Research Output 1961 2019

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2019

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory

Athanasiadou, R., Neymotin, B., Brandt, N., Wang, W., Christiaen, L., Gresham, D. & Tranchina, D., Mar 1 2019, In : PLoS computational biology. 15, 3, p. e1006794

Research output: Contribution to journalArticle

Open Access
Statistical Models
statistical models
RNA
Spike
Calibration

A conserved regulatory program initiates lateral plate mesoderm emergence across chordates

Prummel, K. D., Hess, C., Nieuwenhuize, S., Parker, H. J., Rogers, K. W., Kozmikova, I., Racioppi, C., Brombacher, E. C., Czarkwiani, A., Knapp, D., Burger, S., Chiavacci, E., Shah, G., Burger, A., Huisken, J., Yun, M. H., Christiaen, L., Kozmik, Z., Müller, P., Bronner, M. & 2 others, Krumlauf, R. & Mosimann, C., Dec 1 2019, In : Nature Communications. 10, 1, 3857.

Research output: Contribution to journalArticle

Open Access
Chordata
Mesoderm
Prednisolone
Muscle
Zebrafish

A matter of timing

Perry, M. W. & Desplan, C., Jan 1 2019, In : eLife. 8

Research output: Contribution to journalArticle

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification

Wang, W., Niu, X., Stuart, T., Jullian, E., Mauck, W. M., Kelly, R. G., Satija, R. & Christiaen, L., Jun 1 2019, In : Nature Cell Biology. 21, 6, p. 674-686 13 p.

Research output: Contribution to journalArticle

Pharyngeal Muscles
Chordata
Head
Muscles
Mesoderm

A standardized nomenclature and atlas of the male terminalia of Drosophila melanogaster

Rice, G., David, J. R., Kamimura, Y., Masly, J. P., Mcgregor, A. P., Nagy, O., Noselli, S., Nunes, M. D. S., O’Grady, P., Sánchez-Herrero, E., Siegal, M., Toda, M. J., Rebeiz, M., Courtier-Orgogozo, V. & Yassin, A., Jan 1 2019, (Accepted/In press) In : Fly.

Research output: Contribution to journalArticle

Terminalia
genitalia
Drosophila melanogaster
terminology
rendering

Bacillus subtilis spore resistance to simulated mars surface conditions

Cortesão, M., Fuchs, F. M., Commichau, F. M., Eichenberger, P., Schuerger, A. C., Nicholson, W. L., Setlow, P. & Moeller, R., Jan 1 2019, In : Frontiers in Microbiology. 10, FEB, 333.

Research output: Contribution to journalArticle

Open Access
Mars
Bacillus subtilis
Spores
Radiation
DNA Damage

Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter

Ling, J., Umezawa, K. Y., Scott, T. & Small, S., Sep 19 2019, In : Molecular Cell. 75, 6, p. 1178-1187.e4

Research output: Contribution to journalArticle

Transcriptional Activation
Transcription Factors

Bidirectional sliding of two parallel microtubules generated by multiple identical motors

Allard, J., Doumic, M., Mogilner, A. & Oelz, D., Jan 1 2019, In : Journal of Mathematical Biology.

Research output: Contribution to journalArticle

Microtubules
microtubules
Continuous-time Markov Process
Molecular Motor
Markov Chains

Big Data to the Bench: Transcriptome Analysis for Undergraduates

Procko, C., Morrison, S., Dunar, C., Mills, S., Maldonado, B., Cockrum, C., Peters, N. E., Huang, S-S. & Chory, J., Jun 1 2019, In : CBE life sciences education. 18, 2, p. ar19

Research output: Contribution to journalArticle

Open Access
Gene Expression Profiling
Students
biology
RNA
Computational methods

Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Street, L. A., Morao, A. K., Winterkorn, L. H., Jiao, C. Y., Albritton, S. E., Sadic, M., Kramer, M. & Ercan, S., Jul 1 2019, In : Genetics. 212, 3, p. 729-742 14 p.

