Benjamin L. Miller, Ph.D.

Contact Information

Phone Numbers

Administrative: (585) 275-3871

Office: (585) 275-9805

Fax: (585) 273-1346

Research Labs

Visit Lab Website

Locations

University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 697
Rochester, NY 14642

Faculty Appointments

Professor - Department of Dermatology (SMD)
Professor - Department of Biomedical Engineering (SMD) - Joint

Biography

Research

Research in the Miller group focuses on two fundamental areas: the control of biomolecular interactions through the synthesis of new small-molecule probes, and the observation of biomolecular interactions through the development of novel optical sensing technologies. In the area of control, we are particularly interested in the sequence-selective recognition of RNA. New RNA sequences with important functions in basic biology and human health and disease are being discovered at an ever-increasing rate, and yet our ability to target these sequences specifically is still at a rudimentary stage. To address this gap, we are applying techniques of molecular design and a novel combinatorial method of small-molecule evolution called Dynamic Combinatorial Chemistry, which allows us to rapidly "prototype" sequence-selective RNA binding molecules. Thus far we have used this methodology to RNA targets important in Myotonic Dystrophy and HIV. Protein-targeted small-molecule discovery projects are also of interest, and current projects include the mechanism of tight junction formation and the transport of beta-amyloid across the blood-brain barrier. To the end of achieving better methods of observing biomolecular interactions, our group has a longstanding program in the use of the optical properties of nanostructured materials as the basis for new biosensors and diagnostic tools. Two examples of current efforts include Arrayed Imaging Reflectometry (AIR) and sensors based on two-dimensional photonic crystals (2-D PhC). AIR relies on the creation of a near-perfect antireflection coating on the surface of a silicon chip; binding of a biomolecular target destroys this antireflective condition and is visible by a change in reflected light. This allows for highly multiplexed (10's to 1000's of targets) and quantitative detection. Photonic crystal sensors, on the other hand, offer the possibility of ultrasensitive detection: for example, a major long-term goal of our work is the production of sensors that can effectively detect one virus in a blood sample.

Credentials

Education

1988
BS, Chemistry; B.A. Mathematics; B.A. German | Miami University

1994
PhD | Stanford University
Organic Chemistry

Post-doctoral Training & Residency

1994 - 1996
NIH Postdoctoral Fellow, Department of Chemistry, Harvard University: Professor Stuart L. Schreiber, advisor. Design, synthesis, and evaluation of structure-based, nonpeptide combinatorial libraries for binding to Src homology 3 (SH3) domains.

Awards

2009
Rochester Business Journal Health Care Achievement Award
Sponsor: Rochester Business Journal

2001 - 2006
Camille Dreyfus Teacher-Scholar Award
Sponsor: Dreyfus Foundation

1998 - 2000
Research Corporation Research Innovation Award
Sponsor: Research Corporation

1994 - 1996
NIH Postdoctoral Fellowship
Sponsor: NIH
Location: Harvard University

1991 - 1993
W. R. Grace Graduate Fellow Award
Sponsor: W. R. Grace Corporation
Location: Stanford University

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Patents

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: 9,410,953
Issue Date: Aug 09, 2016
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: 2349009
Issue Date: May 14, 2014
Country: Europe
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: FR2349009
Issue Date: May 14, 2014
Country: France
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: DE2349009
Issue Date: May 14, 2014
Country: Germany
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: CH2349009
Issue Date: May 14, 2014
Country: Switzerland/Liechtenstein
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Use of Non-Nucleophilic Additives for Reduction of Surface Morphological Anomalies in Probe Arrays
Patent #: GB2349009
Issue Date: May 14, 2014
Country: United Kingdom
Invented By: Charles R Mace, Benjamin L Miller, Amrita Urdhwareshe-Yadav

Patent Title: Tripodal Cyclohexane Derivatives And Their Use As Carbohydrate Receptors
Patent #: 8,716,472
Issue Date: May 06, 2014
Country: United States
Invented By: Peter Gareiss, Benjamin L Miller, Prakash B Palde

Patent Title: Small Molecule Modulators of Melanin Expression
Patent #: 9,162,984
Issue Date: Oct 20, 2015
Country: United States
Invented By: Peter Gareiss, Brian R McNaughton, Benjamin L Miller, Glynis A Scott

Patent Title: Rapid Diagnostic Chips for Detection of Immune Responses to HPV (Human Papilloma Virus)
Patent #: 8,450,056
Issue Date: May 28, 2013
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, Robert C Rose

Patent Title: Oligocycloalkanoid Peptidomimetic Compounds and Method of Use
Patent #: 6,562,782
Issue Date: May 13, 2003
Country: United States
Invented By: Robert D Hubbard, Benjamin L Miller

