Research Articles Published

2024

• Deciphering Bladder Cancer-Related circRNA Biomarkers: An Ensemble Model Integrating Deep Learning and Statistics for circRNA Analysis. Ding Y, Pan Y, Geyer CR, Vizeacoumar FJ, Vizeacoumar FS, Wu F. Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 2024. Shenzhen, China. (Conference Publication).
• Systematic comparison of CRISPR and shRNA screens to identify essential genes using graph-based unsupervised learning model. Ding Y, Denomy C, Freywald A, Pan Y, Vizeacoumar FJ, Vizeacoumar FS, Wu F. Cells 2024. Oct4; 13(19):1653.
• The EphA2 Receptor Regulates Invasiveness and Drug Sensitivity in Canine and Human Osteosarcoma Cells. Harris ED, Sharpe JC, Strozen T, Abdi S, Kliewer M, Sanchez MG, Hogan NS, MacDonald-Dickinson V, Vizeacoumar FJ, Toosi BM. Cells. 2024 Jul 16;13(14):1201. 
• Preclinical 3D model screening reveals digoxin as an effective therapy for a rare and aggressive type of endometrial cancer. Kumar PP, Smith D, Key J, Dong H, Ganapathysamy A, Maranda V, Wong NKY, Fernandez ML, Kim H, Zhang G, Ewanowich C, Hopkins L, Freywald A, Postovit LM, Köbel M, Fu Y, Vizeacoumar FS, Vizeacoumar FJ, Carey MS, Lee C-H. Gynecologic Oncology. 2024; 188,162-168.
• MEMO1 binds iron and modulates iron homeostasis in cancer cells. Dolgova N, Uhlemann EE, Boniecki MT, Vizeacoumar FS, Ara A, Nouri P, Ralle M, Tonelli M, Abbas SA, Patry J, Elhasasna H, Freywald A, Vizeacoumar FJ†, Dmitriev OY†. Elife. 2024 Apr 19;13:e86354. doi: 10.7554/eLife.86354. Epub ahead of print. († Corresponding authors)
• AI is a viable alternative to high throughput screening: a 318-target study. The Atomwise AIMS Program. Sci Rep 2024 Apr 2;14(1):7526.
• Breast tumor metastasis and its microenvironment: It takes both seed and soil to grow a tumor and target it for treatment. Bonni S, Brindley DN, Chamberlain MD, Daneshvar-Baghbadorani N, Freywald A, Hemmings DG, Hombach-Klonisch S, Klonisch T, Raouf A, Shemanko CS, Topolnitska D, Visser K, Vizeacoumar FJ, Wang E, Gibson SB. Cancers 2024; 16(5):911.
• hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JWE, Denomy C, Hutchinson C, Abidullah HM, Hammond SA, Pastushok L, Vizeacoumar FS, Levin MC. Nat Commun. 2024 Jan 8;15(1):356.

