Z. Zhao, O. Payan Parra, F. Musella, N. Scrutton-Alvarado, S.I. Fujita, F. Alber, Y. Yang, T. Yamada. Mega-enhancers compartmentalize transcriptionally active long genes in the brain (2026) Nature Cell Biology. 2026 Sep;28(9):1913-1926. doi: 10.1038/s41556-026-02043-2. PMID: 42575995. Epub 2026 Aug 10.
Galasso J, Wang Y, Alber F, Ernst J, Luo C. map3C: a computational tool for processing multiomic single-cell Hi-C data. Bioinformatics (2026) Volume 42, Issue 8, August 2026, btag562, https://doi.org/10.1093/bioinformatics/btag562
Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S*, Phillips-Cremins JE*, Gilbert DM*, Pollard KS*, Alber F*, Ma J*, Noble WS*, Yue F*. An integrated view of the structure and function of the human 4D nucleome. Nature. (2026) Jan;649(8097):759-776. doi: 10.1038/s41586-025-09890-3. Epub 2025 Dec 17. PMID: 41407856
W. Zeng, CC. Liu , S. Li, Y. Zhou, M. Stackpole, Y. Xiao, R. Hu, C. Tang, Q. Liu, W. Zeng, A. Yeh, A. Melehy, B. Tran, Z. Noor, M. Yokomizo, D. Amara, S. Gumate, P. Ahuja, DY. Li, J. Zhao, I. Rose, C. Walker, S. Malik, Y. Zhu, HR Tseng, EB Garon, S.W. French, C. E. Magyar, S. M. Dry, C. Lajonchere, D. H. Geschwind, G. Choi, S. Saab, A. Shetty, C. R. Wong, K. G. King, D. S. Lu, S. Raman, X. Xiang, K. Shetty, L. Mishra, S. Memarzadeh, Y. Liu, F. Alber, W. Hsu, K. Krysan, S. M. Dubinett, D. R. Aberle, V. Agopian, SH B. Han, W. H. Wong, X. Ni, W. Li , X. J. Zhou. Toward the Simultaneous Detection of Multiple Diseases with a Highly Cost-Effective Cell-Free DNA Methylome Test. Proc. Natl. Acad. Sc. USA. (2026) Apr 14;123(15):e2518347123. doi: 10.1073/pnas.2518347123. Epub 2026 Apr 6.
Y. Zhan, F. Musella, F. Alber. Prediction of single-cell chromatin compartments from single-cell chromosome structures by MaxComp. PLOS Computational Biology (2025) May 23;21(5):e1013114. doi: 10.1371/journal.pcbi.1013114. eCollection 2025 May. PMID: 40408515
Y. Wang, A. Yildirim, L. Boninsegna, M. Chester, S.H. Kang, X.J. Zhou, F. Alber. 3D Genome Organization Shapes DNA damage susceptibility to Platinum-based Drugs. Nucleic Acid Research (2025) May 22;53(10):gkaf315. doi: 10.1093/nar/gkaf315. PMID: 40433977
Y. Zhan, A. Yildirim, L. Boninsegna, F. Alber. Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis. Genome Biology (2025) 26(1):30. PMID: 39948644, doi: 10.1186/s13059-024-03472-8.
Y. Zhang, L. Boninsegna, M. Yang, T. Misteli, F. Alber, J. Ma. Computational methods for analysing multiscale 3D genome organization. (2024) Nature Review Genetics (2024) 25(2):123-141. PMID: 37673975, doi: 10.1038/s41576-023-00638-1
A. Yildirim, N. Hua, L. Boninsegna, G. Polles, K. Gong, S. Hao, W. Li, X. Jasmine Zhou, F. Alber. Evaluating the role of the nuclear microenvironment in gene function by population-based modeling. Nature Structural & Molecular Biology (2023), 0(8):1193-1206. PMID: 37580627, doi: 10.1038/s41594-023-01036-1.
