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Items: 1 to 50 of 79

1.

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects.

de Soysa TY, Ranade SS, Okawa S, Ravichandran S, Huang Y, Salunga HT, Schricker A, Del Sol A, Gifford CA, Srivastava D.

Nature. 2019 Aug;572(7767):120-124. doi: 10.1038/s41586-019-1414-x. Epub 2019 Jul 24.

PMID:
31341279
2.

Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks.

Hartmann A, Ravichandran S, Del Sol A.

Methods Mol Biol. 2019;1975:37-51. doi: 10.1007/978-1-4939-9224-9_2.

PMID:
31062304
3.

An integrative method to predict signalling perturbations for cellular transitions.

Zaffaroni G, Okawa S, Morales-Ruiz M, Del Sol A.

Nucleic Acids Res. 2019 Jul 9;47(12):e72. doi: 10.1093/nar/gkz232.

4.

Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain.

Kalamakis G, Brüne D, Ravichandran S, Bolz J, Fan W, Ziebell F, Stiehl T, Catalá-Martinez F, Kupke J, Zhao S, Llorens-Bobadilla E, Bauer K, Limpert S, Berger B, Christen U, Schmezer P, Mallm JP, Berninger B, Anders S, Del Sol A, Marciniak-Czochra A, Martin-Villalba A.

Cell. 2019 Mar 7;176(6):1407-1419.e14. doi: 10.1016/j.cell.2019.01.040. Epub 2019 Feb 28.

PMID:
30827680
5.

A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities.

Okawa S, Del Sol A.

Nucleic Acids Res. 2019 Apr 23;47(7):3333-3343. doi: 10.1093/nar/gkz147.

6.

Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy.

Del Sol A, Okawa S, Ravichandran S.

Trends Biotechnol. 2019 Jul;37(7):687-696. doi: 10.1016/j.tibtech.2019.01.005. Epub 2019 Feb 16. Review.

PMID:
30782480
7.

SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation.

Hartmann A, Okawa S, Zaffaroni G, Del Sol A.

Sci Rep. 2018 Sep 6;8(1):13355. doi: 10.1038/s41598-018-31688-9.

8.

Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift.

Okawa S, Saltó C, Ravichandran S, Yang S, Toledo EM, Arenas E, Del Sol A.

Nat Commun. 2018 Jul 3;9(1):2595. doi: 10.1038/s41467-018-05016-8.

9.

A complex of the ubiquitin ligase TRIM32 and the deubiquitinase USP7 balances the level of c-Myc ubiquitination and thereby determines neural stem cell fate specification.

Nicklas S, Hillje AL, Okawa S, Rudolph IM, Collmann FM, van Wuellen T, Del Sol A, Schwamborn JC.

Cell Death Differ. 2019 Mar;26(4):728-740. doi: 10.1038/s41418-018-0144-1. Epub 2018 Jun 13.

PMID:
29899379
10.

Signaling-Dependent Control of Apical Membrane Size and Self-Renewal in Rosette-Stage Human Neuroepithelial Stem Cells.

Medelnik JP, Roensch K, Okawa S, Del Sol A, Chara O, Mchedlishvili L, Tanaka EM.

Stem Cell Reports. 2018 Jun 5;10(6):1751-1765. doi: 10.1016/j.stemcr.2018.04.018. Epub 2018 May 17.

11.

Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients.

Grosse-Wilde A, Kuestner RE, Skelton SM, MacIntosh E, d'Hérouël AF, Ertaylan G, Del Sol A, Skupin A, Huang S.

Oncotarget. 2018 Apr 13;9(28):20018-20033. doi: 10.18632/oncotarget.25034. eCollection 2018 Apr 13.

12.

Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease.

Ravichandran S, Michelucci A, Del Sol A.

Front Physiol. 2018 Mar 2;9:154. doi: 10.3389/fphys.2018.00154. eCollection 2018.

13.

Regulation of Fn14 Receptor and NF-κB Underlies Inflammation in Meniere's Disease.