2023

• Survey of NF1 inactivation by surrogae immunohistochemistry in ovarian carcinomas. Köbel M, Yong RZ, Kang EY, Al-Shamma Z, Cook LS, Kinloch M, Carey MS, Hopkins L, Nelson GS, McManus KJ, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Fu Y, Reuss DE, Lee CH. Gynecol Oncol. 2023 Oct 9;178:80-88. doi: 10.1016/j.ygyno.2023.09.016. Online ahead of print.
• Integration of cancer-related genetic landscape of Eph receptors and ephrins with proteomics identifies a crosstalk between EPHB6 and EGFR. Hanover G, Vizeacoumar FS, Banerjee SL, Nair R, Dahiya R, Osornio-Hernandez AI, Morales AM, Freywald T, Himanen JP, Toosi BM, Bisson N†, Vizeacoumar FJ†, Freywald A†. Cell Rep. 2023 Jun 30;42(7):112670. doi: 10.1016/j.celrep.2023.112670. Online ahead of print. († Corresponding authors).
• Generation of a SARS-CoV-2 Reverse Genetics System and Novel Human Lung Cell Lines That Exhibit High Virus-Induced Cytopathology. Khan JQ, Rohamare M, Rajamanickam K, Bhanumathy KK, Lew J, Kumar A, Falzarano D, Vizeacoumar FJ, Wilson JA. Viruses. 2023 May 30;15(6):1281. doi: 10.3390/v15061281.
• A multipronged unbiased strategy guides the development of an anti-EGFR/EPHA2-bispecific antibody for combination cancer therayp. El Zawily A, Vizeacoumar FS, Dahiya R, Banerjee SL, Bhanumathy KK, Elhasasna H, Hanover G, Sharpe JC, Sanchez MG, Greidanus P, Stacey RG, Moon KM, Alexandrov I, Himanen JP, Nikolov DB, Fonge H, White AP, Foster LJ, Wang B, Toosi BM†, Bisson N†, Mirzabekov TA†, Vizeacoumar FJ†, Freywald A†. Clin Cancer Res. 2023 Mar 28;OF1-OF16. doi: 10.1158/1078-0432.CCR-22-2535. Online ahead of print. († Corresponding authors).
• Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ†, Wu Y†.  Front. Oncol. 2023 Jan 26;12:1087989. († Corresponding authors).
  
• A CRISPR Platform for Targeted In Vivo Screens. Maranda V, Zhang Y, Vizeacoumar FS, Freywald A†, Vizeacoumar FJ†. Methods Mol Biol. 2023;2614:397-409. doi: 10.1007/978-1-0716-2914-7_24. († Corresponding authors).

2022

• Homoharringtonine demonstrates a cytotoxic effect against triple-negative breast cancer cell lines and acts synergistically with paclitaxel. Plett R, Mellor P, Kendall S, Hammond SA, Boulet A, Plaza K, Vizeacoumar FS, Vizeacoumar FJ†, Anderson DH†. Sci Rep. 2022 Sep 19;12(1):15663. doi: 10.1038/s41598-022-19621-7. († Corresponding authors).
• Activation of the Anaphase Promoting Complex Reverses Multiple Drug Resistant Cancer in a Canine Model of Multiple Drug Resistant Lymphoma. Arnason TG, MacDonald-Dickinson V, Gaunt MC, Davies GF, Lobanova L, Trost B, Gillespie ZE, Waldner M, Baldwin P, Borrowman D, Marwood H, Vizeacoumar FS, Vizeacoumar FJ, Eskiw CH, Kusalik A, Harkness TAA. Cancers. 2022; 14(17):4215. https://doi.org/10.3390/cancers14174215.
• A Drug Repurposing Screen Identifies Fludarabine Phosphate as a Potential Therapeutic Agent for N-MYC Overexpressing Neuroendocrine Prostate Cancers. Elhasasna H, Khan R, Bhanumathy KK, Vizeacoumar FS, Walke P, Bautista M, Dahiya DK, Maranda V, Patel H, Balagopal A, Alli N, Krishnan A, Freywald A† and Vizeacoumar FJ†. Cells 2022, 11(14), 2246; doi.org/10.3390/cells11142246 († Corresponding authors).
• DDX41 is required for cGAS-STING activation against DNA virus infection. Singh RS, Vidhyasagar V, Yang S, Arna AB, Yadav M, Aggarwal A, Aguilera AN, Shinriki S, Bhanumathy KB, Pandey K, Xu A, Rapin N, Bosch M, DeCoteau JF, Xiang J, Vizeacoumar FJ, Zhou Y, Misra V, Matsui H, Ross SR, Wu Y. Cell Rep. 2022 May 24;39(8):110856. doi: 10.1016/j.celrep.2022.110856.
• Differential expression of HNF1A and HNF1A-AS1 in colon cancer cells. Sepehri Z, Banerjee A, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Dolinsky VW, Davie JR. IUBMB Life. 2022 Jun;74(6):496-507. doi: 10.1002/iub.2609. Epub 2022 Mar 2.

