Publications
2024
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Moyer DC, Reimertz J, Segrè D, Fuxman Bass JI. Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models. bioRxiv. 2024 Jun 27:2024.06.24.600481. doi: 10.1101/2024.06.24.600481
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Rottenberg JT, Taslim TH, Soto-Ugaldi LF, Martinez-Cuesta L, Martinez-Calejman C, Fuxman Bass JI. Viral cis-regulatory elements as sensors of cellular states and environmental cues. Trends in Genetics. 2024 May 30:S0168-9525(24)00108-2. doi: 10.1016/j.tig.2024.05.004
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Luke Lambourne, Kaia Mattioli, Clarissa Santoso, Gloria Sheynkman, Sachi Inukai, Babita Kaundal, Anna Berenson, Kerstin Spirohn-Fitzgerald, Anukana Bhattacharjee, Elisabeth Rothman, Shaleen Shrestha, Florent Laval, Zhipeng Yang, Deepa Bisht, Jared A. Sewell, Guangyuan Li, Anisa Prasad, Sabrina Phanor, Ryan Lane, Devlin M. Campbell, Toby Hunt, Dawit Balcha, Marinella Gebbia, Jean-Claude Twizere, Tong Hao, Adam Frankish, Josh A. Riback, Nathan Salomonis, Michael A. Calderwood, David E. Hill, Nidhi Sahni, Marc Vidal, Martha L. Bulyk, Juan I. Fuxman Bass. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. bioRxiv. 2024.03.12.584681. doi: 10.1101/2024.03.12.584681.
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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. Life Science Alliance. 2024 Jan 29:2024.01.24.577099. doi: 10.26508/lsa.202402641
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2023
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Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Emerging questions in transcriptional regulation. Cell Systems​. 2023 Apr 19;14(4):247-251. doi: 10.1016/j.cels.2023.03.005
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Berenson A, Lane R, Soto-Ugaldi LF, Patel M, Ciausu C, Li Z, Chen Y, Shah S, Santoso C, Liu X, Spirohn K, Hao T, Hill DE, Vidal M, Fuxman Bass JI. Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors. Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors. Nature Communications 2023.04.14.536894. doi: 10.1038/s41467-023-42445-6.
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Carrasco Pro S, Hook H, Bray D, Moyer D, Yin M, Labadorf A, Tewhey R, *Siggers T, *Fuxman Bass J. Widespread perturbation of ETS factor binding sites in cancer. Nature Communications. 2023 Feb 17;14(1):913. doi: 10.1038/s41467-023-36535-8. (*co-corresponding authors)
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Patalano SD, Fuxman Bass P, Fuxman Bass JI. Transcription factors in the development and treatment of immune disorders. Transcription. 2023 Dec 15:1-23. doi: 10.1080/21541264.2023.2294623.
He 何璇 XA, Berenson A, Bernard M, Weber C, Cook L, Visel A, Fuxman Bass JI, Fisher S. Identification of conserved skeletal enhancers associated with craniosynostosis risk genes. Human Molecular Genetics 2022.09.01.506150. doi: 10.1093/hmg/ddad182.
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Berenson A, Fuxman Bass JI. Enhanced yeast one-hybrid assays to study protein-DNA interactions. Methods Mol Biol. 2023;2599:11-20.doi: 10.1007/978-1-0716-2847-8_2.
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2022
*Soto LF, *Requena D, *Fuxman Bass JI. Epitope Evaluator: an interactive web application to study predicted T-cell epitopes. PLoS One. 2022 Aug 26;17(8):e0273577. doi: 10.1371/journal.pone.0273577. (*co-corresponding author)
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Soto L, Li Z, Santoso CS, Berenson A, Ho I, Shen VX, Yuan S, Fuxman Bass JI. Compendium of human transcription factor effector domains. Molecular Cell. 2022 Feb 3;82(3):514-526. doi: 10.1016/j.molcel.2021.11.007.
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2021
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Kuniholm J, Armstrong E, Bernabe B, Coote C, Berenson A, Patalano SD, Olson A, He X, Lin N, Fuxman Bass JI, Henderson AJ. Intragenic proviral elements support transcription of defective HIV-1 proviruses. PloS Pathogens. 2021 Dec 28;17(12):e1009982. doi: 10.1371/journal.ppat.1009982.
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Basu J, Reis BS, Peri S, Zha J, Hua X, Ge L, Ferchen K, Nicolas E, Czyzewicz P, Cai KQ, Tan Y, Fuxman Bass JI, Walhout AJM, Grimes HL, Grivennikov SI, Mucida D, Kappes DJ. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function. Nature Immunology. 2021 Aug;22(8):969-982. doi: 10.1038/s41590-021-00980-8.