A. Yildirim, F. Alber. Studying the impact of the nuclear topography on gene function. Nature Structural & Molecular Biology (2023) 30, 1062–1063 (Research Briefing) doi: https://doi.org/10.1038/s41594-023-01051-2.
J. Dekker, F. Alber, S. Aufmkolk, B.J. Beliveau, B.G. Bruneau, A.S. Belmont, L. Bintu, A. Boettiger, R. Calandrelli, C.M. Disteche, D.M. Gilbert, T. Gregor, A.S. Hansen, B. Huang, D. Huangfu, R. Kalhor, C.S. Leslie, W. Li, Y. Li, J. Ma, W.S. Noble, P.J. Park, J.E. Phillips-Cremins, K.S. Pollard, S.M. Rafelski, B. Ren, Y. Ruan, Y. Shav-Tal, Y. Shen, J. Shendure, X. Shu, C. Strambio-De-Castillia, A. Vertii, H. Zhang, S. Zhong. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. (2023) 83(15):2624-2640. PMID: 37419111, doi: 10.1016/j.molcel.2023.06.018.
M.L. Stackpole, W. Zeng, S. Li, C.C. Liu, Y. Zhou, S. He, A. Yeh, Z. Wang, F. Sun, Q. Li, Z. Yuan, A. Yildirim, P.J. Chen, P. Winograd, B. Tran, Y.T. Lee, P.S. Li, Z. Noor, M. Yokomizo, P. Ahuja, Y. Zhu, H.R. Tseng, J. Tomlinson, E. Garon, S. French, C.E. Magyar, S. Dry, C. Lajonchere, D. Geschwind, G. Choi, S. Saab, F. Alber, W.H. Wong, S. M. Dubinett, D. Aberle, V. Agopian, S.H.B. Han, X. Ni, W. Li, X.J. Zhou. (2022). Cost effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nature Communications, 2022,13(1):5566. doi: 10.1038/s41467-022-32995-6.
L. Boninsegna, A. Yildirim, G. Polles, Y. Zhan, SA. Quinodoz, E. Finn, M. Guttman, XJ Zhou, F. Alber (2022) Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations. Nature Methods (2022) 19(8):938-949. doi: 10.1038/s41592-022-01527-x. PMCID: 35817938
L. Boninsegna, & F. Alber. Reconstructing whole genome structures using a multi-modal data integration approach. Nature Methods (2022) 19, 934—935 (Research Briefing). PMID: 35831438 DOI: 10.1038/s41592-022-01528-w
L. Boninsegna, A. Yildirim, Y. Zhan, F. Alber. (2022) Integrative approaches in genome structure analysis. Structure. 2022 Jan 6;30(1):24-36. doi: 10.1016/j.str.2021.12.003. Epub 2021 Dec 27. PMID: 34963059
A. Yildirim, L. Boninsegna, Y. Zhan, F. Alber. (2021) Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Cold Spring Harb Perspect Biol. 2021 Aug 16: a039693. doi: 10.1101/ cshperspect.a039693. Online ahead of print. PMID: 34400556
S. Li, ZS. Noor, W. Zeng, ML. Stackpole, X. Ni, Y. Zhou, Z. Yuan, WH. Wong, VG. Agopian, SM Dubinett, F. Alber, W. Li, EB. Garon, XJ Zhou. (2021) Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nature Communications. 2021 Jul 7;12(1):4172. doi: 10.1038/s41467-021-24457-2.PMID: 34234141
J. Singla, K. White, R. Stevens, F. Alber (2021) Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography. J Struct Biol. 2021 Jun;213(2):107727. doi: 10.1016/j.jsb.2021.107727. Epub 2021 Mar 20. PMID: 33753204
KL. White, J. Singla, V. Loconte, JH. Chen, A. Ekman, L. Sun, X. Zhang, JP. Francis, A. Li, W. Lin, K. Tseng, G. McDermott, F. Alber, A. Sali, C. Larabell, RC. Stevens. (2020) Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Sci Adv. 2020 Dec 9;6(50):eabc8262. doi: 10.1126/sciadv.abc8262. Print 2020 Dec. PMID: 33298443
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 https://doi.org/10.1201/9781315144009
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. PMID: 29570991 DOI: 10.1016/j.cell.2018.03.014
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) Producing genome structure populations with the dynamic and automated PGS software. Nature Protocols (2018) May;13(5):915-926. doi: 10.1038/nprot.2018.008. Epub 2018 Apr 5. PMID: 29622804
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. PMID: 26951677 DOI: 10.1073/pnas.1512577113
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. DOI: 10.1038/ncomms11549 ,PMID: 27240697
