Publications

Xu, M., Singla, J., Tocheva, E. I., Chang, Y. W., Stevens, R. C., Jensen, G. J., & Alber, F. (2019). De novo structural pattern mining in cellular electron cryotomograms. Structure, 27(4), 679-691. (Cover Story)

Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM. (2019) Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. Front Cardiovasc Med. 2019 Jan 15;5:186. doi: 10.3389/fcvm.2018.00186. eCollection 2018. PMID: 30697540

G. Polles, N. Hua, A. Yildirim, F. Alber (2019) Genome Structure Calculation through Comprehensive Data Integration. In Modeling the 3D Conformation of Genomes, Eds. Guido Tiana, Luca Giorgetti, Taylor & Francis Group. CRC Press; pp 253. ISBN 9781138500792 - CAT# K35804

Singla, J., McClary, K. M., White, K. L., Alber, F., Sali, A., & Stevens, R. C. (2018). Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β cell. Cell, 173(1), 11-19.

Dultz, E., Mancini, R., Polles, G., Vallotton, P., Alber, F., & Weis, K. (2018). Quantitative imaging of chromatin decompaction in living cells. Molecular biology of the cell, 29(14), 1763-1777.

Caridi, C. P., Delabaere, L., Tjong, H., Hopp, H., Das, D., Alber, F., & Chiolo, I. (2018). Quantitative methods to investigate the 4D dynamics of heterochromatic repair sites in Drosophila cells. In Methods in enzymology (Vol. 601, pp. 359-389). Academic Press.

Li W, Li Q, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F, Zhou XJ. (2018) CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data. Nucleic Acids Res. 2018 Sep 6;46(15):e89. doi: 10.1093/nar/gky423. PMID: 29897492

Li, H., Kalhor, R., Li, B., Su, T., Berk, A., Kurdistani, S., ... & Chen, L. (2017). Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture. bioRxiv, 142604.

N. Hua, H. Tjong, H. Shin, K. Gong, X.J. Zhou, F. Alber (2017) PGS: a dynamic and automated population-based genome structure software. Nature Protocols

Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., ... & Politz, J. C. R. (2017). The 4D nucleome project. Nature, 549(7671), 219-226. (As part of the 4DN consortium)

Q. Li, H. Tjong, X. Li, K. Gong, X.J. Zhou, I. Chiolo, F. Alber (2017) The 3D genome organization of Drosophila melanogaster through data integration. Genome Biology 18(1):145. doi: 10.1186/s13059-017-1264-5

Joseph, A. P., Polles, G., Alber, F., & Topf, M. (2017). Integrative modelling of cellular assemblies. Current opinion in structural biology, 46, 102-109.

Frazier, Z., Xu, M., & Alber, F. (2017). Tomominer and tomominercloud: A software platform for large-scale subtomogram structural analysis. Structure, 25(6), 951-961.

Zhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M. P., Alber, F., & Murre, C. (2017). Comprehensive characterization of neutrophil genome topology. Genes & development, 31(2), 141-153. (Cover story)

Kang, S., Li, Q., Chen, Q., Zhou, Y., Park, S., Lee, G., ... & Alber, F. (2017). CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome biology, 18(1), 1-12.

Tjong, H., Li, W., Kalhor, R., Dai, C., Hao, S., Gong, K., ... & Larabell, C. A. (2016). Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proceedings of the National Academy of Sciences, 113(12), E1663-E1672.

Dai, C., Li, W., Tjong, H., Hao, S., Zhou, Y., Li, Q., ... & Zhou, X. J. (2016). Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Nature communications, 7(1), 1-11.

Pei, L., Xu, M., Frazier, Z., & Alber, F. (2016). Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking. BMC bioinformatics, 17(1), 405.

Dultz, E., Tjong, H., Weider, E., Herzog, M., Young, B., Brune, C., ... & Weis, K. (2016). Global reorganization of budding yeast chromosome conformation in different physiological conditions. Journal of Cell Biology, 212(3), 321-334.

Shin, H., Shi, Y., Dai, C., Tjong, H., Gong, K., Alber, F., & Zhou, X. J. (2016). TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic acids research, 44(7), e70-e70.

Gong, K., Tjong, H., Zhou, X. J., & Alber, F. (2015). Comparative 3D genome structure analysis of the fission and the budding yeast. PLoS One, 10(3).

Pandurangan, A. P., Vasishtan, D., Alber, F., & Topf, M. (2015). γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly using a genetic algorithm. Structure, 23(12), 2365-2376.

Li, W., Gong, K., Li, Q., Alber, F., & Zhou, X. J. (2015). Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. Bioinformatics, 31(6), 960-962.

Thalassinos, K., Pandurangan, A. P., Xu, M., Alber, F., & Topf, M. (2013). Conformational states of macromolecular assemblies explored by integrative structure calculation. Structure, 21(9), 1500-1508.

Xu, M., & Alber, F. (2013). Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms. Bioinformatics, 29(13), i274-i282.

Tjong, H., Gong, K., Chen, L., & Alber, F. (2012). Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome research, 22(7), 1295-1305. (Cover Story)

Zhou, X. J., & Alber, F. (2012). Zooming in on genome organization. Nature methods, 9(10), 961-963.

Frazier, Z., & Alber, F. (2012). A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling. Journal of Computational Biology, 19(6), 606-618.

Xu, M., Beck, M., & Alber, F. (2012). High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. Journal of structural biology, 178(2), 152-164.

Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2012). Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nature biotechnology, 30(1), 90. (Cover Story)

Xu, M., & Alber, F. (2012). High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization. BMC systems biology, 6(S1), S18.

Xu, M., Beck, M., & Alber, F. (2011). Template-free detection of macromolecular complexes in cryo electron tomograms. Bioinformatics, 27(13), i69-i76.

