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Items: 1 to 50 of 53


De Novo Structural Pattern Mining in Cellular Electron Cryotomograms.

Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F.

Structure. 2019 Apr 2;27(4):679-691.e14. doi: 10.1016/j.str.2019.01.005. Epub 2019 Feb 7.


Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation.

Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM.

Front Cardiovasc Med. 2019 Jan 15;5:186. doi: 10.3389/fcvm.2018.00186. eCollection 2018.


Vigabatrin with hormonal treatment versus hormonal treatment alone (ICISS) for infantile spasms: 18-month outcomes of an open-label, randomised controlled trial.

O'Callaghan FJK, Edwards SW, Alber FD, Cortina Borja M, Hancock E, Johnson AL, Kennedy CR, Likeman M, Lux AL, Mackay MT, Mallick AA, Newton RW, Nolan M, Pressler R, Rating D, Schmitt B, Verity CM, Osborne JP; International Collaborative Infantile Spasms Study (ICISS) investigators.

Lancet Child Adolesc Health. 2018 Oct;2(10):715-725. doi: 10.1016/S2352-4642(18)30244-X. Epub 2018 Aug 29.


CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.

Li W, Li Q, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F, Zhou XJ.

Nucleic Acids Res. 2018 Sep 6;46(15):e89. doi: 10.1093/nar/gky423.


Quantitative imaging of chromatin decompaction in living cells.

Dultz E, Mancini R, Polles G, Vallotton P, Alber F, Weis K.

Mol Biol Cell. 2018 Jul 15;29(13):1763-1777. doi: 10.1091/mbc.E17-11-0648. Epub 2018 May 17. Erratum in: Mol Biol Cell. 2019 Mar 15;30(6):808-809.


Producing genome structure populations with the dynamic and automated PGS software.

Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F.

Nat Protoc. 2018 May;13(5):915-926. doi: 10.1038/nprot.2018.008. Epub 2018 Apr 5.


Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.

Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC.

Cell. 2018 Mar 22;173(1):11-19. doi: 10.1016/j.cell.2018.03.014. Review.


Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.

Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I.

Methods Enzymol. 2018;601:359-389. doi: 10.1016/bs.mie.2017.11.033. Epub 2018 Feb 26.


The three-dimensional genome organization of Drosophila melanogaster through data integration.

Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F.

Genome Biol. 2017 Jul 31;18(1):145. doi: 10.1186/s13059-017-1264-5.


Integrative modelling of cellular assemblies.

Joseph AP, Polles G, Alber F, Topf M.

Curr Opin Struct Biol. 2017 Oct;46:102-109. doi: 10.1016/ Epub 2017 Jul 20. Review.


TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis.

Frazier Z, Xu M, Alber F.

Structure. 2017 Jun 6;25(6):951-961.e2. doi: 10.1016/j.str.2017.04.016. Epub 2017 May 25.


CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.

Kang S, Li Q, Chen Q, Zhou Y, Park S, Lee G, Grimes B, Krysan K, Yu M, Wang W, Alber F, Sun F, Dubinett SM, Li W, Zhou XJ.

Genome Biol. 2017 Mar 24;18(1):53. doi: 10.1186/s13059-017-1191-5.


Comprehensive characterization of neutrophil genome topology.

Zhu Y, Gong K, Denholtz M, Chandra V, Kamps MP, Alber F, Murre C.

Genes Dev. 2017 Jan 15;31(2):141-153. doi: 10.1101/gad.293910.116. Epub 2017 Feb 6.


Safety and effectiveness of hormonal treatment versus hormonal treatment with vigabatrin for infantile spasms (ICISS): a randomised, multicentre, open-label trial.

O'Callaghan FJ, Edwards SW, Alber FD, Hancock E, Johnson AL, Kennedy CR, Likeman M, Lux AL, Mackay M, Mallick AA, Newton RW, Nolan M, Pressler R, Rating D, Schmitt B, Verity CM, Osborne JP; participating investigators.

Lancet Neurol. 2017 Jan;16(1):33-42. doi: 10.1016/S1474-4422(16)30294-0. Epub 2016 Nov 10.


Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.

Dai C, Li W, Tjong H, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F, Jasmine Zhou X.

Nat Commun. 2016 May 31;7:11549. doi: 10.1038/ncomms11549.


Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1663-72. doi: 10.1073/pnas.1512577113. Epub 2016 Mar 7.


Global reorganization of budding yeast chromosome conformation in different physiological conditions.

Dultz E, Tjong H, Weider E, Herzog M, Young B, Brune C, Müllner D, Loewen C, Alber F, Weis K.

J Cell Biol. 2016 Feb 1;212(3):321-34. doi: 10.1083/jcb.201507069. Epub 2016 Jan 25.


TopDom: an efficient and deterministic method for identifying topological domains in genomes.

Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ.

Nucleic Acids Res. 2016 Apr 20;44(7):e70. doi: 10.1093/nar/gkv1505. Epub 2015 Dec 23.


γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm.

Pandurangan AP, Vasishtan D, Alber F, Topf M.

