Recent Publications

An up-to-date list of publications may be found at PubMed (https://pubmed.ncbi.nlm.nih.gov/).

2024

Sugawara N, Towne MJ, Lovett ST, Haber JE.  “Spontaneous and double-strand break repair-associated quasipalindrome and frameshift mutagenesis in budding yeast: role of mismatch repair.” Genetics, May 1 2024, PubMed, https://doi.org/10.1093/genetics/iyad015.

Sapède E, Sugawara N, Tyers RG, Nakajima Y, Afreen MF, Romero Escobar J, Haber JE.  “Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae.” PLoS Genet. vol. 20, no. 2, Feb 5 2024, pp. 2469. PubMed, https://doi.org/10.1371/journal.pgen.1010527.

2023

Haber JE.  “101 years ago: Hermann Muller's remarkable insight.” Genetics, vol. 6, no. 4, Apr. 2023, p. 223 PubMed, https://doi.org/10.1093/genetics/iyad015.

Polleys EJ, Del Priore I, Haber JE, Freudenreich CH.  “Structure-forming CAG/CTG repeats interfere with gap repair to cause repeat expansions and chromosome breaks.” Nat Commun, vol. 14, no. 1, Apr. 2023, pp. 2469. PubMed, https://doi.org/10.1038/s41467-023-37901-2.

2022

Choi, Jihyun, et al. “Repair of Mismatched Templates during Rad51-Dependent Break-Induced Replication.” PLoS Genetics, vol. 18, no. 9, Sept. 2022, p. e1010056. PubMed, https://doi.org/10.1371/journal.pgen.1010056.

Epum, Esther A., and James E. Haber. “DNA Replication: The Recombination Connection.” Trends in Cell Biology, vol. 32, no. 1, Jan. 2022, pp. 45–57. PubMed, https://doi.org/10.1016/j.tcb.2021.07.005.

Esquivel-Chávez, Alfredo, et al. “Euchromatin Factors HULC and Set1C Affect Heterochromatin Organization and Mating-Type Switching in Fission Yeast Schizosaccharomyces Pombe.” Genes & Genetic Systems, vol. 97, no. 3, Oct. 2022, pp. 123–38. PubMed, https://doi.org/10.1266/ggs.22-00012.

Haber, James E. “A Shattering Experience.” Molecular Cell, vol. 82, no. 13, July 2022, pp. 2360–62. PubMed, https://doi.org/10.1016/j.molcel.2022.06.018.

Neal, Sonya, et al. “Quality Control: Maintaining Molecular Order and Preventing Cellular Chaos.” Molecular Cell, vol. 82, no. 8, Apr. 2022, pp. 1390–97. PubMed, https://doi.org/10.1016/j.molcel.2022.04.002.

Takacs, Constantin N., et al. “Cas9-Mediated Endogenous Plasmid Loss in Borrelia Burgdorferi.” PloS One, vol. 17, no. 11, 2022, p. e0278151. PubMed, https://doi.org/10.1371/journal.pone.0278151.

2021

Ait Saada, Anissia, et al. “Structural Parameters of Palindromic Repeats Determine the Specificity of Nuclease Attack of Secondary Structures.” Nucleic Acids Research, vol. 49, no. 7, Apr. 2021, pp. 3932–47. PubMed, https://doi.org/10.1093/nar/gkab168.

Arnould, Coline, et al. “Loop Extrusion as a Mechanism for Formation of DNA Damage Repair Foci.” Nature, vol. 590, no. 7847, Feb. 2021, pp. 660–65. PubMed, https://doi.org/10.1038/s41586-021-03193-z.

Gallagher, Danielle N., and James E. Haber. “Single-Strand Template Repair: Key Insights to Increase the Efficiency of Gene Editing.” Current Genetics, vol. 67, no. 5, Oct. 2021, pp. 747–53. PubMed, https://doi.org/10.1007/s00294-021-01186-z.