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Santoso CS, Li Z, Rottenberg JT, Liu X, Shen VX, Fuxman Bass JI. Therapeutic targeting of transcription factors to control the cytokine release syndrome in COVID-19. Frontiers in Pharmacology. 2021 Jun 7;12:673485. doi: 10.3389/fphar.2021.673485.
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Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass JI, Benson G. Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. Nucleic Acids Research. 2021 Apr 13:gkab224. doi: 10.1093/nar/gkab224.
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Soto LF, Li Z, Santoso CS, Berenson A, Ho I, Shen VX, Yuan S, Fuxman Bass JI. Compendium of human transcription factor effector domains. Mol Cell. 2022 Feb 3;82(3):514-526. doi: 10.1016/j.molcel.2021.11.007
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Pedro KD, Agosto LM, Sewell JA, Eberenz KA, He X, *Fuxman Bass JI, *Henderson AJ. An unbiased functional screen identifies transcriptional networks that regulate HIV-1 and HIV-2. Proc Natl Acad Sci U S A. 2021 Mar 16;118(11):e2012835118. doi: 10.1073/pnas.2012835118. (* co-senior and co-corresponding authors)
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2020
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Santoso CS, Li Z, Lal S, Yuan S, Gan KA, Agosto LM, Liu X, Carrasco Pro S, Sewell JA, Henderson A, Atianand MK, Fuxman Bass JI. Comprehensive mapping of the human cytokine gene regulatory network. Nucleic Acids Research 2020 Dec 2;48(21):12055-12073. doi: 10.1093/nar/gkaa1055.
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Carrasco Pro S, Bulekova K, Gregor B, Labadorf L, Fuxman Bass JI. Prediction of genome-wide effects of single nucleotide variants on transcription factor binding. Scientific Reports. 2020 Oct 19; 10, 1-11. doi: 10.1038/s41598-020-74793-4.
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Liu X, Hong T, Parameswaran S, Ernst K, Marazzi I, Weirauch MT, Fuxman Bass JI. Human Virus Transcriptional Regulators. Cell. 2020 Jul 9;182(1):24-37. doi: 10.1016/j.cell.2020.06.023.
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2019
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*Shrestha S, *Sewell JA, Santoso CS, Forchielli E, Pro SC, Martinez M, Fuxman Bass JI. Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. Genome Res. 2019 Sep;29(9):1533-1544. doi: 10.1101/gr.248823.119. (* co-first authors)
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Shrestha S, Liu X, Santoso CS, Fuxman Bass JI. Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences. J Vis Exp. 2019 Feb 11;(144). doi: 10.3791/59192.
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Mookerjee-Basu J, Hua X, Ge L, Nicolas E, Li Q, Czyzewicz P, Zhongping D, Peri S, Fuxman Bass JI, Walhout AJM, Kappes DJ. Functional conservation of a developmental switch in mammals since the Jurassic age. Mol Biol Evol. 2019 Jan 1;36(1):39-53. doi: 10.1093/molbev/msy191,
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2018
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*Carrasco Pro S, *Dafonte Imedio A, Santoso CS, Gan KA, Sewell JA, Martinez M, Sereda R, Mehta S, Fuxman Bass JI. Global landscape of mouse and human cytokine transcriptional regulation. Nucleic Acids Res. 2018 Oct 12;46(18):9321-9337. doi: 10.1093/nar/gky787. (* co-first authors)
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Demchak B, Kreisberg JF, Fuxman Bass JI. Theory and Application of Network Biology Toward Precision Medicine. J Mol Biol. 2018 Jul 17. pii: S0022-2836(18)30811-8. doi: 10.1016/j.jmb.2018.07.019.
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Sewell JA, Fuxman Bass JI. Options and Considerations When Using a Yeast One-Hybrid System. Methods Mol Biol. 2018;1794:119-130. doi: 10.1007/978-1-4939-7871-7_8.
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*Kok A. Gan, *Sebastian Carrasco Pro, Jared A. Sewell and Juan I. Fuxman Bass. Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. Frontiers in Genetics. 2018 Feb 2;9:16. doi: 10.3389/fgene.2018.00016. (* co-first authors)
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2017
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Sewell JA, Fuxman Bass JI. Cellular network perturbations by disease-associated variants. Curr Opin Sys Biol. 2017 Jun;3:60-66. doi: 10.1016/j.coisb.2017.04.009.
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2016
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Fuxman Bass JI, Reece-Hoyes JS, #Walhout AJ. Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.top077669. doi: 10.1101/pdb.top077669.
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Fuxman Bass JI, Reece-Hoyes JS, #Walhout AJ. Zymolyase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast. Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088971. doi: 10.1101/pdb.prot088971.
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Fuxman Bass JI, Reece-Hoyes JS, #Walhout AJ. Colony Lift Colorimetric Assay for β-Galactosidase Activity. Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088963. doi: 10.1101/pdb.prot088963.
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Fuxman Bass JI, Reece-Hoyes JS, #Walhout AJ. Performing Yeast One-Hybrid Library Screens. Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088955. doi: 10.1101/pdb.prot088955.
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Fuxman Bass JI, Reece-Hoyes JS, #Walhout AJ. Generating Bait Strains for Yeast One-Hybrid Assays. Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088948. doi: 10.1101/pdb.prot088948.
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Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Mol Syst Biol 2016 Oct 24; 12:884. doi: 10.15252/msb.20167131.
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2015
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Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJ. Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants. Cell. 2015 Apr 23;161(3):661-73. doi: 10.1016/j.cell.2015.03.003.
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*Sahni N, *Yi S, *Taipale M, *Fuxman Bass JI, *Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJ, Lindquist S, Vidal M. Widespread Perturbation of Disease-Specific Macromolecular Interactions in Human Genetic Disorders. Cell. 2015 Apr 23;161(3):647-60. doi: 10.1016/j.cell.2015.04.013.
Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 2015 Apr 23;4:e06967. doi: 10.7554/eLife.06967.
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2014
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Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res. Nucleic Acids Res. 2014 Jan;42(1):153-62. doi: 10.1093/nar/gkt858.
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2013
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Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nature Methods. 2013 Dec. 10(12):1169-76. doi: 10.1038/nmeth.2728.
Gabelloni ML, Sabbione F, Jancic C, Fuxman Bass JI, Keitelman I, Iula L, Oleastro M, Geffner JR, Trevani AS. NADPH oxidase derived reactive oxygen species are involved in human neutrophil IL-1β secretion but not in inflammasome activation. Eur J Immunol. 2013 Dec;43(12):3324-35. doi: 10.1002/eji.201243089.
Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJ. Complex expression dynamics and robustness in C. elegans insulin networks. Genome Research. 2013 Jun;23(6):954-65. doi: 10.1101/gr.150466.112.
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Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Research. 2014 Jan;42(1):153-62. doi: 10.1093/nar/gkt858.
Prior to 2013
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Traglia GM, Sala CD, Fuxman Bass JI, Soler-Bistué AJ, Zorreguieta A, Ramírez MS, Tolmasky ME. Internalization of Locked Nucleic Acids/DNA Hybrid Oligomers into Escherichia coli. Biores Open Access. 2012 Oct;1(5):260-3. doi: 10.1089/biores.2012.0257.
Nahmod K, Walther T, Cambados N, Fernandez N, Meiss R, Tappenbeck N, Wang Y, Raffo D, Simian M, Schwiebs A, Pozner R, Fuxman Bass J, Geffner J, Kordon E, Schere Levy C. AT1 receptor blockade delays post-lactational mammary gland involution: a novel role for the renin angiotensin system. FASEB J. 2012 May;26(5):1982-94. doi: 10.1096/fj.11-191932.
Fuxman Bass J, Russo D, Gabelloni M, Geffner J, Giordano M, Catalano M, Zorreguieta A, Trevani A. Extracellular DNA: A Major Proinflammatory Component of P. aeruginosa Biofilms. J Immunol. 2010 Jun 1;184(11):6386-95. doi: 10.4049/jimmunol.0901640.
Salamone G, Petracca Y, Fuxman Bass J, Rumbo M, Geffner J, Trevani A. Flagellin delays spontaneous human neutrophil apoptosis. Lab Invest. 2010 Jul;90(7):1049-59. doi: 10.1038/labinvest.2010.77.
Fuxman Bass J, Alvarez M, Gabelloni M, Geffner J, Vermeulen M, Amaral M, Trevani A. GM-CSF enhances a CpG-independent pathway of neutrophil activation triggered by bacterial DNA. Mol Immunol. 2008 Nov;46(1):37-44. doi: 10.1016/j.molimm.2008.06.033.
Fuxman Bass J, Gabelloni M, Alvarez M, Vermeulen M, Russo D, Zorreguieta A, Geffner J, Trevani A. Characterization of bacterial DNA binding to human neutrophil surface. Lab Invest. 2008 Sep;88(9):926-37. doi: 10.1038/labinvest.2008.59.
Alvarez M, Fuxman Bass J, Geffner J, Fernández Calotti P, Costas M, Coso O, Gamberale R, Vermeulen M, Salamone G, Tanos T, Trevani A. Neutrophil signaling pathways activated by bacterial DNA stimulation. J Immunol. 2006 Sep 15;177(6):4037-46. doi: 10.4049/jimmunol.177.6.4037.