2021

• Highly Specific Sigma Receptor Ligands Exhibit Anti-Viral Properties in SARS-CoV-2 Infected Cells. Ostrov DA, Bluhm AP, Li D, Khan JQ, Rohamare M, Rajamanickam K, K Bhanumathy K, Lew J, Falzarano D, Vizeacoumar FJ, Wilson JA, Mottinelli M, Kanumuri SRR, Sharma A, McCurdy CR, Norris MH. Pathogens. 2021 Nov 20;10(11):1514. doi: 10.3390/pathogens10111514.
• Sympathetic signaling facilitates progression of neuroendocrine prostate cancer. Dwivedi S, Bautista M, Shrestha S, Elhasasna H, Chaphekar T, Vizeacoumar FS, Krishnan A. Cell Death Discov. 2021 Nov 22;7(1):364. doi: 10.1038/s41420-021-00752-1.
• Mapping Genetic Interactions. Volume 2381. 1st Edition.
  Editors: Franco J. Vizeacoumar and Andrew Freywald
  Hardcover ISBN: 978-1-0716-1739-7; eBook ISBN: 978-1-0716-740-3. Springer Nature Publications. Publication Date: October 2021. DOI: 10.1007/978-1-0716-1740-3.
  
• Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. Bhanumathy KK, Abuhussein O, Vizeacoumar FS, Freywald A, Vizeacoumar FJ, Phenix CP, Price EW, Cao R. Methods Mol Biol. 2021;2381:333-358. doi: 10.1007/978-1-0716-1740-3_18.
• Identification of Synthetic Lethal Interactions Using High-Throughput, Arrayed CRISPR/Cas9-Based Platforms. MacAuley MJ, Abuhussein O, Vizeacoumar FS. Methods Mol Biol. 2021;2381:135-149. doi: 10.1007/978-1-0716-1740-3_7.
• INCISOR: An Algorithm to Identify Synthetic Rescue Mediators of Resistance to Targeted and Immunotherapy. Wang X, Vizeacoumar FS, Sahu AD. Methods Mol Biol. 2021;2381:203-215. doi: 10.1007/978-1-0716-1740-3_11.
• Genome-wide synthetic lethal screen unveils novel CAIX – NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors. Chafe SC, Vizeacoumar FS, Venkateswaran G, Nemirovsky O, Awrey S, Brown WS, McDonald PC, Carta F, Metcalfe A, Karasinska JM, Huang L, Muthuswamy SK, Schaeffer DF, Renouf DJ, Supuran CT, Vizeacoumar FJ, Dedhar S.  Science Advances 2021 Aug 27;7(35):eabj0364. doi: 10.1126/sciadv.abj0364. Print 2021 Aug.
  
• Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. Dong SXM, Vizeacoumar FS, Bhanumathy KK, Alli N, Gonzalez-Lopez C, Gajanayaka N, Caballero R, Ali H, Freywald A, Cassol E, Angel JB, Vizeacoumar FJ†, Kumar A†.  BMC Infectious Diseases. 2021 Jul 7;21(1):655.2021 († Corresponding authors).
• Mining the plasma-proteome associated genes in patients with gastro-esophageal cancers for biomarker discovery. Vizeacoumar FS, Guo H, Dwernychuk L, Zaidi A, Freywald A, Wu F, Vizeacoumar FJ† and Ahmed S†. Sci Rep. 2021 Apr 7;11(1):7590. († Corresponding authors).
• Conversion from unresectable to resectable liver metastases in real-world patients with liver-only metastatic colorectal cancer (mCRC) treated with FOLFOXIRI plus bevacizumab: The Conversion trial. Ahmed S, Anderson D, Chalchal HI, Dwernychuk L, Gill D, Gitlin J, Hammond A, Kanthan R, Le D, Lim J, Rakheja R, Sari N, Vizeacoumar FJ, Zaidi A, Moser M. Journal of Clinical Oncology (2021). Volume 39, Issue 3_suppl. DOI: 10.1200/JCO.2021.39.3_suppl.TPS147.
• Protein Tyrosine Kinases: Their Roles and Their Targeting in Leukemia. Bhanumathy KK, Balagopal A, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Giambra V. Cancers 2021, 13(2), 184.
• APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A. Wong L, Vizeacoumar FS, Vizeacoumar FJ, Chelico L. Nucleic Acids Res. 2021 Jan 11;49(1):322-339.

