Mark Bathe

Affiliations

Department of Biological Engineering, MIT, Cambridge 02142, MA anne@broadinstitute.org mark.bathe@mit.edu.

Publications (38)

Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging.

eNeuro

Avec: Eric Danielson , Karen Perez de Arce , Beth Cimini , Eike-Christian Wamhoff , Shantanu Singh , Jeffrey R Cottrell , Anne E Carpenter , Mark Bathe

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.

PLoS computational biology

Avec: Victor Kulikov , Syuan-Ming Guo , Matthew Stone , Allen Goodman , Anne Carpenter , Mark Bathe , Victor Lempitsky

Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.

Nucleic acids research

Avec: Matthew R Adendorff , Guo Qing Tang , David P Millar , Mark Bathe , William P Bricker

Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds.

The journal of physical chemistry letters

Avec: Stephanie M Hart , Xiao Wang , Jiajia Guo , Mark Bathe , Gabriela S Schlau-Cohen

Sculpting photoproducts with DNA origami.

Chem

Avec: Jeffrey Gorman , Stephanie M Hart , Torsten John , Maria A Castellanos , Dvir Harris , Molly F Parsons , James L Banal , Adam P Willard , Gabriela S Schlau-Cohen , Mark Bathe

Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language.

medRxiv : the preprint server for health sciences

Avec: Joseph D Berleant , James L Banal , Dhriti K Rao , Mark Bathe

Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds.

bioRxiv : the preprint server for biology

Avec: Eike-Christian Wamhoff , Larance Ronsard , Jared Feldman , Grant A Knappe , Blake M Hauser , Anna Romanov , Evan Lam , Kerri St Denis , Julie Boucau , Amy K Barczak , Alejandro B Balazs , Aaron Schmidt , Daniel Lingwood , Mark Bathe

3D RNA-scaffolded wireframe origami.

Nature communications

Avec: Molly F Parsons , Matthew F Allan , Shanshan Li , Tyson R Shepherd , Sakul Ratanalert , Kaiming Zhang , Krista M Pullen , Wah Chiu , Silvi Rouskin , Mark Bathe

Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision.

Science advances

Avec: Chi Chen , Xin Luo , Alexander E K Kaplan , Moungi G Bawendi , Robert J Macfarlane , Mark Bathe

Functionalizing DNA origami to investigate and interact with biological systems.

Nature reviews. Materials

Avec: Grant A Knappe , Eike-Christian Wamhoff , Mark Bathe

Tract-specific analysis improves sensitivity of spinal cord diffusion MRI to cross-sectional and longitudinal changes in amyotrophic lateral sclerosis.

Communications biology

Avec: Pramod Kumar Pisharady , Lynn E Eberly , Ian Cheong , Georgios Manousakis , Gaurav Guliani , H Brent Clark , Mark Bathe , David Walk , Christophe Lenglet

Identification of Nonradiative Decay Pathways in Cy3.

The journal of physical chemistry letters

Avec: Stephanie M Hart , James L Banal , Mark Bathe , Gabriela S Schlau-Cohen

A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging.

Cell reports

Avec: Reuven Falkovich , Eric W Danielson , Karen Perez de Arce , Eike-C Wamhoff , Juliana Strother , Anna P Lapteva , Morgan Sheng , Jeffrey R Cottrell , Mark Bathe

Engineering Exciton Dynamics with Synthetic DNA Scaffolds.

Accounts of chemical research

Avec: Stephanie M Hart , Jeffrey Gorman , Mark Bathe , Gabriela S Schlau-Cohen

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

bioRxiv : the preprint server for biology

Avec: Matthew F Allan , Justin Aruda , Jesse S Plung , Scott L Grote , Yves J Martin des Taillades , Albéric A de Lajarte , Mark Bathe , Silvi Rouskin

Role of nanoscale antigen organization on B-cell activation probed using DNA origami.

