC.

Skin Pharmacol Physiol. 2018;31(6):283-291. doi: 10.1159/000490800. Epub 2018 Aug 21.

PMID:
30130788
10.

Whole-transcriptome analysis reveals genetic factors underlying flowering time regulation in rapeseed (Brassica napus L.).

Shah S, Weinholdt C, Jedrusik N, Molina C, Zou J, Große I, Schiessl S, Jung C, Emrani N.

Plant Cell Environ. 2018 Aug;41(8):1935-1947. doi: 10.1111/pce.13353. Epub 2018 Jun 19.

PMID:
29813173
11.

A Viral Suppressor Modulates the Plant Immune Response Early in Infection by Regulating MicroRNA Activity.

Pertermann R, Tamilarasan S, Gursinsky T, Gambino G, Schuck J, Weinholdt C, Lilie H, Grosse I, Golbik RP, Pantaleo V, Behrens SE.

MBio. 2018 Apr 24;9(2). pii: e00419-18. doi: 10.1128/mBio.00419-18.

12.

Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee (Bombus lapidarius L.).

Theodorou P, Radzevičiūtė R, Kahnt B, Soro A, Grosse I, Paxton RJ.

Proc Biol Sci. 2018 Apr 25;285(1877). pii: 20172806. doi: 10.1098/rspb.2017.2806.

13.

Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration.

Melnyk CW, Gabel A, Hardcastle TJ, Robinson S, Miyashima S, Grosse I, Meyerowitz EM.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2447-E2456. doi: 10.1073/pnas.1718263115. Epub 2018 Feb 13.

14.

myTAI: evolutionary transcriptomics with R.

Drost HG, Gabel A, Liu J, Quint M, Grosse I.

Bioinformatics. 2018 May 1;34(9):1589-1590. doi: 10.1093/bioinformatics/btx835.

15.

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7.

Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D.

Genome Biol. 2017 Oct 31;18(1):204. doi: 10.1186/s13059-017-1332-x.

16.

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colomé-Tatché M, Durka W, Engelhardt J, Gaspar B, Gogol-Döring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska SJ, Rensing SA, Stadler PF, Trucchi E, Ullrich K, Verhoeven KJF.

Ecol Lett. 2017 Dec;20(12):1576-1590. doi: 10.1111/ele.12858. Epub 2017 Oct 12. Review.

PMID:
29027325
17.

Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana.

Cherenkov P, Novikova D, Omelyanchuk N, Levitsky V, Grosse I, Weijers D, Mironova V.

J Exp Bot. 2018 Jan 4;69(2):329-339. doi: 10.1093/jxb/erx254. Review.

18.

Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots.

Omelyanchuk NA, Wiebe DS, Novikova DD, Levitsky VG, Klimova N, Gorelova V, Weinholdt C, Vasiliev GV, Zemlyanskaya EV, Kolchanov NA, Kochetov AV, Grosse I, Mironova VV.

Sci Rep. 2017 May 30;7(1):2489. doi: 10.1038/s41598-017-02476-8.

19.

Optimal Block-Based Trimming for Next Generation Sequencing.

Hedtke I, Lemnian I, Grosse I, Muller-Hannemann M.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):364-376. doi: 10.1109/TCBB.2017.2696525. Epub 2017 Apr 24.

PMID:
28436887
20.

Cross-kingdom comparison of the developmental hourglass.

Drost HG, Janitza P, Grosse I, Quint M.

Curr Opin Genet Dev. 2017 Aug;45:69-75. doi: 10.1016/j.gde.2017.03.003. Epub 2017 Mar 24. Review.

21.

Erratum to: Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens.

Doublet V, Poeschl Y, Gogol-Döring A, Alaux C, Annoscia D, Aurori C, Barribeau SM, Bedoya-Reina OC, Brown MJ, Bull JC, Flenniken ML, Galbraith DA, Genersch E, Gisder S, Grosse I, Holt HL, Hultmark D, Lattorff HM, Le Conte Y, Manfredini F, McMahon DP, Moritz RF, Nazzi F, Niño EL, Nowick K, van Rij RP, Paxton RJ, Grozinger CM.

BMC Genomics. 2017 Mar 23;18(1):256. doi: 10.1186/s12864-017-3624-7. No abstract available.

22.

Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens.

Doublet V, Poeschl Y, Gogol-Döring A, Alaux C, Annoscia D, Aurori C, Barribeau SM, Bedoya-Reina OC, Brown MJ, Bull JC, Flenniken ML, Galbraith DA, Genersch E, Gisder S, Grosse I, Holt HL, Hultmark D, Lattorff HM, Le Conte Y, Manfredini F, McMahon DP, Moritz RF, Nazzi F, Niño EL, Nowick K, van Rij RP, Paxton RJ, Grozinger CM.

BMC Genomics. 2017 Mar 2;18(1):207. doi: 10.1186/s12864-017-3597-6. Erratum in: BMC Genomics. 2017 Mar 23;18(1):256.

23.

Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies.

Nettling M, Treutler H, Cerquides J, Grosse I.

BMC Bioinformatics. 2017 Mar 1;18(1):141. doi: 10.1186/s12859-017-1495-1.

24.

Functional and evolutionary consequences of cranial fenestration in birds.

Gussekloo SWS, Berthaume MA, Pulaski DR, Westbroek I, Waarsing JH, Heinen R, Grosse IR, Dumont ER.

Evolution. 2017 May;71(5):1327-1338. doi: 10.1111/evo.13210. Epub 2017 Mar 17.

PMID:
28230246
25.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

Nettling M, Treutler H, Cerquides J, Grosse I.

Bioinformatics. 2017 Jun 1;33(11):1639-1646. doi: 10.1093/bioinformatics/btx033.

26.

The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana.

Zemlyanskaya EV, Levitsky VG, Oshchepkov DY, Grosse I, Mironova VV.

Front Plant Sci. 2017 Jan 9;7:2044. doi: 10.3389/fpls.2016.02044. eCollection 2016.

27.

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

28.

InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites.

Eggeling R, Grosse I, Grau J.

Bioinformatics. 2017 Feb 15;33(4):580-582. doi: 10.1093/bioinformatics/btw689.

29.

The Biomechanics of Bony Facial "Buttresses" in South African Australopiths: An Experimental Study Using Finite Element Analysis.

Ledogar JA, Benazzi S, Smith AL, Weber GW, Carlson KB, Dechow PC, Grosse IR, Ross CF, Richmond BG, Wright BW, Wang Q, Byron C, Carlson KJ, De Ruiter DJ, Pryor Mcintosh LC, Strait DS.

Anat Rec (Hoboken). 2017 Jan;300(1):171-195. doi: 10.1002/ar.23492.

30.

A Detailed Analysis of the BR1 Locus Suggests a New Mechanism for Bolting after Winter in Sugar Beet (Beta vulgaris L.).

Tränkner C, Lemnian IM, Emrani N, Pfeiffer N, Tiwari SP, Kopisch-Obuch FJ, Vogt SH, Müller AE, Schilhabel M, Jung C, Grosse I.

Front Plant Sci. 2016 Nov 14;7:1662. eCollection 2016.

31.

Phylogenetic distribution of plant snoRNA families.

Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF.

BMC Genomics. 2016 Nov 24;17(1):969.

32.

The Biomechanics of Zygomatic Arch Shape.

Smith AL, Grosse IR.

Anat Rec (Hoboken). 2016 Dec;299(12):1734-1752. doi: 10.1002/ar.23484.

33.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

34.

Human feeding biomechanics: performance, variation, and functional constraints.

Ledogar JA, Dechow PC, Wang Q, Gharpure PH, Gordon AD, Baab KL, Smith AL, Weber GW, Grosse IR, Ross CF, Richmond BG, Wright BW, Byron C, Wroe S, Strait DS.

PeerJ. 2016 Jul 26;4:e2242. doi: 10.7717/peerj.2242. eCollection 2016.

35.

An information model to support user-centered design of medical devices.

Hagedorn TJ, Krishnamurty S, Grosse IR.

J Biomed Inform. 2016 Aug;62:181-94. doi: 10.1016/j.jbi.2016.07.010. Epub 2016 Jul 8.

36.

3D finite element modeling of pelvic organ prolapse.

Yang Z, Hayes J, Krishnamurty S, Grosse IR.

Comput Methods Biomech Biomed Engin. 2016 Dec;19(16):1772-1784. Epub 2016 May 13.

PMID:
27174200
37.

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information.

Nettling M, Treutler H, Cerquides J, Grosse I.

