Publications

2020

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.

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. bioRxiv doi: https://doi.org/10.1101/2020.05.05.079657

 

 

2019

*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)

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.

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,

2018

*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)

 

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.

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.

*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)

2017

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.

2016

#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. (#co-corresponding author).

#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. (#co-corresponding author).

#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. (#co-corresponding author).

#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. (#co-corresponding author).

#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. (#co-corresponding author).

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.

2015

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.

*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. (* co-first author).

 

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.

 

2014

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

2013

#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. (#co-corresponding author).

 

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.

 

 

Prior to 2013

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.

 

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.

 

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.

 

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.

 

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.

 

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.

 

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.

Juan Fuxman Bass, PhD

Assistant Professor of Biology

 

Boston University

5 Cummington mall

Boston, MA 02215

e-mail: fuxman[at]bu.edu

Phone: (617) 353-2448

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