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. PMID: 27716029 DOI: 10.1186/s12859-016-1283-3
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. PMID: 26811423 DOI: 10.1083/jcb.201507069
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. PMID: 26704975 DOI: 10.1093/nar/gkv1505
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). PMID: 25799503 DOI: 10.1371/journal.pone.0119672
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. PMID: 26655474 DOI: 10.1016/j.str.2015.10.013
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. PMID: 25391400 DOI: 10.1093/bioinformatics/btu747
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. PMID: 24010709 DOI: 10.1016/j.str.2013.08.006
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. PMID: 23812994 DOI: 10.1093/bioinformatics/btt22
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) PMID: 22619363, DOI: 10.1101/gr.129437.111
Zhou, X. J., & Alber, F. (2012). Zooming in on genome organization. Nature methods, 9(10), 961-963. PMID: 23018997 DOI: 10.1038/nmeth.2181
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. PMID: 22697237 DOI: 10.1089/cmb.2012.0027
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. PMID: 22420977 DOI: 10.1016/j.jsb.2012.02.01.
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) PMID: 22198700, DOI: 10.1038/nbt.2057
Xu, M., & Alber, F. (2012). High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization. BMC systems biology, 6(S1), S18. PMID: 23046491 DOI: 10.1186/1752-0509-6-S1-S18
Xu, M., Beck, M., & Alber, F. (2011). Template-free detection of macromolecular complexes in cryo electron tomograms. Bioinformatics, 27(13), i69-i76. PMID: 21685103 DOI: 10.1093/bioinformatics/btr207
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. PMID: 25068871 DOI: 10.1109/ISB.2011.6033166
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. PMID: 21094684 DOI: 10.1016/j.jsb.2010.11.011
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. PMID: 20529915 DOI: 10.1093/bioinformatics/btq201
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. Date Added to IEEE Xplore: 01 December 2009 Print ISBN:978-0-7695-3885-3 DOI: 10.1109/BIBM.2009.32
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. PMID: 18318657 DOI: 10.1146/annurev.biochem.77.060407.135530
Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D., Suprapto, A. , Karni-Schmidt, O., Williams, R. , Chait, B.T., Rout, M. P., Sali, A. (2007). Determining the architectures of macromolecular assemblies. Nature, 450(7170), 683-694. PMID: 18046405 DOI: 10.1038/nature06404
Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D., Suprapto, A. , Karni-Schmidt, O. , Williams, R., Chait, B.T., Sali, A., Rout, M.P. (2007). The molecular architecture of the nuclear pore complex. Nature, 450(7170), 695-701. PMID: 18046406 DOI: 10.1038/nature06405 (Cover Story).
Korkin, D., Davis, F. P., Alber, F., Luong, T., Shen, M. Y., Lucic, V., Kennedy, M.B., Sali, A. (2006). Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Computational Biology, 2(11). PMID: 17096593 DOI: 10.1371/journal.pcbi.0020153
Devos, D., Dokudovskaya, S., Williams, R., Alber, F., Eswar, N., Chait, B. T., Rout, M. P., 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. PMID: 16461911 DOI: 10.1073/pnas.0506345103
Alber, F., Kim, M. F., & Sali, A. (2005). Structural characterization of assemblies from overall shape and subcomplex compositions. Structure, 13(3), 435-445. PMID: 15766545 DOI: 10.1016/j.str.2005.01.01
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). PMID: 15523559 PMCID: PMC524472 DOI: 10.1371/journal.pbio.002038
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.
Z. Zhao, O. Payan Parra, F. Musella, N. Scrutton-Alvarado, S.I. Fujita, F. Alber, Y. Yang, T. Yamada. Mega-enhancers compartmentalize transcriptionally active long genes in the brain (2026) Nat Cell Biol. 2026 Sep;28(9):1913-1926. doi: 10.1038/s41556-026-02043-2. Epub 2026 Aug 10.
Galasso J, Wang Y, Alber F, Ernst J, Luo C. map3C: a computational tool for processing multiomic single-cell Hi-C data. Bioinformatics (2026) Volume 42, Issue 8, August 2026, btag562, https://doi.org/10.1093/bioinformatics/btag562
Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S*, Phillips-Cremins JE*, Gilbert DM*, Pollard KS*, Alber F*, Ma J*, Noble WS*, Yue F*. An integrated view of the structure and function of the human 4D nucleome. Nature. (2026) Jan;649(8097):759-776. doi: 10.1038/s41586-025-09890-3. Epub 2025 Dec 17. PMID: 41407856
W. Zeng, CC. Liu , S. Li, Y. Zhou, M. Stackpole, Y. Xiao, R. Hu, C. Tang, Q. Liu, W. Zeng, A. Yeh, A. Melehy, B. Tran, Z. Noor, M. Yokomizo, D. Amara, S. Gumate, P. Ahuja, DY. Li, J. Zhao, I. Rose, C. Walker, S. Malik, Y. Zhu, HR Tseng, EB Garon, S.W. French, C. E. Magyar, S. M. Dry, C. Lajonchere, D. H. Geschwind, G. Choi, S. Saab, A. Shetty, C. R. Wong, K. G. King, D. S. Lu, S. Raman, X. Xiang, K. Shetty, L. Mishra, S. Memarzadeh, Y. Liu, F. Alber, W. Hsu, K. Krysan, S. M. Dubinett, D. R. Aberle, V. Agopian, SH B. Han, W. H. Wong, X. Ni, W. Li , X. J. Zhou. Toward the Simultaneous Detection of Multiple Diseases with a Highly Cost-Effective Cell-Free DNA Methylome Test. Proc. Natl. Acad. Sc. USA. (2026) Apr 14;123(15):e2518347123. doi: 10.1073/pnas.2518347123. Epub 2026 Apr 6.
Y. Zhan, F. Musella, F. Alber. Prediction of single-cell chromatin compartments from single-cell chromosome structures by MaxComp. PLOS Computational Biology (2025) May 23;21(5):e1013114. doi: 10.1371/journal.pcbi.1013114. eCollection 2025 May. PMID: 40408515
Y. Wang, A. Yildirim, L. Boninsegna, M. Chester, S.H. Kang, X.J. Zhou, F. Alber. 3D Genome Organization Shapes DNA damage susceptibility to Platinum-based Drugs. Nucleic Acid Research (2025) May 22;53(10):gkaf315. doi: 10.1093/nar/gkaf315. PMID: 40433977
Y. Zhan, A. Yildirim, L. Boninsegna, F. Alber. Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis. Genome Biology (2025) 26(1):30. PMID: 39948644, doi: 10.1186/s13059-024-03472-8.
Y. Zhang, L. Boninsegna, M. Yang, T. Misteli, F. Alber, J. Ma. Computational methods for analysing multiscale 3D genome organization. (2024) Nature Review Genetics (2024) 25(2):123-141. PMID: 37673975, doi: 10.1038/s41576-023-00638-1
A. Yildirim, F. Alber. Studying the impact of the nuclear topography on gene function. Nature Structural & Molecular Biology (2023) 30, 1062–1063 (Research Briefing) doi: https://doi.org/10.1038/s41594-023-01051-2.
A. Yildirim, N. Hua, L. Boninsegna, G. Polles, K. Gong, S. Hao, W. Li, X. Jasmine Zhou, F. Alber. Evaluating the role of the nuclear microenvironment in gene function by population-based modeling. Nature Structural & Molecular Biology (2023), 0(8):1193-1206. PMID: 37580627, doi: 10.1038/s41594-023-01036-1.