Research output: Contribution to journalArticle

Histone Code
Regulator Genes
Gene Expression
Chromosome Segregation
Heterochromatin

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

Pokrovskii, M., Hall, J. A., Ochayon, D. E., Yi, R., Chaimowitz, N. S., Seelamneni, H., Carriero, N., Watters, A., Waggoner, S. N., Littman, D. R., Bonneau, R. & Miraldi, E. R., Jul 16 2019, In : Immunity. 51, 1, p. 185-197.e6

Research output: Contribution to journalArticle

Gene Regulatory Networks
Homeostasis
Transcription Factors
Genome
Lymphocytes

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis

Beltran, T., Barroso, C., Birkle, T. Y., Stevens, L., Schwartz, H. T., Sternberg, P. W., Fradin, H., Gunsalus, K., Piano, F., Sharma, G., Cerrato, C., Ahringer, J., Martínez-Pérez, E., Blaxter, M. & Sarkies, P., Mar 25 2019, In : Developmental Cell. 48, 6, p. 793-810.e6

Research output: Contribution to journalArticle

Open Access
RNA Polymerase II
Epigenomics
Small Interfering RNA
Chromatin
Caenorhabditis elegans

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P. & Satija, R., Jun 13 2019, In : Cell. 177, 7, p. 1888-1902.e21

Research output: Contribution to journalArticle

Small Cytoplasmic RNA
Anchors
Gene expression
Gene Expression
Lymphocytes

Contributions of crust proteins to spore surface properties in Bacillus subtilis

Shuster, B., Khemmani, M., Abe, K., Huang, X., Nakaya, Y., Maryn, N., Buttar, S., Gonzalez, A. N., Driks, A., Sato, T. & Eichenberger, P., Jan 1 2019, In : Molecular Microbiology.

Research output: Contribution to journalArticle

Surface Properties
Bacillus subtilis
Spores
Hydrophobic and Hydrophilic Interactions
Polysaccharides

Cross-species hybridization and the origin of North African date palms

Flowers, J., Hazzouri, K. M., Gros-Balthazard, M., Mo, Z., Koutroumpa, K., Perrakis, A., Ferrand, S., Khierallah, H. S. M., Fuller, D. Q., Aberlenc, F., Fournaraki, C. & Purugganan, M., Jan 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 5, p. 1651-1658 8 p.

Research output: Contribution to journalArticle

Middle East
Northern Africa
Population
Genome
Phoeniceae

Dengue, chikungunya, and scrub typhus are important etiologies of non-malarial febrile illness in Rourkela, Odisha, India

Rao, P. N., Van Eijk, A. M., Choubey, S., Ali, S. Z., Dash, A., Barla, P., Oraon, R. R., Patel, G., Nandini, P., Acharya, S., Mohanty, S., Carlton, J. & Satpathi, S., Jul 3 2019, In : BMC Infectious Diseases. 19, 1, 572.

Research output: Contribution to journalArticle

Open Access
Scrub Typhus
Dengue
India
Fever
Routine Diagnostic Tests

Directions for research and training in plant omics: Big Questions and Big Data

Argueso, C. T., Assmann, S. M., Birnbaum, K., Chen, S., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Friesner, J., Greenlee, V. R., Law, J. A., Marshall-Colón, A., Mason, G. A., O'Lexy, R., Peck, S. C., Schmitz, R. J., Song, L., Stern, D., Varagona, M. J., Walley, J. W. & Williams, C. M., Apr 1 2019, In : Plant Direct. 3, 4, e00133.

Research output: Contribution to journalArticle

Open Access
training (plants)
Education
plant biology
Research
Arabidopsis

Discoidin-domain receptor coordinates cell-matrix adhesion and collective polarity in migratory cardiopharyngeal progenitors

Bernadskaya, Y. Y., Brahmbhatt, S., Gline, S. E., Wang, W. & Christiaen, L., Dec 1 2019, In : Nature Communications. 10, 1, 57.

Research output: Contribution to journalArticle

Cell-Matrix Junctions
polarity
adhesion
Adhesion
Light trailers

EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data

Koh, H. W. L., Zhang, Y., Vogel, C. & Choi, H., Feb 1 2019, In : Journal of Proteome Research. 18, 2, p. 748-752 5 p.

Research output: Contribution to journalArticle

Proteomics
Labeling
Peptides
Proteins
Labels

Elites tweet to get feet off the streets: Measuring regime social media strategies during protest

Munger, K., Bonneau, R., Nagler, J. & Tucker, J., Oct 1 2019, In : Political Science Research and Methods. 7, 4, p. 815-834 20 p.

Research output: Contribution to journalArticle

Open Access
social media
protest
elite
regime
twitter

Evolution at the edge of expanding populations

Deforet, M., Carmona Fontaine, C., Korolev, K. S. & Xavier, J. B., Jan 1 2019, In : American Naturalist.

