Faculty of Arts and Science

Research Output 1960 2018

2018

A (+)-Larixol Congener with High Affinity and Subtype Selectivity toward TRPC6

Häfner, S., Burg, F., Kannler, M., Urban, N., Mayer, P., Dietrich, A., Trauner, D., Broichhagen, J. & Schaefer, M. Jan 1 2018 (Accepted/In press) In : ChemMedChem.

Research output: Contribution to journalArticle

Computer operating procedures
Lung
Reperfusion
Edema
Ischemia
Students
Self Report
Micrococcal Nuclease
Ionization
Protonation
Proteins
Molecular Dynamics Simulation

Adventures with RNA graphs

Schlick, T. Jan 1 2018 (Accepted/In press) In : Methods.

Research output: Contribution to journalArticle

Thermionic emission
RNA
Polynucleotides
Intake systems
Research laboratories

A Dynamic Structure of Social Trait Space

Stolier, R. M., Hehman, E. & Freeman, J. B. Jan 1 2018 (Accepted/In press) In : Trends in Cognitive Sciences.

Research output: Contribution to journalArticle

Cognitive systems
Personality
Research
Sociological Factors

Afterglow solid-state NMR spectroscopy

Abramov, G. & Traaseth, N. J. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1688, p. 55-66 12 p. (Methods in Molecular Biology; vol. 1688)

Research output: Chapter in Book/Report/Conference proceedingChapter

Magnetic Resonance Spectroscopy
Membrane Transport Proteins
Multiple Drug Resistance
Spectrum Analysis
Membrane Proteins

Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin

Lee, C. H., Yu, J. R., Kumar, S., Jin, Y., LeRoy, G., Bhanu, N., Kaneko, S., Garcia, B. A., Hamilton, A. D. & Reinberg, D. Jan 1 2018 (Accepted/In press) In : Molecular Cell.

Research output: Contribution to journalArticle

Chromatin
Mutation
Personnel Selection
Neoplasms
Clinical Trials

Amygdala structure and the tendency to regard the social system as legitimate and desirable

Hannah Nam, H., Jost, J. T., Kaggen, L., Campbell-Meiklejohn, D. & Van Bavel, J. J. Feb 1 2018 In : Nature Human Behaviour. 2, 2, p. 133-138 6 p.

Research output: Contribution to journalArticle

Amygdala
Vulnerable Populations
Prefrontal Cortex
Neuroimaging
Extremities

An Enduring Dialogue between Computational and Empirical Vision

Martinez-Conde, S., Macknik, S. L. & Heeger, D. J. Apr 1 2018 In : Trends in Neurosciences. 41, 4, p. 163-165 3 p.

Research output: Contribution to journalShort survey

Psychophysics
Neurophysiology

An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time

Razy-Krajka, F., Gravez, B., Kaplan, N., Racioppi, C., Wang, W. & Christiaen, L. Feb 6 2018 In : eLife. 7, e29656

Research output: Contribution to journalArticle

Mesoderm
Muscles
Pharyngeal Muscles
Urochordata
Cardiac Myocytes

ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Brozovic, M. , Dantec, C. , Dardaillon, J. , Dauga, D. , Faure, E. , Gineste, M. , Louis, A. , Naville, M. , Nitta, K. R. , Piette, J. , Reeves, W. , Scornavacca, C. , Simion, P. , Vincentelli, R. , Bellec, M. , Aicha, S. B. , Fagotto, M. , Guéroult-Bellone, M. , Haeussler, M. , Jacox, E. & 19 others Lowe, E. K., Mendez, M., Roberge, A., Stolfi, A., Yokomori, R., Brown, C. T., Cambillau, C., Christiaen, L., Delsuc, F., Douzery, E., Dumollard, R., Kusakabe, T., Nakai, K., Nishida, H., Satou, Y., Swalla, B., Veeman, M., Volff, J. N. & Lemaire, P. Jan 1 2018 In : Nucleic acids research. 46, D1, p. D718-D725

Research output: Contribution to journalArticle

Urochordata
Genome
Databases
Gene Expression
Vertebrates

A non-invasive, quantitative study of broadband spectral responses in human visual cortex

Kupers, E. R., Wang, H. X., Amano, K., Kay, K. N., Heeger, D. J. & Winawer, J. Mar 1 2018 In : PLoS ONE. 13, 3, e0193107

Research output: Contribution to journalArticle

Magnetoencephalography
Visual Cortex
Noise
Brain
brain
Reheat cycle
Quantum theory
Potential energy
quantum theory
Molecular dynamics

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures

Koehler Leman, J. & Bonneau, R. Apr 3 2018 In : Biochemistry. 57, 13, p. 1939-1944 6 p.