2020

• Biological Mechanisms and the Advancing Approaches to Overcoming Cancer Drug Resistance, Volume 12, 1st Edition.
  Editors: Andrew Freywald and Franco J. Vizeacoumar.
  Hardcover ISBN: 9780128213100; eBook ISBN: 9780128213117. Imprint: Academic Press. Published Date: 18th November 2020.
• The CINs of Polo-Like Kinase 1 in Cancer. Cunningham CE†, MacAuley MJ, Vizeacoumar FS, Abuhussein O, Freywald A†, Vizeacoumar FJ†. Cancers 2020, 12(10), 2953. († Corresponding authors).

2019

• Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Database. Denomy C, Germain S, Haave B, Vizeacoumar FS, Freywald A, Weaver B, Vizeacoumar FJ†. Cancer Research. 2019 Aug 15 DOI: 10.1158/0008-5472.CAN-19-0585 († Corresponding author).
• A Low-cost and portable smart instrumentation for detecting colorectal cancer cells. Alam MW, Wahid KA, Islam MF, Bernhard W, Geyer CR, Vizeacoumar FJ. Appl. Sci. 2019. 9(17); 3510; doi.org/10.3390/app9173510.
• Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. Kirzinger MWB, Vizeacoumar FS, Haave B, Gonzalez-Lopez C, Bonham K, Kusalik A†, Vizeacoumar FJ†. BMC Med Genomics. 2019 Jul 27;12(1):112. doi: 10.1186/s12920-019-0554-z († Corresponding authors).
• Targeting the CINful genome: Strategies to overcome tumor heterogeneity. Cunningham CE, MacAuley MJ, Yadav G, Vizeacoumar FS, Freywald A†, Vizeacoumar FJ†. Prog Biophys Mol Biol. 2019 Feb 25. pii: S0079-6107(18)30284-0. doi: 10.1016/j.pbiomolbio.2019.02.006. [Epub ahead of print] († Corresponding authors).
• Estrogen receptor signaling regulates the expression of breast tumor kinase in breast cancer cells. Miah S, Bagu E, Goel R, Yetunde O, Dai C, Ward A, Vizeacoumar FS, Davies G, Vizeacoumar FJ, Anderson D and Lukng KE. BMC Cancer (2019) 19:78. DOI: https://doi.org/10.1186/s12885-018-5186-8.
• A Road map to personalizing targeted cancer therapies using synthetic lethality. Parameswaran S, Kundapur D, Vizeacoumar FS, Freywald A†, Uppalapati MC†, Vizeacoumar FJ†. Trends in Cancer 2019 Jan;5(1):11-29. doi: 10.1016/j.trecan.2018.11.001. Epub 2018 Dec 7. Review († Corresponding authors).
• Molecular characterization of a MLL1 fusion and its role in chromosomal instability. Parameswaran S, Vizeacoumar FS, Kalyanasundaram Bhanumathy K, Qin F, Islam MF, Toosi BM, Cunningham CE, Mousseau DD, Uppalapati MC, Stirling PC, Wu Y, Bonham K, Freywald A, Li H, Vizeacoumar FJ†. Mol Oncol. 2019 Feb;13(2):422-440. doi: 10.1002/1878-0261.12423. Epub 2018 Dec 31(† Corresponding author).