Research output: Contribution to journalArticle

mutants
reproductive cost
swarming
bacterium
bacteria

Expansion of the Spore Surface Polysaccharide Layer in Bacillus subtilis by Deletion of Genes Encoding Glycosyltransferases and Glucose Modification Enzymes

Shuster, B., Khemmani, M., Nakaya, Y., Holland, G., Iwamoto, K., Abe, K., Imamura, D., Maryn, N., Driks, A., Sato, T. & Eichenberger, P., Oct 1 2019, In : Journal of bacteriology. 201, 19

Research output: Contribution to journalArticle

Glycosyltransferases
Gene Deletion
Bacillus subtilis
Spores
Polysaccharides

Faculty perceptions and knowledge of career development of trainees in biomedical science: What do we (think we) know?

Watts, S. W., Chatterjee, D., Rojewski, J. W., Reiss, C., Baas, T., Gould, K. L., Brown, A. M., Chalkley, R., Brandt, P., Wefes, I., Hyman, L. & Kevin Ford, J., Jan 1 2019, In : PLoS One. 14, 1, e0210189.

Research output: Contribution to journalArticle

career development
education programs
Education
professional development
mentoring

Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

Xiong, K., Lancaster, A. K., Siegal, M. & Masel, J., Dec 1 2019, In : Nature Communications. 10, 1, 2418.

Research output: Contribution to journalArticle

Open Access
Diamond
Noise
topology
Topology
diamonds

For Whom the Bot Tolls: A Neural Networks Approach to Measuring Political Orientation of Twitter Bots in Russia

Stukal, D., Sanovich, S., Tucker, J. & Bonneau, R., Apr 1 2019, In : SAGE Open. 9, 2

Research output: Contribution to journalArticle

Open Access
twitter
political attitude
neural network
Russia
social media

High-definition spatial transcriptomics for in situ tissue profiling

Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., Gould, J., Griffin, G. K., Borg, Å., Ronaghi, M., Frisén, J., Lundeberg, J., Regev, A. & Ståhl, P. L., Oct 1 2019, In : Nature methods. 16, 10, p. 987-990 4 p.

Research output: Contribution to journalArticle

Tissue
Spatial Analysis
Brain
RNA
Breast Neoplasms

Infection-generated electric field in gut epithelium drives bidirectional migration of macrophages

Sun, Y., Reid, B., Ferreira, F., Luxardi, G., Ma, L., Lokken, K. L., Zhu, K., Xu, G., Sun, Y., Ryzhuk, V., Guo, B. P., Lebrilla, C. B., Maverakis, E., Mogilner, A. & Zhao, M., Apr 1 2019, In : PLoS biology. 17, 4, p. e3000044

Research output: Contribution to journalArticle

Open Access
Macrophages
electric field
macrophages
epithelium
Epithelium

Inferring bacterial recombination rates from large-scale sequencing datasets

Lin, M. & Kussell, E., Feb 1 2019, In : Nature Methods. 16, 2, p. 199-204 6 p.

Research output: Contribution to journalArticle

Genetic Recombination
Gene Pool
Genes
Metagenomics
Bacterial DNA

Initial characterization of Wnt-Tcf functions during Ciona heart development

Kaplan, N. A., Wang, W. & Christiaen, L., Jan 1 2019, (Accepted/In press) In : Developmental Biology.

Research output: Contribution to journalArticle

Wnt Signaling Pathway
Pharyngeal Muscles
Muscle Development
Cardiac Myocytes
Vertebrates

Integrative single-cell analysis

Stuart, T. & Satija, R., Jan 1 2019, In : Nature Reviews Genetics.

Research output: Contribution to journalArticle

Single-Cell Analysis
Technology
RNA Sequence Analysis
Epigenomics
Proteomics

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery

Koh, H. W. L., Fermin, D., Vogel, C., Choi, K. P., Ewing, R. M. & Choi, H., Dec 1 2019, In : npj Systems Biology and Applications. 5, 1, 22.

Research output: Contribution to journalArticle

Open Access
Molecular interactions
Gene Regulatory Networks
Statistical Models
Data integration
Joints

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Miraldi, E. R., Pokrovskii, M., Watters, A., Castro, D. M., De Veaux, N., Hall, J. A., Lee, J. Y., Ciofani, M., Madar, A., Carriero, N., