Faculty of Arts and Science

Research Output 1960 2019

2019

Brief, daily meditation enhances attention, memory, mood, and emotional regulation in non-experienced meditators

Basso, J. C., McHale, A., Ende, V., Oberlin, D. J. & Suzuki, W., Jan 1 2019, In : Behavioural Brain Research. 356, p. 208-220 13 p.

Research output: Contribution to journalArticle

Meditation
Webcasts
Exercise Test
Control Groups
Short-Term Memory

Developmental evidence for a link between the inherence bias in explanation and psychological essentialism

Sutherland, S. L. & Cimpian, A., Jan 1 2019, In : Journal of experimental child psychology. 177, p. 265-281 17 p.

Research output: Contribution to journalArticle

Psychology

Oculomotor inhibition reflects temporal expectations

Amit, R., Abeles, D., Carrasco-Queijeiro, M. & Yuval-Greenberg, S., Jan 1 2019, In : NeuroImage. 184, p. 279-292 14 p.

Research output: Contribution to journalArticle

Cues
Saccades
Social Adjustment
Inhibition (Psychology)
Electroencephalography

Preference for speech in infancy differentially predicts language skills and autism-like behaviors

Sorcinelli, A., Ference, J., Curtin, S. & Vouloumanos, A., Feb 1 2019, In : Journal of experimental child psychology. 178, p. 295-316 22 p.

Research output: Contribution to journalArticle

Autistic Disorder
Language
Haplorhini
Vocabulary
Parturition

Temporal orientation

Maglio, S. J. & Trope, Y., Apr 1 2019, In : Current Opinion in Psychology. 26, p. 62-66 5 p.

Research output: Contribution to journalReview article

Social Distance
Direction compound
2018

5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells

Ji, S., Fu, I., Naldiga, S., Shao, H., Basu, A. K., Broyde, S. & Tretyakova, N. Y., Oct 12 2018, In : Nucleic acids research. 46, 18, 1 p.

Research output: Contribution to journalArticle

DNA Replication
Mutation
DNA
link protein
5-formylcytosine

5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells

Ji, S., Fu, I., Naldiga, S., Shao, H., Basu, A. K., Broyde, S. & Tretyakova, N. Y., Jan 1 2018, In : Nucleic acids research. 46, 13, p. 6455-6469 15 p.

Research output: Contribution to journalArticle

DNA Replication
Mutation
DNA
Proteins
Peptides

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

Lung
Transplantation (surgical)
Reperfusion
Transient Receptor Potential Channels
Edema
Students
Self Report

A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease

Liu, J., Swails, J., Zhang, J., He, X. & Roitberg, A. E., Feb 7 2018, In : Journal of the American Chemical Society. 140, 5, p. 1639-1648 10 p.

Research output: Contribution to journalArticle

Micrococcal Nuclease
Ionization
Protonation
Proteins
Molecular Dynamics Simulation

Actin-myosin force generation and symmetry breaking in the model contractile fiber

Fogelson, B. & Mogilner, A., Jan 1 2018, In : SIAM Journal on Applied Mathematics. 78, 3, p. 1754-1777 24 p.

Research output: Contribution to journalArticle

Myosin
Actin
Symmetry Breaking
Fiber
Fibers

Activation of a novel p70 S6 kinase 1-dependent intracellular cascade in the basolateral nucleus of the amygdala is required for the acquisition of extinction memory

Huynh, T. N., Santini, E., Mojica, E., Fink, A. E., Hall, B. S., Fetcho, R. N., Grosenick, L., Deisseroth, K., Ledoux, J., Liston, C. & Klann, E., Jun 1 2018, In : Molecular Psychiatry. 23, 6, p. 1394-1401 8 p.

Research output: Contribution to journalArticle

70-kDa Ribosomal Protein S6 Kinases
Amygdala
Ribosomal Protein S6 Kinases
Extracellular Signal-Regulated MAP Kinases
Basolateral Nuclear Complex

Acute Stress Throughout the Memory Cycle: Diverging Effects on Associative and Item Memory

Goldfarb, E. V., Tompary, A., Davachi, L. & Phelps, E., Sep 17 2018, (Accepted/In press) In : Journal of Experimental Psychology: General.

Research output: Contribution to journalArticle

Hydrocortisone
Arousal
Recognition (Psychology)

A dataset and architecture for visual reasoning with a working memory

Yang, G. R., Ganichev, I., Wang, X-J., Shlens, J. & Sussillo, D., Jan 1 2018, Computer Vision – ECCV 2018 - 15th European Conference, 2018, Proceedings. Hebert, M., Ferrari, V., Sminchisescu, C. & Weiss, Y. (eds.). Springer-Verlag, p. 729-745 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11214 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Working Memory
Reasoning
Data storage equipment
Video Analysis
Network architecture

Addendum: Preventing the return of fear in humans using reconsolidation update mechanisms

Schiller, D., Monfils, M. H., Raio, C. M., Johnson, D. C., Ledoux, J. & Phelps, E., Oct 1 2018, In : Nature. 562, 7727, p. E21

Research output: Contribution to journalArticle

A disinhibitory circuit motif and flexible information routing in the brain

Wang, X-J. & Yang, G. R., Apr 1 2018, In : Current Opinion in Neurobiology. 49, p. 75-83 9 p.