2018

• Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability. Jing A, Vizeacoumar FS, Parameswaran S, Haave B, Cunningham CE, Wu Y, Arnold R, Bonham K, Freywald A, Han J†, Vizeacoumar FJ†. NPJ Syst Biol Appl. 2018 Oct 24;4:38. doi: 10.1038/s41540-018-0074-z. eCollection 2018. († Corresponding authors).
• Discovering Selective Binders for Photoswitchable Proteins Using Phage Display. Reis JM, Xu X, McDonald S, Woloschuk RM, Jaikaran ASI, Vizeacoumar FS, Woolley GA, Uppalapati M. ACS Synth Biol. 2018 Oct 19;7(10):2355-2364. doi: 10.1021/acssynbio.8b00123. Epub 2018 Sep 27.
• Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates. Goel RK, Meyer M, Paczkowska M, Reimand J, Vizeacoumar FS, Vizeacoumar FJ, Lam TT, Lukong KE. Proteome Sci. 2018 Aug 18;16:16. doi: 10.1186/s12953-018-0143-7.
• EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours. Toosi BM, El Zawily A, Truitt L, Shannon M, Allonby O, Babu M, DeCoteau J, Mousseau D5, Ali M, Freywald T, Gall A, Vizeacoumar FS, Kirzinger MW, Geyer CR, Anderson DH, Kim T, Welm AL, Siegel P, Vizeacoumar FJ, Kusalik A, Freywald A. Oncogene. 2018 Apr 27. doi: 10.1038/s41388-018-0228-x. [Epub ahead of print].
• Biochemical characterization of INTS3 and C9ORF80, two subunits of hNABP1/2 heterotrimeric complex in nucleic acid binding. Vidhyasagar V, He Y, Guo M, Talwar T, Singh RS, Yadav M, Katselis G, Vizeacoumar FJ, Lukong E, Wu Y. Biochem J. 2018 Jan 2;475(1):45-60. doi: 10.1042/BCJ20170351.

2017

• FRK inhibits breast cancer cell migration and invasion by suppressing epithelial-mesenchymal transition. Ogunbolude Y, Dai C, Bagu ET, Goel RK, Miah S, MacAusland-Berg J, Ng CY, Chibbar R, Napper S, Raptis L, Vizeacoumar FS, Vizeacoumar FJ, Bonham K, Lukong KE. Oncotarget. 2017 Dec 6;8(68):113034-113065. doi: 10.18632/oncotarget.22958. eCollection 2017 Dec 22.
• An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer. Auslander N†, Cunningham CE, Toosi BM, McEwen EJ, Yizhak K, Vizeacoumar FS, Parameswaran S, Gonen N, Freywald T, Bhanumathy KK, Freywald A†, Vizeacoumar FJ†, Ruppin E†. Mol Syst Biol. 2017 Dec 1;13(12):956. doi: 10.15252/msb.20177739. († Corresponding authors).
• The EphB6 receptor is overexpressed in pediatric T cell acute lymphoblastic leukemia and increases its sensitivity to doxorubicin treatment. El Zawily A, McEwen E, Toosi B, Vizeacoumar FS, Freywald T, Vizeacoumar FJ†, Freywald A†. Sci Rep. 2017 Nov 7;7(1):14767. doi: 10.1038/s41598-017-15200-3. († Corresponding authors).
• Molecular characterization of breast cancer cell lines through multiple omic approaches. Smith SE, Mellor P, Ward AK, Kendall S, McDonald M, Vizeacoumar FS, Vizeacoumar FJ, Napper S, Anderson DH. Breast Cancer Research 2017 Jun 5; 19(1):65. Doi:10.1186/s13058-017-0855-0.
• Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens. Islam MF, Watanabe A, Wong L, Lazarou C, Vizeacoumar FS, Abuhussein O, Hill W, Uppalapati M, Geyer CR, Vizeacoumar FJ†.  Sci Rep. 2017 Apr 21;7(1):1040. doi: 10.1038/s41598-017-01170-z. († Corresponding author).