Research output: Contribution to journalArticle

Photosensitizers
Membrane Proteins
Slip forming
Membranes
Hand

Antibody pull-down experiments in fission yeast

Dong, Q. & Li, F. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1721, p. 117-123 7 p. (Methods in Molecular Biology; vol. 1721)

Research output: Chapter in Book/Report/Conference proceedingChapter

Schizosaccharomyces
Antibodies
Proteins

A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity

Dubay, K. H., Iwan, K., Osorio-Planes, L., Geissler, P. L., Groll, M., Trauner, D. & Broichhagen, J. Mar 16 2018 In : ACS Chemical Biology. 13, 3, p. 793-800 8 p.

Research output: Contribution to journalArticle

Carbonic Anhydrase II
Cysteine
Carbonic Anhydrases
Iron plating
Maleimides

A sibling method for identifying vQTLs

Conley, D., Johnson, R., Domingue, B., Dawes, C., Boardman, J. & Siegal, M. Apr 1 2018 In : PLoS ONE. 13, 4, e0194541

Research output: Contribution to journalArticle

Siblings
genetic relationships
Single Nucleotide Polymorphism
Genotype
Phenotype

Assessing accuracy in close relationships research: A truth and bias approach

Stern, C. & West, T. V. Jan 1 2018 In : Journal of Social and Personal Relationships. 35, 1, p. 89-111 23 p.

Research output: Contribution to journalArticle

Research Personnel
trend
Research
Testing
psychology

Assessing Interactions between a Polytopic Membrane Protein and Lipid Bilayers Using Differential Scanning Calorimetry and Solid-State NMR

Banigan, J. R., Leninger, M., Her, A. S. & Traaseth, N. J. Mar 1 2018 In : Journal of Physical Chemistry B. 122, 8, p. 2314-2322 9 p.

Research output: Contribution to journalArticle

Differential Scanning Calorimetry
Lipid Bilayers
Membrane Lipids
Membrane Proteins
Phase Transition

Astrocyte glycogen and lactate: New insights into learning and memory mechanisms

Alberini, C. M., Cruz, E., Descalzi, G., Bessières, B. & Gao, V. Jun 1 2018 In : GLIA. 66, 6, p. 1244-1262 19 p.

Research output: Contribution to journalReview article

Glycogen
Astrocytes
Lactic Acid
Learning
Glycogenolysis

Availability of Data Supporting Tables and Figures in Articles

Reiss, C. S. Jan 1 2018 In : DNA and Cell Biology. 37, 1, 1 p.

Research output: Contribution to journalEditorial

Azomethine Ylide Cycloaddition Approach toward Dendrobine: Synthesis of 5-Deoxymubironine C

Williams, B. M. & Trauner, D. Mar 16 2018 In : Journal of Organic Chemistry. 83, 6, p. 3061-3068 8 p.

Research output: Contribution to journalArticle

Cycloaddition
Cyclization
Carbon

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: The nonequilibrium stratification

Wang, X., Tu, X., Zhang, J. Z. H. & Sun, Z. Jan 1 2018 In : Physical Chemistry Chemical Physics. 20, 3, p. 2009-2021 13 p.

Research output: Contribution to journalArticle

stratification
sampling
optimization
acceptability
free energy

Beyond Markov: Accounting for independence violations in causal reasoning

Rehder, B. Jun 1 2018 In : Cognitive Psychology. 103, p. 42-84 43 p.

Research output: Contribution to journalArticle

Cognition
Decision Making
Learning
cause
cognition

cAMPr: A single-wavelength fluorescent sensor for cyclic AMP

Hackley, C. R., Mazzoni, E. O. & Blau, J. Mar 6 2018 In : Science Signaling. 11, 520, eaah3738

Research output: Contribution to journalArticle

Acoustic logging
Cyclic AMP
Photons
Drosophila
Neurons

Cavefishes

Borowsky, R. Jan 22 2018 In : Current Biology. 28, 2, p. R60-R64

Research output: Contribution to journalShort survey

caves
Fishes
fish
Food
food availability

Cell-Type Specificity of Callosally Evoked Excitation and Feedforward Inhibition in the Prefrontal Cortex

Anastasiades, P. G., Marlin, J. J. & Carter, A. G. Jan 16 2018 In : Cell Reports. 22, 3, p. 679-692 14 p.