Research output: Contribution to journalReview article

Auditory Pathways
Visual Pathways
Neocortex
Brain
carbosulfan

Adventures with RNA graphs

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

Research output: Contribution to journalArticle

RNA
Polynucleotides
Hydrogen

A Dynamic Bayesian Observer Model Reveals Origins of Bias in Visual Path Integration

Lakshminarasimhan, K. J., Petsalis, M., Park, H., DeAngelis, G. C., Pitkow, X. & Angelaki, D., Jul 11 2018, In : Neuron. 99, 1, p. 194-206.e5

Research output: Contribution to journalArticle

Optic Flow
Uncertainty
Reward

A Dynamic Structure of Social Trait Space

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

Research output: Contribution to journalArticle

Personality
Research
Sociological Factors

Aesthetics

Brielmann, A. A. & Pelli, D., Aug 20 2018, In : Current Biology. 28, 16, p. R859-R863

Research output: Contribution to journalShort survey

aesthetics
Esthetics
Sun
Wear of materials
Solar System

A feed-forward relay integrates the regulatory activities of bicoid and orthodenticle via sequential binding to suboptimal sites

Datta, R. R., Ling, J., Kurland, J., Ren, X., Xu, Z., Yucel, G., Moore, J., Shokri, L., Baker, I., Bishop, T., Struffi, P., Levina, R., Bulyk, M. L., Johnston, R. J. & Small, S., May 1 2018, In : Genes and Development. 32, 9-10, p. 723-736 14 p.

Research output: Contribution to journalArticle

Nucleotide Motifs
Embryonic Structures
Homeodomain Proteins
Drosophila melanogaster
Transcriptional Activation

A force balanced fragmentation method for ab initio molecular dynamic simulation of protein

Xu, M., Zhu, T. & Zhang, J., May 1 2018, In : Frontiers in Chemistry. 6, MAY, 189.

Research output: Contribution to journalArticle

Molecular dynamics
Computer simulation
Proteins
Peptides
Atoms

Afterglow solid-state NMR spectroscopy

Abramov, G. & Traaseth, N., 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

Airway microbiota is associated with upregulation of the PI3K pathway in lung cancer

Tsay, J. C. J., Wu, B. G., Badri, M. H., Clemente, J. C., Shen, N., Meyn, P., Li, Y., Yie, T. A., Lhakhang, T., Olsen, E., Murthy, V., Michaud, G., Sulaiman, I., Tsirigos, A., Heguy, A., Pass, H., Weiden, M. D., Rom, W. N., Sterman, D. H., Bonneau, R. & 2 othersBlaser, M. J. & Segal, L. N., Nov 1 2018, In : American Journal of Respiratory and Critical Care Medicine. 198, 9, p. 1188-1198 11 p.

Research output: Contribution to journalArticle

1-Phosphatidylinositol 4-Kinase
Microbiota
Lung Neoplasms
Mitogen-Activated Protein Kinase 6
Up-Regulation

Alcohol Intake Can Reduce Gambling Behavior

Wagner, G., Sevincer, A. T., Keim, R., Fähnrich, M. & Oettingen, G., Jan 1 2018, (Accepted/In press) In : Psychology of Addictive Behaviors.

Research output: Contribution to journalArticle

Gambling
Alcohols
Myopia
Cues
Placebos

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. & Reinberg, D., Jan 1 2018, (Accepted/In press) In : Molecular Cell.

Research output: Contribution to journalArticle

Chromatin
Mutation
Personnel Selection
Neoplasms
Clinical Trials

A Modular Implant System for Multimodal Recording and Manipulation of the Primate Brain

Kleinbart, J. E., Orsborn, A. L., Choi, J. S., Wang, C., Qiao, S., Viventi, J. & Pesaran, B., Oct 26 2018, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2018. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-July. p. 3362-3365 4 p. 8512993

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Primates
Brain
Optical recording
Neurons
Imaging techniques

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

Hannah Nam, H., Jost, J., Kaggen, L., Campbell-Meiklejohn, D. & Van Bavel, 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

Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

Liu, Q., Onal, P., Datta, R. R., Rogers, J. M., Schmidt-Ott, U., Bulyk, M. L., Small, S. & Thornton, J. W., Oct 9 2018, In : eLife. 7

Research output: Contribution to journalArticle

Genetically Modified Animals
Diptera
Animals
Substitution reactions
Genes

An Enduring Dialogue between Computational and Empirical Vision

Martinez-Conde, S., Macknik, S. L. & Heeger, D., 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
Muscle
Siphons
Muscles
Networks (circuits)

An incoherent feedforward loop facilitates adaptive tuning of gene expression

Hong, J., Brandt, N., Abdul-Rahman, F., Yang, A., Hughes, T. & Gresham, D., Apr 5 2018, In : eLife. 7, e32323.

Research output: Contribution to journalArticle

Gene expression
Tuning
Ammonium Compounds
Gene Expression
Genes

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 othersLowe, 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. & Winawer, J., Mar 1 2018, In : PLoS One. 13, 3, e0193107.

Research output: Contribution to journalArticle

Magnetoencephalography
Visual Cortex
Brain
Noise
brain
sampling
Sampling
Molecular dynamics
Mathematical operators
Trajectories

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

Membrane Proteins
Membranes
Computational methods
Hand
Protein Domains

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Zhang, X. S., Li, J., Krautkramer, K. A., Badri, M., Battaglia, T., Borbet, T. C., Koh, H., Ng, S., Sibley, R. A., Li, Y., Pathmasiri, W., Jindal, S., Shields-Cutler, R. R., Hillmann, B., Al-Ghalith, G. A., Ruiz, V. E., Livanos, A., Van‘t Wout, A. B., Nagalingam, N., Rogers, A. B. & 9 othersSumner, S. J., Knights, D., Denu, J. M., Li, H., Ruggles, K. V., Bonneau, R., Williamson, R. A., Rauch, M. & Blaser, M. J., Jul 24 2018, In : eLife. 7, e37816.

Research output: Contribution to journalArticle

Medical problems
Type 1 Diabetes Mellitus
Innate Immunity
Anti-Bacterial Agents
Gene expression

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

Anti-prion Protein Antibody 6D11 Restores Cellular Proteostasis of Prion Protein Through Disrupting Recycling Propagation of PrPSc and Targeting PrPSc for Lysosomal Degradation

Pankiewicz, J. E., Sanchez, S., Kirshenbaum, K., Kascsak, R. B., Kascsak, R. J. & Sadowski, M. J., Jul 9 2018, (Accepted/In press) In : Molecular Neurobiology. p. 1-19 19 p.

Research output: Contribution to journalArticle

Recycling
Antibodies
Prions
Cell Membrane
Scrapie

A pipeline for computational design of novel RNA-like topologies

Jain, S., Laederach, A., Ramos, S. B. V. & Schlick, T., Jan 1 2018, In : Nucleic acids research. 46, 14, p. 7040-7051 12 p.

Research output: Contribution to journalArticle

RNA
Nucleotides
Databases

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
Maleimides
Optogenetics

A principled method to identify individual differences and behavioral shifts in signaled active avoidance

Krypotos, A. M., Moscarello, J. M., Sears, R. M., Ledoux, J. & Galatzer-Levy, I., Nov 1 2018, In : Learning & memory (Cold Spring Harbor, N.Y.). 25, 11, p. 564-568 5 p.

Research output: Contribution to journalArticle

Individuality
Cues
Linear Models
Software
Learning

A resource-rational theory of set size effects in human visual working memory

van den Berg, R. & Ma, W. J., Aug 7 2018, In : eLife. 7, e34963.

Research output: Contribution to journalArticle

Short-Term Memory
Data storage equipment
Costs and Cost Analysis
Costs
Brain

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

Genes
genetic relationships
Single Nucleotide Polymorphism
Genotype
Phenotype

Asking Children to “Be Helpers” Can Backfire After Setbacks

Foster-Hanson, E., Cimpian, A., Leshin, R. A. & Rhodes, M., Jan 1 2018, (Accepted/In press) In : Child development.

Research output: Contribution to journalArticle

helper
Milk
Helping Behavior
scenario
Social Behavior

Asking the right questions about the psychology of human inquiry: Nine open challenges

Coenen, A., Nelson, J. D. & Gureckis, T., Jun 4 2018, (Accepted/In press) In : Psychonomic Bulletin and Review. p. 1-41 41 p.

Research output: Contribution to journalArticle

Psychology
Aptitude
Intelligence
Experiment
Research

A spatial frequency spectral peakedness model predicts discrimination performance of regularity in dot patterns

Protonotarios, E. D., Griffin, L. D., Johnston, A. & Landy, M., Aug 1 2018, In : Vision Research. 149, p. 102-114 13 p.

Research output: Contribution to journalArticle

Developmental Biology

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

Stern, C. & West, T., 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., Mar 1 2018, In : Journal of Physical Chemistry B. 122, 8, p. 2314-2322 9 p.

Research output: Contribution to journalArticle

Lipid bilayers
Membrane Lipids
Lipids
lipids
Differential scanning calorimetry

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

Sun, H., Duan, L., Chen, F., Liu, H., Wang, Z., Pan, P., Zhu, F., Zhang, J. & Hou, T., Jan 1 2018, In : Physical Chemistry Chemical Physics. 20, 21, p. 14450-14460 11 p.

Research output: Contribution to journalArticle

Free energy
Entropy
free energy
entropy
field theory (physics)