J. Dekker, F. Alber, S. Aufmkolk, B.J. Beliveau, B.G. Bruneau, A.S. Belmont, L. Bintu, A. Boettiger, R. Calandrelli, C.M. Disteche, D.M. Gilbert, T. Gregor, A.S. Hansen, B. Huang, D. Huangfu, R. Kalhor, C.S. Leslie, W. Li, Y. Li, J. Ma, W.S. Noble, P.J. Park, J.E. Phillips-Cremins, K.S. Pollard, S.M. Rafelski, B. Ren, Y. Ruan, Y. Shav-Tal, Y. Shen, J. Shendure, X. Shu, C. Strambio-De-Castillia, A. Vertii, H. Zhang, S. Zhong. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. (2023) 83(15):2624-2640. PMID: 37419111, doi: 10.1016/j.molcel.2023.06.018.
M.L. Stackpole, W. Zeng, S. Li, C.C. Liu, Y. Zhou, S. He, A. Yeh, Z. Wang, F. Sun, Q. Li, Z. Yuan, A. Yildirim, P.J. Chen, P. Winograd, B. Tran, Y.T. Lee, P.S. Li, Z. Noor, M. Yokomizo, P. Ahuja, Y. Zhu, H.R. Tseng, J. Tomlinson, E. Garon, S. French, C.E. Magyar, S. Dry, C. Lajonchere, D. Geschwind, G. Choi, S. Saab, F. Alber, W.H. Wong, S. M. Dubinett, D. Aberle, V. Agopian, S.H.B. Han, X. Ni, W. Li, X.J. Zhou. (2022). Cost effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nature Communications, 2022,13(1):5566. doi: 10.1038/s41467-022-32995-6.
L. Boninsegna, & F. Alber. Reconstructing whole genome structures using a multi-modal data integration approach. Nature Methods (2022) 19, 934—935 (Research Briefing). PMID: 35831438 DOI: 10.1038/s41592-022-01528-w
L. Boninsegna, A. Yildirim, G. Polles, Y. Zhan, SA. Quinodoz, E. Finn, M. Guttman, XJ Zhou, F. Alber (2022) Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations. Nature Methods (2022) 19(8):938-949. doi: 10.1038/s41592-022-01527-x. PMCID: 35817938
L. Boninsegna, A. Yildirim, Y. Zhan, F. Alber. (2022) Integrative approaches in genome structure analysis. Structure. 2022 Jan 6;30(1):24-36. doi: 10.1016/j.str.2021.12.003. Epub 2021 Dec 27. PMID: 34963059
A. Yildirim, L. Boninsegna, Y. Zhan, F. Alber. (2021) Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Cold Spring Harb Perspect Biol. 2021 Aug 16: a039693. doi: 10.1101/ cshperspect.a039693. Online ahead of print. PMID: 34400556
S. Li, ZS. Noor, W. Zeng, ML. Stackpole, X. Ni, Y. Zhou, Z. Yuan, WH. Wong, VG. Agopian, SM Dubinett, F. Alber, W. Li, EB. Garon, XJ Zhou. (2021) Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nature Communications. 2021 Jul 7;12(1):4172. doi: 10.1038/s41467-021-24457-2.PMID: 34234141
J. Singla, K. White, R. Stevens, F. Alber (2021) Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography. J Struct Biol. 2021 Jun;213(2):107727. doi: 10.1016/j.jsb.2021.107727. Epub 2021 Mar 20. PMID: 33753204
KL. White, J. Singla, V. Loconte, JH. Chen, A. Ekman, L. Sun, X. Zhang, JP. Francis, A. Li, W. Lin, K. Tseng, G. McDermott, F. Alber, A. Sali, C. Larabell, RC. Stevens. (2020) Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Sci Adv. 2020 Dec 9;6(50):eabc8262. doi: 10.1126/sciadv.abc8262. Print 2020 Dec. PMID: 33298443
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.