Frejo L, Requena T, Okawa S, Gallego-Martinez A, Martinez-Bueno M, Aran I, Batuecas-Caletrio A, Benitez-Rosario J, Espinosa-Sanchez JM, Fraile-Rodrigo JJ, García-Arumi AM, González-Aguado R, Marques P, Martin-Sanz E, Perez-Fernandez N, Pérez-Vázquez P, Perez-Garrigues H, Santos-Perez S, Soto-Varela A, Tapia MC, Trinidad-Ruiz G, Del Sol A, Alarcon Riquelme ME, Lopez-Escamez JA.

Front Immunol. 2017 Dec 13;8:1739. doi: 10.3389/fimmu.2017.01739. eCollection 2017.

14.

The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity.

Lynch CJ, Bernad R, Calvo I, Nóbrega-Pereira S, Ruiz S, Ibarz N, Martinez-Val A, Graña-Castro O, Gómez-López G, Andrés-León E, Espinosa Angarica V, Del Sol A, Ortega S, Fernandez-Capetillo O, Rojo E, Munoz J, Serrano M.

Cell Rep. 2018 Jan 9;22(2):396-410. doi: 10.1016/j.celrep.2017.12.062.

15.

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons.

Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW.

Genome Res. 2017 Nov;27(11):1783-1794. doi: 10.1101/gr.223313.117. Epub 2017 Oct 13.

16.

Absence of regulator of G-protein signaling 4 does not protect against dopamine neuron dysfunction and injury in the mouse 6-hydroxydopamine lesion model of Parkinson's disease.

Ashrafi A, Garcia P, Kollmus H, Schughart K, Del Sol A, Buttini M, Glaab E.

Neurobiol Aging. 2017 Oct;58:30-33. doi: 10.1016/j.neurobiolaging.2017.06.008. Epub 2017 Jun 19.

17.

Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data.

Jung S, Angarica VE, Andrade-Navarro MA, Buckley NJ, Del Sol A.

Sci Rep. 2017 Jul 5;7(1):4660. doi: 10.1038/s41598-017-04929-6.

18.

Bioinformatics Tools for Genome-Wide Epigenetic Research.

Angarica VE, Del Sol A.

Adv Exp Med Biol. 2017;978:489-512. doi: 10.1007/978-3-319-53889-1_25. Review.

PMID:
28523562
19.

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus.

De Jaime-Soguero A, Aulicino F, Ertaylan G, Griego A, Cerrato A, Tallam A, Del Sol A, Cosma MP, Lluis F.

PLoS Genet. 2017 Mar 27;13(3):e1006682. doi: 10.1371/journal.pgen.1006682. eCollection 2017 Mar.

20.

RefBool: a reference-based algorithm for discretizing gene expression data.

Jung S, Hartmann A, Del Sol A.

Bioinformatics. 2017 Jul 1;33(13):1953-1962. doi: 10.1093/bioinformatics/btx111.

PMID:
28334101
21.

Big-Data-Driven Stem Cell Science and Tissue Engineering: Vision and Unique Opportunities.

Del Sol A, Thiesen HJ, Imitola J, Carazo Salas RE.

Cell Stem Cell. 2017 Feb 2;20(2):157-160. doi: 10.1016/j.stem.2017.01.006.

22.

Identifying niche-mediated regulatory factors of stem cell phenotypic state: a systems biology approach.

Ravichandran S, Del Sol A.

FEBS Lett. 2017 Feb;591(3):560-569. doi: 10.1002/1873-3468.12559. Epub 2017 Jan 30. Review.

23.

A systems biology approach to identify niche determinants of cellular phenotypes.

Ravichandran S, Okawa S, Martínez Arbas S, Del Sol A.

Stem Cell Res. 2016 Sep;17(2):406-412. doi: 10.1016/j.scr.2016.09.006. Epub 2016 Sep 15.

24.

A Generalized Gene-Regulatory Network Model of Stem Cell Differentiation for Predicting Lineage Specifiers.

Okawa S, Nicklas S, Zickenrott S, Schwamborn JC, Del Sol A.