Nature nanotechnology

Avec: Rémi Veneziano , Tyson J Moyer , Matthew B Stone , Eike-Christian Wamhoff , Benjamin J Read , Sayak Mukherjee , Tyson R Shepherd , Jayajit Das , William R Schief , Darrell J Irvine , Mark Bathe

Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes.

Nature communications

Avec: Syuan-Ming Guo , Remi Veneziano , Simon Gordonov , Li Li , Eric Danielson , Karen Perez de Arce , Demian Park , Anthony B Kulesa , Eike-Christian Wamhoff , Paul C Blainey , Edward S Boyden , Jeffrey R Cottrell , Mark Bathe

Bioproduction of pure, kilobase-scale single-stranded DNA.

Scientific reports

Avec: Tyson R Shepherd , Rebecca R Du , Hellen Huang , Eike-Christian Wamhoff , Mark Bathe

Programming Structured DNA Assemblies to Probe Biophysical Processes.

Annual review of biophysics

Avec: Eike-Christian Wamhoff , James L Banal , William P Bricker , Tyson R Shepherd , Molly F Parsons , Rémi Veneziano , Matthew B Stone , Hyungmin Jun , Xiao Wang , Mark Bathe

Autonomously designed free-form 2D DNA origami.

Science advances

Avec: Hyungmin Jun , Fei Zhang , Tyson Shepherd , Sakul Ratanalert , Xiaodong Qi , Hao Yan , Mark Bathe

Planar 2D wireframe DNA origami.

Science advances

Avec: Xiao Wang , Shanshan Li , Hyungmin Jun , Torsten John , Kaiming Zhang , Hannah Fowler , Jonathan P K Doye , Wah Chiu , Mark Bathe

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells.

Nature communications

Avec: Tammy C T Lan , Matty F Allan , Lauren E Malsick , Jia Z Woo , Chi Zhu , Fengrui Zhang , Stuti Khandwala , Sherry S Y Nyeo , Yu Sun , Junjie U Guo , Mark Bathe , Anders Näär , Anthony Griffiths , Silvi Rouskin

ACS nano

Avec: Grant A Knappe , Eike-Christian Wamhoff , Benjamin J Read , Darrell J Irvine , Mark Bathe

Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds.

Nature communications

Avec: Eike-Christian Wamhoff , Larance Ronsard , Jared Feldman , Grant A Knappe , Blake M Hauser , Anna Romanov , James Brett Case , Shilpa Sanapala , Evan C Lam , Kerri J St Denis , Julie Boucau , Amy K Barczak , Alejandro B Balazs , Michael S Diamond , Aaron G Schmidt , Daniel Lingwood , Mark Bathe

Versatile Dehydration-Assisted Functionalization of Quantum Dots and Rods.

Angewandte Chemie (International ed. in English)

Avec: Chi Chen , Xin Luo , Mark Bathe

Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology.

ACS nano

Avec: Kirill A Afonin , Marina A Dobrovolskaia , George Church , Mark Bathe

Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges.

ACS nano

Avec: Hyungmin Jun , Tyson R Shepherd , Kaiming Zhang , William P Bricker , Shanshan Li , Wah Chiu , Mark Bathe

A Bayesian framework for high-throughput T cell receptor pairing.

Bioinformatics (Oxford, England)

Avec: Patrick V Holec , Joseph Berleant , Mark Bathe , Michael E Birnbaum

Random access DNA memory using Boolean search in an archival file storage system.

Nature materials

Avec: James L Banal , Tyson R Shepherd , Joseph Berleant , Hellen Huang , Miguel Reyes , Cheri M Ackerman , Paul C Blainey , Mark Bathe

Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging.

Communications biology

Avec: Martin L Tomov , Alison O'Neil , Hamdah S Abbasi , Beth A Cimini , Anne E Carpenter , Lee L Rubin , Mark Bathe

Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation.

Advanced drug delivery reviews

Avec: Kirill A Afonin , Marina A Dobrovolskaia , Weina Ke , Piotr Grodzinski , Mark Bathe

Programming 2D Supramolecular Assemblies with Wireframe DNA Origami.