BMC Genomics. 2016 May 10;17:347. doi: 10.1186/s12864-016-2682-6.

38.

Normoxic accumulation of HIF1α is associated with glutaminolysis.

Kappler M, Pabst U, Rot S, Taubert H, Wichmann H, Schubert J, Bache M, Weinholdt C, Immel UD, Grosse I, Vordermark D, Eckert AW.

Clin Oral Investig. 2017 Jan;21(1):211-224. doi: 10.1007/s00784-016-1780-9. Epub 2016 Mar 9.

PMID:
26955835
39.

Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development.

Drost HG, Bellstädt J, Ó'Maoiléidigh DS, Silva AT, Gabel A, Weinholdt C, Ryan PT, Dekkers BJ, Bentsink L, Hilhorst HW, Ligterink W, Wellmer F, Grosse I, Quint M.

Mol Biol Evol. 2016 May;33(5):1158-63. doi: 10.1093/molbev/msw039. Epub 2016 Feb 23.

40.

Mechanical evidence that Australopithecus sediba was limited in its ability to eat hard foods.

Ledogar JA, Smith AL, Benazzi S, Weber GW, Spencer MA, Carlson KB, McNulty KP, Dechow PC, Grosse IR, Ross CF, Richmond BG, Wright BW, Wang Q, Byron C, Carlson KJ, de Ruiter DJ, Berger LR, Tamvada K, Pryor LC, Berthaume MA, Strait DS.

Nat Commun. 2016 Feb 8;7:10596. doi: 10.1038/ncomms10596.

41.

DiffLogo: a comparative visualization of sequence motifs.

Nettling M, Treutler H, Grau J, Keilwagen J, Posch S, Grosse I.

BMC Bioinformatics. 2015 Nov 17;16:387. doi: 10.1186/s12859-015-0767-x.

42.

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data.

Eggeling R, Roos T, Myllymäki P, Grosse I.

BMC Bioinformatics. 2015 Nov 9;16:375. doi: 10.1186/s12859-015-0797-4.

43.

Joint Analysis of Dependent Features within Compound Spectra Can Improve Detection of Differential Features.

Trutschel D, Schmidt S, Grosse I, Neumann S.

Front Bioeng Biotechnol. 2015 Sep 24;3:129. doi: 10.3389/fbioe.2015.00129. eCollection 2015.

44.

Divergent Evolution of the Transcriptional Network Controlled by Snf1-Interacting Protein Sip4 in Budding Yeasts.

Mehlgarten C, Krijger JJ, Lemnian I, Gohr A, Kasper L, Diesing AK, Grosse I, Breunig KD.

PLoS One. 2015 Oct 6;10(10):e0139464. doi: 10.1371/journal.pone.0139464. eCollection 2015.

45.

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation.

Ryan PT, Ó'Maoiléidigh DS, Drost HG, Kwaśniewska K, Gabel A, Grosse I, Graciet E, Quint M, Wellmer F.

BMC Genomics. 2015 Jul 1;16:488. doi: 10.1186/s12864-015-1699-6.

46.

A concept ideation framework for medical device design.

Hagedorn TJ, Grosse IR, Krishnamurty S.

J Biomed Inform. 2015 Jun;55:218-30. doi: 10.1016/j.jbi.2015.04.010. Epub 2015 May 6.

47.

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C.

BMC Bioinformatics. 2015 Feb 21;16:56. doi: 10.1186/s12859-015-0486-3.

48.

Men and women differ in their diurnal expression of monocyte peroxisome proliferator-activated receptor-α in the fed but not in the fasted state.

Wege N, Schutkowski A, Boenn M, Bialek J, Schlitt A, Noack F, Grosse I, Stangl GI.

FASEB J. 2015 Jul;29(7):2905-11. doi: 10.1096/fj.14-267575. Epub 2015 Mar 30.

PMID:
25825462
49.

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R.

Grau J, Grosse I, Keilwagen J.

Bioinformatics. 2015 Aug 1;31(15):2595-7. doi: 10.1093/bioinformatics/btv153. Epub 2015 Mar 24.

50.

Evidence for active maintenance of phylotranscriptomic hourglass patterns in animal and plant embryogenesis.

Drost HG, Gabel A, Grosse I, Quint M.

Mol Biol Evol. 2015 May;32(5):1221-31. doi: 10.1093/molbev/msv012. Epub 2015 Jan 27.

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