Research output: Contribution to journalArticle

Prefrontal Cortex
Neurons
Corpus Callosum
Physiology
Parvalbumins

Charge splitters and charge transport junctions based on guanine quadruplexes

Sha, R., Xiang, L., Liu, C., Balaeff, A., Zhang, Y., Zhang, P., Li, Y., Beratan, D. N., Tao, N. & Seeman, N. C. Feb 26 2018 (Accepted/In press) In : Nature Nanotechnology. p. 1-6 6 p.

Research output: Contribution to journalArticle

guanines
Charge transfer
DNA
Electric charge
Carrier transport

Cherub versus brat

Malin, J. A. & Desplan, C. Mar 27 2018 In : eLife. 7, e36030

Research output: Contribution to journalArticle

Long Noncoding RNA
Neoplasms

Chiroptical structure-property relations in cyclo[18]carbon and its in silico hydrogenation products

Murphy, V. L., Farfan, C. & Kahr, B. Jan 1 2018 (Accepted/In press) In : Chirality.

Research output: Contribution to journalArticle

Optical Rotation
Hydrogenation
Computer Simulation
Carbon
Electric dipole moments

Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding

Bascom, G. D. & Schlick, T. Jan 1 2018 (Accepted/In press) In : Biophysical Journal.

Research output: Contribution to journalArticle

Acetylation
Histones
Chromatin
Islands
Intergenic DNA

C-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R. & Littman, D. R. Feb 15 2018 In : Nature. 554, 7692, p. 373-377 5 p.

Research output: Contribution to journalArticle

Regulatory T-Lymphocytes
Helicobacter hepaticus
Bacteria
T-Lymphocytes
Inflammatory Bowel Diseases

Cognitive behavior classification from scalp EEG signals

Dvorak, D., Shang, A., Abdel-Baki, S., Suzuki, W. & Fenton, A. A. Jan 23 2018 (Accepted/In press) In : IEEE Transactions on Neural Systems and Rehabilitation Engineering.

Research output: Contribution to journalArticle

Job analysis
Electrophysiology
Cognitive systems
Neurology
Electroencephalography

Compressive temporal summation in human visual cortex

Zhou, J., Benson, N. C., Kay, K. N. & Winawer, J. Jan 17 2018 In : Journal of Neuroscience. 38, 3, p. 691-709 19 p.

Research output: Contribution to journalArticle

Visual Cortex
Magnetic Resonance Imaging
Visual Pathways
Neuroimaging
Brain

Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies

Liu, X., Peng, L., Zhou, Y., Zhang, Y. & Zhang, J. Z. H. Mar 13 2018 In : Journal of Chemical Theory and Computation. 14, 3, p. 1772-1780 9 p.

Research output: Contribution to journalArticle

Slip forming
alanine
Free energy
Entropy
free energy

Computational Protein Design with Deep Learning Neural Networks

Wang, J., Cao, H., Zhang, J. Z. H. & Qi, Y. Dec 1 2018 In : Scientific Reports. 8, 1, 6349

Research output: Contribution to journalArticle

Neural networks
Proteins
Deep learning
Multilayer neural networks
Learning systems

Computational study of PCSK9-EGFA complex with effective polarizable bond force field

Chen, J., Duan, L., Ji, C. & Zhang, J. Z. H. Jan 15 2018 In : Frontiers in Molecular Biosciences. 4, JAN, 101

Research output: Contribution to journalArticle

LDL Receptors
Epidermal Growth Factor
Rails
Intake systems
Hydrogen

Conditional and Reversible Activation of Class A and B G Protein-Coupled Receptors Using Tethered Pharmacology

Podewin, T., Ast, J., Broichhagen, J., Fine, N. H. F., Nasteska, D., Leippe, P., Gailer, M., Buenaventura, T., Kanda, N., Jones, B. J., M'Kadmi, C., Baneres, J. L., Marie, J., Tomas, A., Trauner, D., Hoffmann-Röder, A. & Hodson, D. J. Feb 28 2018 In : ACS Central Science. 4, 2, p. 166-179 14 p.

Research output: Contribution to journalArticle

Peptides
Chemical activation
Proteins
Hormones
Unsaturated polymers

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

Tchourine, K., Vogel, C. & Bonneau, R. Apr 10 2018 In : Cell Reports. 23, 2, p. 376-388 13 p.