Xu, M., & Alber, F. (2011, September). Gradient-based high precision alignment of cryo-electron subtomograms. In 2011 IEEE International Conference on Systems Biology (ISB) (pp. 279-284). IEEE.

Beck, M., Topf, M., Frazier, Z., Tjong, H., Xu, M., Zhang, S., & Alber, F. (2011). Exploring the spatial and temporal organization of a cell’s proteome. Journal of structural biology, 173(3), 483-496.

Zhang, S., Vasishtan, D., Xu, M., Topf, M., & Alber, F. (2010). A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. Bioinformatics, 26(12), i261-i268.

Xu, M., Zhang, S., & Alber, F. (2009, November). 3d rotation invariant features for the characterization of molecular density maps. In 2009 IEEE International Conference on Bioinformatics and Biomedicine (pp. 74-78). IEEE.

Alber, F., Förster, F., Korkin, D., Topf, M., & Sali, A. (2008). Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem., 77, 443-477.

Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D., ... & Rout, M. P. (2007). Determining the architectures of macromolecular assemblies. Nature, 450(7170), 683-694. (Cover Story)

Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D., ... & Sali, A. (2007). The molecular architecture of the nuclear pore complex. Nature, 450(7170), 695-701.

Korkin, D., Davis, F. P., Alber, F., Luong, T., Shen, M. Y., Lucic, V., ... & Sali, A. (2006). Structural modeling of protein interactions by analogy: application to PSD-95. PLoS computational biology, 2(11).

Devos, D., Dokudovskaya, S., Williams, R., Alber, F., Eswar, N., Chait, B. T., ... & Sali, A. (2006). Simple fold composition and modular architecture of the nuclear pore complex. Proceedings of the National Academy of Sciences, 103(7), 2172-2177.

Alber, F., Kim, M. F., & Sali, A. (2005). Structural characterization of assemblies from overall shape and subcomplex compositions. Structure, 13(3), 435-445.

Devos, D., Dokudovskaya, S., Alber, F., Williams, R., Chait, B. T., Sali, A., & Rout, M. P. (2004). Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS biology, 2(12).

Chu, F., Shan, S. O., Moustakas, D. T., Alber, F., Egea, P. F., Stroud, R. M., ... & Burlingame, A. L. (2004). Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry. Proceedings of the National Academy of Sciences, 101(47), 16454-16459.

Russell, R. B., Alber, F., Aloy, P., Davis, F. P., Korkin, D., Pichaud, M., ... & Sali, A. (2004). A structural perspective on protein–protein interactions. Current opinion in structural biology, 14(3), 313-324.

Pantano, S., Alber, F., Lamba, D., & Carloni, P. (2002). NADH interactions with WT‐and S94A‐acyl carrier protein reductase from Mycobacterium tuberculosis: An ab initio study. Proteins: Structure, Function, and Bioinformatics, 47(1), 62-68.

Dal Peraro, M., Alber, F., & Carloni, P. (2001). Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study. European Biophysics Journal, 30(1), 75-81.

Alber, F., & Carloni, P. (2000). Ab initio molecular dynamics studies on HIV-1 reverse transcriptase triphosphate binding site: Implications for nucleoside–analog drug resistance. Protein Science, 9(12), 2535-2546.

Frigyes, D., Alber, F., Pongor, S., & Carloni, P. (2001). Arginine–phosphate salt bridges in protein–DNA complexes: a Car–Parrinello study. Journal of Molecular Structure: THEOCHEM, 574(1-3), 39-45.

Zhou, X., Alber, F., Folkers, G., Gonnet, G. H., & Chelvanayagam, G. (2000). An analysis of the helix‐to‐strand transition between peptides with identical sequence. Proteins: Structure, Function, and Bioinformatics, 41(2), 248-256.

Pantano, S., Alber, F., & Carloni, P. (2000). Proton dynamics in an enzyme model substrate: an ab initio molecular dynamics study. Journal of Molecular Structure: THEOCHEM, 530(1-2), 177-181.

Alber, F., Folkers, G., & Carloni, P. (1999). Dimethyl phosphate: Stereoelectronic versus environmental effects. The Journal of Physical Chemistry B, 103(29), 6121-6126.

Alber, F., Folkers, G., & Carloni, P. (1999). Conformational analysis of dimethyl phosphate in aqueous solution: a density functional theory-based molecular dynamics study. Journal of Molecular Structure: THEOCHEM, 489(2-3), 237-245.

Pilger, B. D., Perozzo, R., Alber, F., Wurth, C., Folkers, G., & Scapozza, L. (1999). Substrate Diversity of Herpes Simplex Virus Thymidine Kinase IMPACT OF THE KINEMATICS OF THE ENZYME. Journal of Biological Chemistry, 274(45), 31967-31973.

Alber, F., Kuonen, O., Scapozza, L., Folkers, G., & Carloni, P. (1998). Density functional studies on herpes simplex virus type 1 thymidine kinase–substrate interactions: The role of Tyr‐172 and Met‐128 in thymine fixation. Proteins: Structure, Function, and Bioinformatics, 31(4), 453-459.

Folkers, G., Alber, F., Pilger, B., Wurth, C., & Scapozza, L. (1998). Integrated approaches for the functional description of protein-ligand interaction complexes. ACTUALITES DE CHIMIE THERAPEUTIQUE, 24, 41-48.

Folkers, G., Alber, F., Amrhein, I., Behrends, H., Bohner, T., Gerber, S., ... & Scapozza, L. (1997). Integrated homology modelling and X-ray study of herpes simplex virus I thymidine kinase: a case study. Journal of Receptors and Signal Transduction, 17(1-3), 475-494.