Journal of the American Chemical Society

Avec: Xiao Wang , Hyungmin Jun , Mark Bathe

Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots.

ACS nano

Avec: Xingfei Wei , Chi Chen , Yinong Zhao , Ewa Harazinska , Mark Bathe , Rigoberto Hernandez

Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds.

Chemical science

Avec: Stephanie M Hart , James L Banal , Maria A Castellanos , Larysa Markova , Yuliia Vyborna , Jeffrey Gorman , Robert Häner , Adam P Willard , Mark Bathe , Gabriela S Schlau-Cohen

Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami.

Nature communications

Avec: Chi Chen , Xingfei Wei , Molly F Parsons , Jiajia Guo , James L Banal , Yinong Zhao , Madelyn N Scott , Gabriela S Schlau-Cohen , Rigoberto Hernandez , Mark Bathe

Evaluation of non-modified wireframe DNA origami for acute toxicity and biodistribution in mice.

bioRxiv : the preprint server for biology

Avec: Eike-Christian Wamhoff , Grant A Knappe , Aurora A Burds , Rebecca R Du , Barry W Neun , Simone Difilippantonio , Chelsea Sanders , Elijah F Edmondson , Jennifer L Matta , Marina A Dobrovolskaia , Mark Bathe

Force-free activation of Notch with DNA origami.

Trends in genetics : TIG

Avec: Hyun-Min Kim , Mark Bathe

Charge Detection Mass Spectrometry Enables Molecular Characterization of Nucleic Acid Nanoparticles.

ACS nano

Avec: Polycarp C Ofoegbu , Grant A Knappe , Anna Romanov , Benjamin E Draper , Mark Bathe , Martin F Jarrold