Structure. 2015 Dec 1;23(12):2365-2376. doi: 10.1016/j.str.2015.10.013. Epub 2015 Nov 19.


Comparative 3D genome structure analysis of the fission and the budding yeast.

Gong K, Tjong H, Zhou XJ, Alber F.

PLoS One. 2015 Mar 23;10(3):e0119672. doi: 10.1371/journal.pone.0119672. eCollection 2015.


Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

Li W, Gong K, Li Q, Alber F, Zhou XJ.

Bioinformatics. 2015 Mar 15;31(6):960-2. doi: 10.1093/bioinformatics/btu747. Epub 2014 Nov 12.


Conformational States of macromolecular assemblies explored by integrative structure calculation.

Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M.

Structure. 2013 Sep 3;21(9):1500-8. doi: 10.1016/j.str.2013.08.006.


High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.

Xu M, Alber F.

BMC Syst Biol. 2012;6 Suppl 1:S18. doi: 10.1186/1752-0509-6-S1-S18. Epub 2012 Jul 16.


Zooming in on genome organization.

Zhou XJ, Alber F.

Nat Methods. 2012 Oct;9(10):961-3. doi: 10.1038/nmeth.2181. No abstract available.


A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.

Frazier Z, Alber F.

J Comput Biol. 2012 Jun;19(6):606-18. doi: 10.1089/cmb.2012.0027.


Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.

Tjong H, Gong K, Chen L, Alber F.

Genome Res. 2012 Jul;22(7):1295-305. doi: 10.1101/gr.129437.111. Epub 2012 May 22.


High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.

Xu M, Beck M, Alber F.

J Struct Biol. 2012 May;178(2):152-64. doi: 10.1016/j.jsb.2012.02.014. Epub 2012 Mar 7.


Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.

Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L.

Nat Biotechnol. 2011 Dec 25;30(1):90-8. doi: 10.1038/nbt.2057.


Template-free detection of macromolecular complexes in cryo electron tomograms.

Xu M, Beck M, Alber F.

Bioinformatics. 2011 Jul 1;27(13):i69-76. doi: 10.1093/bioinformatics/btr207.


Gradient-based high precision alignment of cryo-electron subtomograms.

Xu M, Alber F.

IEEE Int Conf Systems Biol. 2011:279-284.


Exploring the spatial and temporal organization of a cell's proteome.

Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F.

J Struct Biol. 2011 Mar;173(3):483-96. doi: 10.1016/j.jsb.2010.11.011. Epub 2010 Nov 19. Review.


A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.

Zhang S, Vasishtan D, Xu M, Topf M, Alber F.

Bioinformatics. 2010 Jun 15;26(12):i261-8. doi: 10.1093/bioinformatics/btq201.


Cognitive outcome in children with rhombencephalosynapsis.

Poretti A, Alber FD, Bürki S, Toelle SP, Boltshauser E.

Eur J Paediatr Neurol. 2009 Jan;13(1):28-33. doi: 10.1016/j.ejpn.2008.02.005. Epub 2008 Apr 14.


Gomez-Lopez-Hernandez syndrome: an easily missed diagnosis.

Poretti A, Bartholdi D, Gobara S, Alber FD, Boltshauser E.

Eur J Med Genet. 2008 May-Jun;51(3):197-208. doi: 10.1016/j.ejmg.2008.01.004. Epub 2008 Feb 8.


Integrating diverse data for structure determination of macromolecular assemblies.

Alber F, Förster F, Korkin D, Topf M, Sali A.

Annu Rev Biochem. 2008;77:443-77. doi: 10.1146/annurev.biochem.77.060407.135530. Review.


The molecular architecture of the nuclear pore complex.

Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP.

Nature. 2007 Nov 29;450(7170):695-701.


Determining the architectures of macromolecular assemblies.

Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A.

Nature. 2007 Nov 29;450(7170):683-94.


Structural modeling of protein interactions by analogy: application to PSD-95.

Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A.

PLoS Comput Biol. 2006 Nov 10;2(11):e153. Epub 2006 Oct 4.


Simple fold composition and modular architecture of the nuclear pore complex.

Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A.

Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2172-7. Epub 2006 Feb 6.


Outcome of medulloblastoma in children: long-term complications and quality of life.

Ribi K, Relly C, Landolt MA, Alber FD, Boltshauser E, Grotzer MA.

Neuropediatrics. 2005 Dec;36(6):357-65.


Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.

Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Burlingame AL.

Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16454-9. Epub 2004 Nov 16.


Components of coated vesicles and nuclear pore complexes share a common molecular architecture.

Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP.

PLoS Biol. 2004 Dec;2(12):e380. Epub 2004 Nov 2. Erratum in: PLoS Biol. 2005 Feb;3(2):e80.


A structural perspective on protein-protein interactions.

Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A.

Curr Opin Struct Biol. 2004 Jun;14(3):313-24. Review.


Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study.

Dal Peraro M, Alber F, Carloni P.

Eur Biophys J. 2001;30(1):75-81.


An analysis of the helix-to-strand transition between peptides with identical sequence.

Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G.

Proteins. 2000 Nov 1;41(2):248-56.


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