Patent Title: Nucleic Acid Binding Compounds and Methods of Use
Patent #: 9,212,205
Issue Date: Dec 15, 2015
Country: United States
Invented By: Peter Gareiss, Brian R McNaughton, Benjamin L Miller, Krzysztof Sobczak, Charles A Thornton, Joseph E Wedekind

Patent Title: Nanocrystal-based Colorimetric Sensors for Human Pathogens
Patent #: 1407265
Issue Date: Dec 19, 2002
Country: Europe
Invented By: Todd D Krauss, Benjamin L Miller

Patent Title: Microcavity Biosensor, Methods of Making, and Uses Thereof
Patent #: 1373894
Issue Date: Dec 13, 2006
Country: Europe
Invented By: Selena Chan, Philippe Fauchet, Scott R Horner, Benjamin L Miller

Patent Title: Microcavity Biosensor and Uses Thereof
Patent #: 7,226,733
Issue Date: Jun 05, 2007
Country: United States
Invented By: Selena Chan, Philippe Fauchet, Scott R Horner, Benjamin L Miller

Patent Title: Method of Identifying Hairpin DNA Probes by Partial Fold Analysis
Patent #: 7,598,034
Issue Date: Oct 06, 2009
Country: United States
Invented By: Benjamin L Miller, Christopher M Strohsahl

Patent Title: Method of Identifying Hairpin DNA Probes by Partial Fold Analysis
Patent #: 7,442,510
Issue Date: Oct 28, 2008
Country: United States
Invented By: Benjamin L Miller, Christopher M Strohsahl

Patent Title: Method for the Topographically -Selective Passivation of Micro- and Nanoscale Devices
Patent #: 10,215,753
Issue Date: Feb 26, 2019
Country: United States
Invented By: Mark A Lifson, Benjamin L Miller, Dhruba Jyoti Basu Roy

Patent Title: Method Of Identifying Hairpin DNA Probes By Partial Fold Analysis
Patent #: 2005237396
Issue Date: Jun 10, 2010
Country: Australia
Invented By: Benjamin L Miller, Christopher M Strohsahl

Patent Title: Inhibiting Amyloid-Beta Peptide/RAGE Interaction at the Blood-Brain Barrier
Patent #: 8,778,985
Issue Date: Jul 15, 2014
Country: United States
Invented By: Rashid Deane, Benjamin L Miller, Berislav V Zlokovic

Patent Title: Hybridization --Based Biosensor Containing Hairpin Probes and Use Thereof
Patent #: 7,811,764
Issue Date: Oct 12, 2010
Country: United States
Invented By: Benjamin L Miller, Christopher M Strohsahl

Patent Title: Flow Cell and System for Detection of Target in Aqueous Environment Using Arrayed Imaging Reflectometry
Patent #: 8,502,982
Issue Date: Aug 06, 2013
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Lewis Rothberg

Patent Title: Designed Peptides for Tight Junction Barrier Modulation
Patent #: ZL 201480052086.0
Issue Date: Jun 02, 2020
Country: China, People's Republic of
Invented By: Elizabeth A Anderson, Lisa A Beck, Anna De Benedetto, Benjamin L Miller

Patent Title: Designed Peptides for Tight Junction Barrier Modulation
Patent #: 9,757,428
Issue Date: Sep 12, 2017
Country: United States
Invented By: Elizabeth A Anderson, Lisa A Beck, Anna De Benedetto, Benjamin L Miller

Patent Title: DNA Microarray Having Hairpin Probes Tethered to Nanostructured Metal Surface
Patent #: 8,957,002
Issue Date: Feb 17, 2015
Country: United States
Invented By: Todd D Krauss, Benjamin L Miller, Hsin-I Peng, Lewis Rothberg

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: 3055433
Issue Date: May 22, 2019
Country: Europe
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: FR3055433
Issue Date: May 22, 2019
Country: France
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: 602014047396.2
Issue Date: May 22, 2019
Country: Germany
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: CH3055433
Issue Date: May 22, 2019
Country: Switzerland/Liechtenstein
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: GB3055433
Issue Date: May 22, 2019
Country: United Kingdom
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Chips, Detection Systems, and Methods for Multiplex Pneumococcus Serology
Patent #: 10,209,254
Issue Date: Feb 19, 2019
Country: United States
Invented By: Benjamin L Miller, Moon Nahm

Patent Title: Biphasic Reaction Vessel and Methods of Use
Patent #: 6,599,754
Issue Date: Jul 29, 2003
Country: United States
Invented By: Bryan Klekota, Benjamin L Miller

Patent Title: Biphasic Reaction Vessel and Methods of Use
Patent #: 1311345
Issue Date: Nov 01, 2001
Country: Europe
Invented By: Bryan Klekota, Benjamin L Miller

