Stephen Floor, PhD
Assistant Professor
Cell and Tissue Biology
School of Dentistry

Some questions we’re interested in are: how do DEAD-box proteins influence RNA structure and bound proteins in cells? How do these changes affect cell state? Do DEAD-box proteins act as molecular dispersants for RNA? How can we measure translation and protein binding on single RNA molecules in cells? We use diverse deep sequencing approaches, biochemistry, imaging, computational analysis, and develop new methods to answer these questions.

• RNA molecular recording with an engineered RNA deaminase.
  Nature methods 2023 Lin Y, Kwok S, Hein AE, Thai BQ, Alabi Y, Ostrowski MS, Wu K, Floor SN
• Nucleolar dynamics are determined by the ordered assembly of the ribosome.
  bioRxiv : the preprint server for biology 2023 Sheu-Gruttadauria J, Yan X, Stuurman N, Floor SN, Vale RD
• Determinants of DDX3X sensitivity uncovered using a helicase activity in translation reporter.
  bioRxiv : the preprint server for biology 2023 Wilkins KC, Schroeder T, Gu S, Revalde JL, Floor SN
• Dynamic regulation of messenger RNA structure controls translation.
  Nature 2023 Lin Y, Floor SN
• The variant landscape and function of DDX3X in cancer and neurodevelopmental disorders.
  Trends in molecular medicine 2023 Gadek M, Sherr EH, Floor SN
• Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression.
  Cell reports 2023 Campbell AE, Dyle MC, Albanese R, Matheny T, Sudheendran K, Cortázar MA, Forman T, Fu R, Gillen AE, Caruthers MH, Floor SN, Calviello L, Jagannathan S
• Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model.
  eLife 2022 Hoye ML, Calviello L, Poff AJ, Ejimogu NE, Newman CR, Montgomery MD, Ou J, Floor SN, Silver DL
• Lysate and cell-based assays to probe the translational role of RNA helicases.
  Methods in enzymology 2022 Wilkins KC, Venkataramanan S, Floor SN
• SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal.
  Developmental cell 2022 Yu T, Cazares O, Tang AD, Kim HY, Wald T, Verma A, Liu Q, Barcellos-Hoff MH, Floor SN, Jung HS, Brooks AN, Klein OD
• Determining the impact of stress granule composition on cell survival.
  Biophysical Journal 2022 Jesslyn Park, Srivats Venkataramanan, José Liboy-Lugo, Virginia K. Blackwell, Stephen N. Floor
• Mapping the regulatory landscape of membraneless organelle assembly and dynamics.
  Biophysical Journal 2022 Jessica Sheu-Gruttadauria, Xiaowei Yan, Nico Stuurman, Stephen Floor, Ronald D. Vale
• The impact of periodic stress on stress granules in human cells.
  Biophysical Journal 2022 Angela L. Gao, Jose Liboy-Lugo, Jesslyn Park, Stephen N. Floor
• The role of G3BP stress granules assembly in cell fitness during the integrated stress response.
  Biophysical Journal 2022 Jose Liboy-Lugo, Jessica Sheu-Gruttadauria, Stephen N. Floor
• Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.
  eLife 2022 Tsai K, Stojkovic V, Noda-Garcia L, Young ID, Myasnikov AG, Kleinman J, Palla A, Floor SN, Frost A, Fraser JS, Tawfik DS, Fujimori DG
• DDX3X and DDX3Y are redundant in protein synthesis.
  RNA (New York, N.Y.) 2021 Venkataramanan S, Gadek M, Calviello L, Wilkins K, Floor SN
• DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
  Nucleic acids research 2021 Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN
• Control of ribosomal protein synthesis by the Microprocessor complex.
  Science signaling 2021 Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A
• Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A.
  Cell chemical biology 2020 Chen M, Asanuma M, Takahashi M, Shichino Y, Mito M, Fujiwara K, Saito H, Floor SN, Ingolia NT, Sodeoka M, Dodo K, Ito T, Iwasaki S
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, …
• Pathogenic DDX3X Mutations Impair RNA Metabolism and Neurogenesis during Fetal Cortical Development.
  Neuron 2020 Lennox AL, Hoye ML, Jiang R, Johnson-Kerner BL, Suit LA, Venkataramanan S, Sheehan CJ, Alsina FC, Fregeau B, Aldinger KA, Moey C, Lobach I, Afenjar A, Babovic-Vuksanovic D, Bézieau S, Blackburn PR, …
• PTBP1 mRNA isoforms and regulation of their translation.