García Fernández, Fabiola, et al. “Modified Chromosome Structure Caused by Phosphomimetic H2A Modulates the DNA Damage Response by Increasing Chromatin Mobility in Yeast.” Journal of Cell Science, vol. 134, no. 6, Mar. 2021, p. jcs258500. PubMed, https://doi.org/10.1242/jcs.258500.

Haber, James E. “Learning Yeast Genetics from Miro Radman.” Cells, vol. 10, no. 4, Apr. 2021, p. 945. PubMed, https://doi.org/10.3390/cells10040945.

Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition)1.” Autophagy, vol. 17, no. 1, Jan. 2021, pp. 1–382. PubMed, https://doi.org/10.1080/15548627.2020.1797280.

Liu, Liping, et al. “Determining the Kinetics of Break-Induced Replication (BIR) by the Assay for Monitoring BIR Elongation Rate (AMBER).” Methods in Enzymology, vol. 661, 2021, pp. 139–54. PubMed, https://doi.org/10.1016/bs.mie.2021.09.004.

Pham, Nhung, et al. “Mechanisms Restraining Break-Induced Replication at Two-Ended DNA Double-Strand Breaks.” The EMBO Journal, vol. 40, no. 10, May 2021, p. e104847. PubMed, https://doi.org/10.15252/embj.2020104847.

Tripuraneni, Vinay, et al. “Local Nucleosome Dynamics and Eviction Following a Double-Strand Break Are Reversible by NHEJ-Mediated Repair in the Absence of DNA Replication.” Genome Research, vol. 31, no. 5, May 2021, pp. 775–88. PubMed, https://doi.org/10.1101/gr.271155.120.

Yamaguchi, Miyuki, and James E. Haber. “Monitoring Gene Conversion in Budding Yeast by Southern Blot Analysis.” Methods in Molecular Biology (Clifton, N.J.), vol. 2153, 2021, pp. 221–38. PubMed, https://doi.org/10.1007/978-1-0716-0644-5_16.

2020

Braberg, Hannes, et al. “Genetic Interaction Mapping Informs Integrative Structure Determination of Protein Complexes.” Science (New York, N.Y.), vol. 370, no. 6522, Dec. 2020, p. eaaz4910. PubMed, https://doi.org/10.1126/science.aaz4910.

Gallagher, Danielle N., et al. “A Rad51-Independent Pathway Promotes Single-Strand Template Repair in Gene Editing.” PLoS Genetics, vol. 16, no. 10, Oct. 2020, p. e1008689. PubMed, https://doi.org/10.1371/journal.pgen.1008689.

Li, Kevin, et al. “Yeast ATM and ATR Kinases Use Different Mechanisms to Spread Histone H2A Phosphorylation around a DNA Double-Strand Break.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 35, Sept. 2020, pp. 21354–63. PubMed, https://doi.org/10.1073/pnas.2002126117.

Li, Yilong, et al. “Patterns of Somatic Structural Variation in Human Cancer Genomes.” Nature, vol. 578, no. 7793, Feb. 2020, pp. 112–21. PubMed, https://doi.org/10.1038/s41586-019-1913-9.

Rheinbay, Esther, et al. “Analyses of Non-Coding Somatic Drivers in 2,658 Cancer Whole Genomes.” Nature, vol. 578, no. 7793, Feb. 2020, pp. 102–11. PubMed, https://doi.org/10.1038/s41586-020-1965-x.

Waterman, David P., et al. “Checkpoint Responses to DNA Double-Strand Breaks.” Annual Review of Biochemistry, vol. 89, June 2020, pp. 103–33. PubMed, https://doi.org/10.1146/annurev-biochem-011520-104722.

2019

Klein, Hannah L., et al. “Guidelines for DNA Recombination and Repair Studies: Cellular Assays of DNA Repair Pathways.” Microbial Cell (Graz, Austria), vol. 6, no. 1, Jan. 2019, pp. 1–64. PubMed, https://doi.org/10.15698/mic2019.01.664.