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: ZL200980125645.5
Issue Date: Mar 22, 2017
Country: China, People's Republic of
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: 2286223
Issue Date: Jul 06, 2016
Country: Europe
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: FR2286223
Issue Date: Jul 06, 2016
Country: France
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: 60200903959
Issue Date: Jul 06, 2016
Country: Germany
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: CH2286223
Issue Date: Jul 06, 2016
Country: Switzerland/Liechtenstein
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: GB2286223
Issue Date: Jul 06, 2016
Country: United Kingdom
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Influenza Immune Response
Patent #: 9,217,745
Issue Date: Dec 22, 2015
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: Arrayed Detector System for Measurement of Anti-Viral Immune Response
Patent #: 9,034,638
Issue Date: May 19, 2015
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, Robert C Rose

Patent Title: Arrayed Detector System For Measurement of Influenza Immune Response
Patent #: 8,486,619
Issue Date: Jul 16, 2013
Country: United States
Invented By: Charles R Mace, Benjamin L Miller, Tim R Mosmann, David J Topham

Patent Title: A Method for Biomolecular Sensing and a System Thereof
Patent #: 7,292,349
Issue Date: Nov 06, 2007
Country: United States
Invented By: Benjamin L Miller, Lewis Rothberg

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Publications

Journal Articles

4/2020
Martinez-Sobrido L, Blanco-Lobo P, Rodriguez L, Fitzgerald T, Zhang H, Nguyen P, Anderson CS, Holden-Wiltse J, Bandyopadhyay S, Nogales A, DeDiego ML, Wasik BR, Miller BL, Henry C, Wilson PC, Sangster MY, Treanor JJ, Topham DJ, Byrd-Leotis L, Steinhauer DA, Cummings RD, Luczo JM, Tompkins SM, Sakamoto K, Jones CA, Steel J, Lowen AC, Danzy S, Tao H, Fink AL, Klein SL, Wohlgemuth N, Fenstermacher KJ, El Najjar F, Pekosz A, Sauer L, Lewis MK, Shaw-Saliba K, Rothman RE, Liu ZY, Chen KF, Parrish CR, Voorhees IEH, Kawaoka Y, Neumann G, Chiba S, Fan S, Hatta M, Kong H, Zhong G, Wang G, Uccellini MB, García-Sastre A, Perez DR, Ferreri LM, Herfst S, Richard M, Fouchier R, Burke D, Pattinson D, Smith DJ, Meliopoulos V, Freiden P, Livingston B, Sharp B, Cherry S, Dib JC, Yang G, Russell CJ, Barman S, Webby RJ, Krauss S, Danner A, Woodard K, Peiris M, Perera RAPM, Chan MCW, Govorkova EA, Marathe BM, Pascua PNQ, Smith G, Li YT, Thomas PG, Schultz-Cherry S. "Characterizing Emerging Canine H3 Influenza Viruses." PLoS pathogens.. 2020 Apr 0; 16(4):e1008409. Epub 2020 Apr 14.

3/27/2020
Tyndall NF, Stievater TH, Kozak DA, Pruessner MW, Roxworthy BJ, Rabinovich WS, Roberts CA, McGill RA, Miller BL, Luta E, Yates MZ. "Figure-of-Merit Characterization of Hydrogen-Bond Acidic Sorbents for Waveguide-Enhanced Raman Spectroscopy." ACS sensors.. 2020 Mar 27; 5(3):831-836. Epub 2020 Mar 19.

10/30/2019
Farrar CS, Rouin GT, Miller BL, Raeman CH, Mooney NA, Hocking DC. "A Matricryptic Conformation of the Integrin-Binding Domain of Fibronectin Regulates Platelet-Derived Growth Factor-Induced Intracellular Calcium Release." Cells.. 2019 Oct 30; 8(11)Epub 2019 Oct 30.

Books & Chapters

2010
Chapter Title: Nanostructured Silicon Optical Sensors
Book Title: Optical Guided-wave Chemical and Biosensors II
Author List: Miller, B. L.
Edited By: Zourob, M.; Lakhtakia, A.
Published By: Springer-Verlag 2010

2009
Book Title: Dynamic Combinatorial Chemistry
Author List: Miller, B. L. (Ed.)
Published By: Wiley & Sons 2009

2008
Chapter Title: Porous and Planar Silicon Technologies for Biomolecular Sensing
Book Title: Principles of Bacterial Detection: Biosensors, Recognition...
Author List: Mace, C. R.; Miller, B. L.
Edited By: Zourob, M.; Elwary, S.; Turner, A.
Published By: Springer-Verlag 2008 in Berlin, Germany

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