2016

• The intrinsically kinase-inactive EPHB6 receptor predisposes cancer cells to DR5-induced apoptosis by promoting mitochondrial fragmentation. El Zawily AM, Toosi BM, Freywald T, Indukuri VV, Vizeacoumar FJ, Leary SC, Freywald A. Oncotarget 2016 Nov 22;7(47):77865-77877. doi: 10.18632/oncotarget.12838.
• Therapeutic relevance of the protein phosphatase 2A in cancer. Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KK, Lee JS, Parameswaran S, Furber L, Abuhussain O, Paul JM, McDonald M, Templeton SD, Shukla H, Boyd F, Alli N, Mousseau D, Geyer R, Bonham K, Anderson DH, Yan J, Yu-Lee L, Weaver BA, Uppalapati1 M, Ruppin E, Sablina A, Freywald A, Vizeacoumar FJ†. Oncotarget. 2016 Sep 20;7(38):61544-61561. doi: 10.18632/oncotarget.11399. († Corresponding author).
• Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment. Paul JM, Toosi B, Vizeacoumar FS, Bhanumathy KK, Li Y, Gerger C, El Zawily A, Freywald T, Anderson DH, Mousseau D, Kanthan R, Zhang Z, Vizeacoumar FJ†, Freywald A†. Oncotarget. 2016 Aug 2;7(31):50027-50042. doi: 10.18632/oncotarget.10569. († Corresponding authors).
• Epigenetic silencing of CREB3L1 by DNA methylation is associated with high-grade metastatic breast cancers with poor prognosis and is prevalent in triple negative breast cancers. Ward AK, Mellor P, Smith SE, Kendall S, Just NA, Vizeacoumar FS, Sarker S, Phillips Z, Alvi R, Saxena A, Vizeacoumar FJ, Carlsen SA, Anderson DH. Breast Cancer Research 2016 Jan 25;18(1):12. doi: 10.1186/s13058-016-0672-x.

2015

• A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. Mol Cell Proteomics. 2015 Oct;14(10):2833-47. doi: 10.1074/mcp.O115.052209. Epub 2015 Aug 19.
• Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double Strand Break Repair by Non-Homologous End Joining. Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, Zhang Z, Vizeacoumar F, Krogan NJ, Freywald A, Golshani A, Babu M. Mol Cell Biol. 2015 May 11. pii: MCB.00007-15. Epub 2015 May 11.

2014

• Building high-resolution synthetic lethal networks: a 'Google map' of the cancer cell. Paul JM, Templeton SD, Baharani A, Freywald A, Vizeacoumar FJ†. Trends Mol Med. 2014 Oct 22;20(12):704-715. doi: 10.1016/j.molmed.2014.09.009. Epub 2014 Oct22. († Corresponding author).

2013

• A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar FJ, Arnold R, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J. Mol Syst Biol. 2013 Oct 8;9:696. doi: 10.1038/msb.2013.54.

2012

• Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae. Orij R, Urbanus ML, Vizeacoumar FJ, Giaever G, Boone C, Nislow C, Brul S, Smits GJ. Genome Biol. 2012 Sep 10;13(9):R80. doi: 10.1186/gb-2012-13-9-r80.
• Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, Chandran S, Punna T, Christopolous C, Wong V, Yu A, Zhong G, Li J, Stagljar I, Conibear E, Wodak SJ, Emili A, Greenblatt JF. Nature. 2012 Sep 27;489(7417):585-9. doi: 10.1038/nature11354. Epub 2012 Sep 2.
• Hsp110 is required for spindle length control. Makhnevych T, Wong P, Pogoutse O, Vizeacoumar FJ, Greenblatt JF, Emili A, Houry WA. J Cell Biol. 2012 Aug 20;198(4):623-36. doi: 10.1083/jcb.201111105.
• Essential gene profiles in breast, pancreas and ovarian cancer cells. Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JL, van Dyk D, Fedyshyn B, Luhova M, Brito GC, Vizeacoumar FJ, Vizeacoumar FS, Datti A, Kasimer D, Buzina A, Mero P, Misquitta C, Normand J, Haider M, Ketela T, Wrana JL, Rottapel R, Neel BG, Moffat J. Cancer Discov. 2012 Feb;2(2):172-89. Epub 2011 Dec 29.
• PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. Jin K, Li J, Vizeacoumar FS, Li Z, Min R, Zamparo L, Vizeacoumar FJ, Datti A, Andrews B, Boone C, Zhang Z. Nucleic Acids Res. 2012 Jan;40(Database issue):D687-94. doi: 10.1093/nar/gkr827. Epub 2011 Oct 18.