Memisoglu, Gonen, Michael C. Lanz, et al. “Mec1ATR Autophosphorylation and Ddc2ATRIP Phosphorylation Regulates DNA Damage Checkpoint Signaling.” Cell Reports, vol. 28, no. 4, 23 2019, pp. 1090-1102.e3. PubMed, https://doi.org/10.1016/j.celrep.2019.06.068.

Memisoglu, Gonen, Vinay V. Eapen, et al. “PP2C Phosphatases Promote Autophagy by Dephosphorylation of the Atg1 Complex.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 5, 29 2019, pp. 1613–20. PubMed, https://doi.org/10.1073/pnas.1817078116.

Memisoglu, Gonen, and James E. Haber. “Dephosphorylation of the Atg1 Kinase Complex by Type 2C Protein Phosphatases.” Molecular & Cellular Oncology, vol. 6, no. 3, 2019, p. 1588658. PubMed, https://doi.org/10.1080/23723556.2019.1588658.

Thon, Geneviève, et al. “Mating-Type Switching by Homology-Directed Recombinational Repair: A Matter of Choice.” Current Genetics, vol. 65, no. 2, Apr. 2019, pp. 351–62. PubMed, https://doi.org/10.1007/s00294-018-0900-2.

Waterman, David P., et al. “Live Cell Monitoring of Double Strand Breaks in S. Cerevisiae.” PLoS Genetics, vol. 15, no. 3, 2019, p. e1008001. PubMed, https://doi.org/10.1371/journal.pgen.1008001.

Wild, Philipp, et al. “Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis.” Molecular Cell, vol. 75, no. 4, 22 2019, pp. 859-874.e4. PubMed, https://doi.org/10.1016/j.molcel.2019.06.022.

2018

Botchkarev, Vladimir V., and James E. Haber. “Functions and Regulation of the Polo-like Kinase Cdc5 in the Absence and Presence of DNA Damage.” Current Genetics, vol. 64, no. 1, Feb. 2018, pp. 87–96. PubMed, https://doi.org/10.1007/s00294-017-0727-2.

Dwivedi, Gajendrahar, and James E. Haber. “Assaying Mutations Associated With Gene Conversion Repair of a Double-Strand Break.” Methods in Enzymology, vol. 601, 2018, pp. 145–60. PubMed, https://doi.org/10.1016/bs.mie.2017.11.029.

Gallagher, Danielle N., and James E. Haber. “Repair of a Site-Specific DNA Cleavage: Old-School Lessons for Cas9-Mediated Gene Editing.” ACS Chemical Biology, vol. 13, no. 2, 16 2018, pp. 397–405. PubMed, https://doi.org/10.1021/acschembio.7b00760.

Garbacz, Marta A., et al. “Evidence That DNA Polymerase δ Contributes to Initiating Leading Strand DNA Replication in Saccharomyces Cerevisiae.” Nature Communications, vol. 9, no. 1, 27 2018, p. 858. PubMed, https://doi.org/10.1038/s41467-018-03270-4.

Haber, James E. “DNA Repair: The Search for Homology.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, vol. 40, no. 5, 2018, p. e1700229. PubMed, https://doi.org/10.1002/bies.201700229.

Lemos, Brenda R., et al. “CRISPR/Cas9 Cleavages in Budding Yeast Reveal Templated Insertions and Strand-Specific Insertion/Deletion Profiles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 9, 27 2018, pp. E2040–47. PubMed, https://doi.org/10.1073/pnas.1716855115.

Maki, Takahisa, et al. “New Insights into Donor Directionality of Mating-Type Switching in Schizosaccharomyces Pombe.” PLoS Genetics, vol. 14, no. 5, 2018, p. e1007424. PubMed, https://doi.org/10.1371/journal.pgen.1007424.

Roy, Kevin R., et al. “Multiplexed Precision Genome Editing with Trackable Genomic Barcodes in Yeast.” Nature Biotechnology, vol. 36, no. 6, 2018, pp. 512–20. PubMed, https://doi.org/10.1038/nbt.4137.

Publications from 2011 to 2017.   Next->