Stem Cell Reports. 2016 Sep 13;7(3):307-315. doi: 10.1016/j.stemcr.2016.07.014. Epub 2016 Aug 18.

25.

Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation.

Espinosa Angarica V, Del Sol A.

Bioessays. 2016 Aug;38(8):758-68. doi: 10.1002/bies.201600103. Epub 2016 Jun 19. Review.

26.

Prox1 Is Required for Oligodendrocyte Cell Identity in Adult Neural Stem Cells of the Subventricular Zone.

Bunk EC, Ertaylan G, Ortega F, Pavlou MA, Gonzalez Cano L, Stergiopoulos A, Safaiyan S, Völs S, van Cann M, Politis PK, Simons M, Berninger B, Del Sol A, Schwamborn JC.

Stem Cells. 2016 Aug;34(8):2115-29. doi: 10.1002/stem.2374. Epub 2016 Apr 21.

27.

Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages.

Tallam A, Perumal TM, Antony PM, Jäger C, Fritz JV, Vallar L, Balling R, Del Sol A, Michelucci A.

PLoS One. 2016 Feb 12;11(2):e0149050. doi: 10.1371/journal.pone.0149050. eCollection 2016.

28.

Prediction of disease-gene-drug relationships following a differential network analysis.

Zickenrott S, Angarica VE, Upadhyaya BB, del Sol A.

Cell Death Dis. 2016 Jan 14;7:e2040. doi: 10.1038/cddis.2015.393.

29.

A differential network analysis approach for lineage specifier prediction in stem cell subpopulations.

Okawa S, Angarica VE, Lemischka I, Moore K, Del Sol A.

NPJ Syst Biol Appl. 2015 Nov 12;1:15012. doi: 10.1038/npjsba.2015.12. eCollection 2015.

30.

A computational strategy for predicting lineage specifiers in stem cell subpopulations.

Okawa S, del Sol A.

Stem Cell Res. 2015 Sep;15(2):427-34. doi: 10.1016/j.scr.2015.08.006. Epub 2015 Sep 2.

31.

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability.

Bahnassawy L, Perumal TM, Gonzalez-Cano L, Hillje AL, Taher L, Makalowski W, Suzuki Y, Fuellen G, del Sol A, Schwamborn JC.

Sci Rep. 2015 Aug 26;5:13456. doi: 10.1038/srep13456.

32.

Identification of large-scale genomic variation in cancer genomes using in silico reference models.

Killcoyne S, Del Sol A.

Nucleic Acids Res. 2016 Jan 8;44(1):e5. doi: 10.1093/nar/gkv828. Epub 2015 Aug 11.

33.

Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells.

van den Berg CW, Okawa S, Chuva de Sousa Lopes SM, van Iperen L, Passier R, Braam SR, Tertoolen LG, del Sol A, Davis RP, Mummery CL.

Development. 2015 Sep 15;142(18):3231-8. doi: 10.1242/dev.123810. Epub 2015 Jul 24.

34.

Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET.

Rodriguez A, Crespo I, Androsova G, del Sol A.

PLoS One. 2015 Jun 9;10(6):e0127216. doi: 10.1371/journal.pone.0127216. eCollection 2015.

35.

Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.

Grosse-Wilde A, Fouquier d'Hérouël A, McIntosh E, Ertaylan G, Skupin A, Kuestner RE, del Sol A, Walters KA, Huang S.

PLoS One. 2015 May 28;10(5):e0126522. doi: 10.1371/journal.pone.0126522. eCollection 2015.

36.

The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs.

Nicklas S, Okawa S, Hillje AL, González-Cano L, Del Sol A, Schwamborn JC.

Nucleic Acids Res. 2015 Mar 11;43(5):2638-54. doi: 10.1093/nar/gkv138. Epub 2015 Feb 26.

37.

Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain.

Ertaylan G, Okawa S, Schwamborn JC, Del Sol A.

Front Cell Neurosci. 2014 Dec 18;8:437. doi: 10.3389/fncel.2014.00437. eCollection 2014.

38.

Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline.

Végh MJ, Rausell A, Loos M, Heldring CM, Jurkowski W, van Nierop P, Paliukhovich I, Li KW, del Sol A, Smit AB, Spijker S, van Kesteren RE.

Mol Cell Proteomics. 2014 Nov;13(11):2975-85. doi: 10.1074/mcp.M113.032086. Epub 2014 Jul 20.

39.

Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs.

Liu GH, Suzuki K, Li M, Qu J, Montserrat N, Tarantino C, Gu Y, Yi F, Xu X, Zhang W, Ruiz S, Plongthongkum N, Zhang K, Masuda S, Nivet E, Tsunekawa Y, Soligalla RD, Goebl A, Aizawa E, Kim NY, Kim J, Dubova I, Li Y, Ren R, Benner C, Del Sol A, Bueren J, Trujillo JP, Surralles J, Cappelli E, Dufour C, Esteban CR, Belmonte JCI.

Nat Commun. 2014 Jul 7;5:4330. doi: 10.1038/ncomms5330.

40.

Sorting signal targeting mRNA into hepatic extracellular vesicles.

Szostak N, Royo F, Rybarczyk A, Szachniuk M, Blazewicz J, del Sol A, Falcon-Perez JM.

RNA Biol. 2014;11(7):836-44. doi: 10.4161/rna.29305. Epub 2014 Jun 12.

41.

FIGG: simulating populations of whole genome sequences for heterogeneous data analyses.

Killcoyne S, del Sol A.

BMC Bioinformatics. 2014 May 19;15:149. doi: 10.1186/1471-2105-15-149.

42.

Efficacy and safety of vitamin K-antagonists (VKA) for atrial fibrillation in non-dialysis dependent chronic kidney disease.

Kooiman J, van Rein N, Spaans B, van Beers KA, Bank JR, van de Peppel WR, del Sol AI, Cannegieter SC, Rabelink TJ, Lip GY, Klok FA, Huisman MV.

PLoS One. 2014 May 9;9(5):e94420. doi: 10.1371/journal.pone.0094420. eCollection 2014.

43.

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes.

Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC.

Protein Cell. 2014 Jan;5(1):59-68. doi: 10.1007/s13238-013-0016-x. Epub 2014 Jan 29.

44.

Concise review: a population shift view of cellular reprogramming.

Del Sol A, Buckley NJ.

Stem Cells. 2014 Jun;32(6):1367-72. doi: 10.1002/stem.1627. Review.

45.

Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks.

Crespo I, Perumal TM, Jurkowski W, del Sol A.

BMC Syst Biol. 2013 Dec 19;7:140. doi: 10.1186/1752-0509-7-140.

46.

Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes.

Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Belmonte JC.

Protein Cell. 2013 Aug 27. [Epub ahead of print]

PMID:
23982742
47.

A general strategy for cellular reprogramming: the importance of transcription factor cross-repression.

Crespo I, Del Sol A.

Stem Cells. 2013 Oct;31(10):2127-35. doi: 10.1002/stem.1473.

48.

Integrating pathways of Parkinson's disease in a molecular interaction map.

Fujita KA, Ostaszewski M, Matsuoka Y, Ghosh S, Glaab E, Trefois C, Crespo I, Perumal TM, Jurkowski W, Antony PM, Diederich N, Buttini M, Kodama A, Satagopam VP, Eifes S, Del Sol A, Schneider R, Kitano H, Balling R.

Mol Neurobiol. 2014 Feb;49(1):88-102. doi: 10.1007/s12035-013-8489-4. Epub 2013 Jul 7. Review.

49.

PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells.

He F, Chen H, Probst-Kepper M, Geffers R, Eifes S, Del Sol A, Schughart K, Zeng AP, Balling R.

Mol Syst Biol. 2012;8:624. doi: 10.1038/msb.2012.56.

50.

Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.

Crespo I, Roomp K, Jurkowski W, Kitano H, del Sol A.

BMC Syst Biol. 2012 Oct 15;6:132. doi: 10.1186/1752-0509-6-132.

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