Research output: Contribution to journalArticle

Thermionic emission
RNA Stability
Chaperonin Containing TCP-1
Chaperonins
Gene Regulatory Networks

Consequences for peers differentially bias computations about risk across development

Powers, K. E., Yaffe, G., Hartley, C. A., Davidow, J. Y., Kober, H. & Somerville, L. H. May 1 2018 In : Journal of Experimental Psychology: General. 147, 5, p. 671-682 12 p.

Research output: Contribution to journalArticle

Decision Making
Motivation
Peer Influence
Economics

Construction of a DNA Origami Based Molecular Electro-optical Modulator

Wang, X., Li, C., Niu, D., Sha, R., Seeman, N. C. & Canary, J. W. Mar 14 2018 In : Nano Letters. 18, 3, p. 2112-2115 4 p.

Research output: Contribution to journalArticle

Optical signal processing
Light modulation
light modulation
Light modulators
Polyaniline

Construction of an improved multi-tetrode hyperdrive for large-scale neural recording in behaving rats

Lu, L., Popeney, B., Dickman, J. D. & Angelaki, D. E. May 9 2018 In : Journal of Visualized Experiments. 2018, 135, e57388

Research output: Contribution to journalArticle

Tetrodes
Neurons
Rats
Brain
Electrodes

Control of recollection by slow gamma dominating mid-frequency gamma in hippocampus CA1

Dvorak, D., Radwan, B., Sparks, F. T., Talbot, Z. N. & Fenton, A. A. Jan 1 2018 In : PLoS Biology. 16, 1, e2003354

Research output: Contribution to journalArticle

hippocampus
Hippocampus
Data storage equipment
Shock
Relocation

Cortical double-opponent cells in color perception: Perceptual scaling and chromatic visual evoked potentials

Nunez, V., Shapley, R. M. & Gordon, J. Jan 1 2018 In : i-Perception. 9, 1

Research output: Contribution to journalArticle

Color Perception
Visual Evoked Potentials
Bioelectric potentials
Color
Neurons

CRISPR knockouts in Ciona embryos

Gandhi, S., Razy-Krajka, F., Christiaen, L. & Stolfi, A. Jan 1 2018 Advances in Experimental Medicine and Biology. Springer New York LLC, p. 141-152 12 p. (Advances in Experimental Medicine and Biology; vol. 1029)

Research output: Chapter in Book/Report/Conference proceedingChapter

Clustered Regularly Interspaced Short Palindromic Repeats
Gene Knockout Techniques
Embryonic Structures
Zinc plating
Urochordata

Dendrites of the dorsal and ventral hippocampal CA1 pyramidal neurons of singly housed female rats exhibit lamina-specific growths and retractions during adolescence that are responsive to pair housing

Chen, Y. W., Akad, A., Aderogba, R., Chowdhury, T. G. & Aoki, C. Jan 1 2018 (Accepted/In press) In : Synapse.

Research output: Contribution to journalArticle

Pyramidal Cells
Dendrites
Hippocampus
Growth
Cognition

De novo sequencing and initial annotation of the Mongolian gerbil (Meriones unguiculatus) genome

Zorio, D. A. R., Monsma, S., Sanes, D. H., Golding, N. L., Rubel, E. W. & Wang, Y. Jan 1 2018 (Accepted/In press) In : Genomics.

Research output: Contribution to journalArticle

Gerbillinae
Genome
Nucleic Acid Databases
Genes
Learning Disorders

Design formalism for DNA self-assembly of polyhedral skeletons using rigid tiles

Ferrari, M. M., Cook, A., Houlihan, A., Rouleau, R., Seeman, N. C., Pangborn, G. & Ellis-Monaghan, J. Jan 31 2018 (Accepted/In press) In : Journal of Mathematical Chemistry. p. 1-28 28 p.

Research output: Contribution to journalArticle

Platonic solid
Self-assembly
Tile
Skeleton
Self assembly

Determining mRNA decay rates using RNA approach to equilibrium sequencing (RATE-seq)

Abdul-Rahman, F. & Gresham, D. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1720, p. 15-24 10 p. (Methods in Molecular Biology; vol. 1720)

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Stability
RNA
Nonlinear Dynamics
Streptavidin
Uracil

Developmental diversification of cortical inhibitory interneurons

Mayer, C., Hafemeister, C., Bandler, R. C., Machold, R., Batista Brito, R., Jaglin, X., Allaway, K., Butler, A., Fishell, G. & Satija, R. Mar 22 2018 In : Nature. 555, 7697, p. 457-462 6 p.

Research output: Contribution to journalArticle

Interneurons
Transcription Factors
RNA Sequence Analysis
Parvalbumins
Gene Regulatory Networks