2011

• Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Li Z*, Vizeacoumar FJ*, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C. Nat Biotechnol. 2011 Apr;29(4):361-7. doi: 10.1038/nbt.1832. Epub 2011 Mar 27. * Both authors contributed equally.

2010

• Genetic interactions reveal the evolutionary trajectories of duplicate genes. VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL. Mol Syst Biol. 2010 Nov 16;6:429. doi: 10.1038/msb.2010.82.
• Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C. Methods Enzymol. 2010;470:145-79. doi: 10.1016/S0076-6879(10)70007-0. Epub 2010 Mar 1.
• A novel mechanism for SUMO system control: regulated Ulp1 nucleolar sequestration. Sydorskyy Y, Srikumar T, Jeram SM, Wheaton S, Vizeacoumar FJ, Makhnevych T, Chong YT, Gingras AC, Raught B. Mol Cell Biol. 2010 Sep;30(18):4452-62. doi: 10.1128/MCB.00335-10. Epub 2010 Jul 20.
• Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Li J, Min R, Vizeacoumar FJ, Jin K, Xin X, Zhang Z. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10472-7. doi: 10.1073/pnas.0914302107. Epub 2010 May 20.
• The genetic landscape of a cell. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.
• Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ. J Cell Biol. 2010 Jan 11;188(1):69-81. doi: 10.1083/jcb.200909013.

2009

• A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. Vizeacoumar FJ, Chong Y, Boone C, Andrews BJ. FEBS Lett. 2009 Jun 5;583(11):1656-61. doi: 10.1016/j.febslet.2009.03.068. Epub 2009 Apr 5.
• Global map of SUMO function revealed by protein-protein interaction and genetic networks. Makhnevych T, Sydorskyy Y, Xin X, Srikumar T, Vizeacoumar FJ, Jeram SM, Li Z, Bahr S, Andrews BJ, Boone C, Raught B. Mol Cell. 2009 Jan 16;33(1):124-35. doi: 10.1016/j.molcel.2008.12.025.

2006

• Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals. Vizeacoumar FJ, Vreden WN, Aitchison JD, Rachubinski RA. J Biol Chem. 2006 May 26;281(21):14805-12. Epub 2006 Mar 21.
• The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA. iol Chem. 2006 May 5;281(18):12817-23. Epub 2006 Mar 6.

2004

• Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA. Mol Biol Cell. 2004 Feb;15(2):665-77. Epub 2003 Nov 14.

2003

• Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae. Tam YY, Torres-Guzman JC, Vizeacoumar FJ , Smith JJ, Marelli M, Aitchison JD, Rachubinski RA. Mol Biol Cell. 2003 Oct;14(10):4089-102. Epub 2003 May 18.
• YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae. Vizeacoumar FJ , Torres-Guzman JC, Tam YY, Aitchison JD, Rachubinski RA. J Cell Biol. 2003 Apr 28;161(2):321-32. Epub 2003 Apr 21.

2002

• Transcriptome profiling to identify genes involved in peroxisome assembly and function. Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ , Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. J Cell Biol. 2002 Jul 22;158(2):259-71. Epub 2002 Jul 22.