Réseau de co-auteurs

Eike-Christian Wamhoff 10 collaborations

James L Banal 7 collaborations

Gabriela S Schlau-Cohen 6 collaborations

Grant A Knappe 6 collaborations

Tyson R Shepherd 6 collaborations

Stephanie M Hart 5 collaborations

Hyungmin Jun 5 collaborations

Xiao Wang 4 collaborations

Molly F Parsons 4 collaborations

Chi Chen 4 collaborations

Karen Perez de Arce 3 collaborations

Jeffrey R Cottrell 3 collaborations

William P Bricker 3 collaborations

Jeffrey Gorman 3 collaborations

Anna Romanov 3 collaborations

Shanshan Li 3 collaborations

Kaiming Zhang 3 collaborations

Wah Chiu 3 collaborations

Silvi Rouskin 3 collaborations

Marina A Dobrovolskaia 3 collaborations

Eric Danielson 2 collaborations

Anne E Carpenter 2 collaborations

Syuan-Ming Guo 2 collaborations

Jiajia Guo 2 collaborations

Torsten John 2 collaborations

Maria A Castellanos 2 collaborations

Adam P Willard 2 collaborations

Larance Ronsard 2 collaborations

Jared Feldman 2 collaborations

Blake M Hauser 2 collaborations

Julie Boucau 2 collaborations

Amy K Barczak 2 collaborations

Alejandro B Balazs 2 collaborations

Daniel Lingwood 2 collaborations

Matthew F Allan 2 collaborations

Sakul Ratanalert 2 collaborations

Xin Luo 2 collaborations

Rémi Veneziano 2 collaborations

Matthew B Stone 2 collaborations

Benjamin J Read 2 collaborations

Darrell J Irvine 2 collaborations

Paul C Blainey 2 collaborations

Rebecca R Du 2 collaborations

Hellen Huang 2 collaborations

Kirill A Afonin 2 collaborations

Joseph Berleant 2 collaborations

Xingfei Wei 2 collaborations

Yinong Zhao 2 collaborations

Rigoberto Hernandez 2 collaborations

Beth Cimini 1 collaboration

Shantanu Singh 1 collaboration

Victor Kulikov 1 collaboration

Matthew Stone 1 collaboration

Allen Goodman 1 collaboration

Anne Carpenter 1 collaboration

Victor Lempitsky 1 collaboration

Matthew R Adendorff 1 collaboration

Guo Qing Tang 1 collaboration

David P Millar 1 collaboration

Dvir Harris 1 collaboration

Joseph D Berleant 1 collaboration

Dhriti K Rao 1 collaboration

Evan Lam 1 collaboration

Kerri St Denis 1 collaboration

Aaron Schmidt 1 collaboration

Krista M Pullen 1 collaboration

Alexander E K Kaplan 1 collaboration

Moungi G Bawendi 1 collaboration

Robert J Macfarlane 1 collaboration

Pramod Kumar Pisharady 1 collaboration

Lynn E Eberly 1 collaboration

Ian Cheong 1 collaboration

Georgios Manousakis 1 collaboration

Gaurav Guliani 1 collaboration

H Brent Clark 1 collaboration

David Walk 1 collaboration

Christophe Lenglet 1 collaboration

Reuven Falkovich 1 collaboration

Eric W Danielson 1 collaboration

Eike-C Wamhoff 1 collaboration

Juliana Strother 1 collaboration

Anna P Lapteva 1 collaboration

Morgan Sheng 1 collaboration

Justin Aruda 1 collaboration

Jesse S Plung 1 collaboration

Scott L Grote 1 collaboration

Yves J Martin des Taillades 1 collaboration

Albéric A de Lajarte 1 collaboration

Tyson J Moyer 1 collaboration

Sayak Mukherjee 1 collaboration

Jayajit Das 1 collaboration

William R Schief 1 collaboration

Remi Veneziano 1 collaboration

Simon Gordonov 1 collaboration

Li Li 1 collaboration

Demian Park 1 collaboration

Anthony B Kulesa 1 collaboration

Edward S Boyden 1 collaboration

Fei Zhang 1 collaboration

Tyson Shepherd 1 collaboration

Xiaodong Qi 1 collaboration

Hao Yan 1 collaboration

Hannah Fowler 1 collaboration

Jonathan P K Doye 1 collaboration

Tammy C T Lan 1 collaboration

Matty F Allan 1 collaboration

Lauren E Malsick 1 collaboration

Jia Z Woo 1 collaboration

Chi Zhu 1 collaboration

Fengrui Zhang 1 collaboration

Stuti Khandwala 1 collaboration

Sherry S Y Nyeo 1 collaboration

Yu Sun 1 collaboration

Junjie U Guo 1 collaboration

Anders Näär 1 collaboration

Anthony Griffiths 1 collaboration

James Brett Case 1 collaboration

Shilpa Sanapala 1 collaboration

Evan C Lam 1 collaboration

Kerri J St Denis 1 collaboration

Michael S Diamond 1 collaboration

Aaron G Schmidt 1 collaboration

George Church 1 collaboration

Patrick V Holec 1 collaboration

Michael E Birnbaum 1 collaboration

Miguel Reyes 1 collaboration

Cheri M Ackerman 1 collaboration

Martin L Tomov 1 collaboration

Alison O'Neil 1 collaboration

Hamdah S Abbasi 1 collaboration

Beth A Cimini 1 collaboration

Lee L Rubin 1 collaboration

Weina Ke 1 collaboration

Piotr Grodzinski 1 collaboration

Ewa Harazinska 1 collaboration

Larysa Markova 1 collaboration

Yuliia Vyborna 1 collaboration

Robert Häner 1 collaboration

Madelyn N Scott 1 collaboration

Aurora A Burds 1 collaboration

Barry W Neun 1 collaboration

Simone Difilippantonio 1 collaboration

Chelsea Sanders 1 collaboration

Elijah F Edmondson 1 collaboration

Jennifer L Matta 1 collaboration

Hyun-Min Kim 1 collaboration

Polycarp C Ofoegbu 1 collaboration

Benjamin E Draper 1 collaboration

Martin F Jarrold 1 collaboration