  RNA (New York, N.Y.) 2019 Arake de Tacca LM, Pulos-Holmes MC, Floor SN, Cate JHD
• The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.
  Molecular cell 2018 Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, Ingolia NT
• CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway.
  Nature genetics 2018 Richardson CD, Kazane KR, Feng SJ, Zelin E, Bray NL, Schäfer AJ, Floor SN, Corn JE
• The Traffic Jam: Polyamine Prevalence Pauses Protein Production.
  Molecular cell 2018 Venkataramanan S, Floor SN
• Move Over, Genomes: Here Comes Transcriptome Engineering.
  The CRISPR journal 2018 Thai B, Floor SN
• Widespread Translational Remodeling during Human Neuronal Differentiation.
  Cell reports 2017 Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN
• Widespread translational remodeling during human neuronal differentiation
  bioRxiv preprint 2017 John D Blair, Dirk Hockemeyer, Jennifer A Doudna, Helen S Bateup, Stephen N Floor
• CRISPR-Cas9 Genome Editing In Human Cells Works Via The Fanconi Anemia Pathway
  bioRxiv preprint 2017 Chris D. Richardson, Katelynn R. Kazane, Sharon J. Feng, Nicholas L. Bray, Axel J. Schaefer, Stephen Floor, Jacob Corn
• Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes.
  Nature biotechnology 2017 Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A, Doudna JA
• Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor.
  Nature 2016 Iwasaki S, Floor SN, Ingolia NT
• Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
  Oncotarget 2016 Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, …
• Tunable protein synthesis by transcript isoforms in human cells.
  eLife 2016 Floor SN, Doudna JA
• Analog sensitive chemical inhibition of the DEAD-box protein DDX3.
  Protein science : a publication of the Protein Society 2015 Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA
• Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome.
  Molecular cell 2015 Floor SN, Doudna JA
• Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
  The Journal of biological chemistry 2015 Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA
• Engineering Inhibitor Specificity in the Dead-Box Protein Family.
  Biophysical Journal 2014 Kendall Condon, Stephen Floor, Jennifer Doudna
• Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2.
  Structure (London, England : 1993) 2013 Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD
• Preliminary in vitro functional analysis of the DEAD-box protein DDX3.
  The FASEB Journal 2012 Stephen N Floor, Alison Smith, Kaihong Zhou, Jennifer A Doudna
• Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Floor SN, Borja MS, Gross JD
• A split active site couples cap recognition by Dcp2 to activation.
  Nature structural & molecular biology 2010 Floor SN, Jones BN, Hernandez GA, Gross JD
• Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid (13)C-p-methoxyphenylalanine.
  Journal of the American Chemical Society 2008 Lampe JN, Floor SN, Gross JD, Nishida CR, Jiang Y, Trnka MJ, Ortiz de Montellano PR
• Control of mRNA decapping by Dcp2: An open and shut case?
  RNA biology 2008 Floor SN, Jones BN, Gross JD
• SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction.
  Nature structural & molecular biology 2008 Neher SB, Bradshaw N, Floor SN, Gross JD, Walter P
• mRNA decapping is promoted by an RNA-binding channel in Dcp2.
  Molecular cell 2008 Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross JD
• Simulated Versus Observed Cluster Eccentricity Evolution.
  The Astrophysical Journal 2004 Stephen N. Floor, Adrian L. Melott, Patrick M. Motl
• Simulated versus observed cluster eccentricity evolution
  The Astrophysical Journal 2004 Floor, S. N., Melott, A. L., & Motl, P. M.
• Eccentricity Evolution in Simulated Galaxy Clusters.
  The Astrophysical Journal 2003 Stephen N. Floor, Adrian L. Melott, Christopher J. Miller, Greg L. Bryan
• Eccentricity evolution in simulated galaxy clusters
  The Astrophysical Journal 2003 Floor, S. N., Melott, A. L., Miller, C. J., & Bryan, G. L.
• Empirical investigation of extreme single-particle behavior of nuclear quadrupole moments in highly collective A~150 superdeformed bands.
  AIP Conference Proceedings 2002 S. T. Clark, G. Hackman, R. V. F. Janssens, R. M. Clark, P. Fallon, S. N. Floor, G. J. Lane, A. O. Macchiavelli, J. Norris, S. J. Sanders, C. Svensson
• Empirical investigation of extreme single-particle behavior of nuclear quadrupole moments in highly collective A approximately 150 superdeformed bands.
  Physical review letters 2001 Clark ST, Hackman G, Janssens RV, Clark RM, Fallon P, Floor SN, Lane GJ, Macchiavelli AO, Norris J, Sanders SJ, Svensson CE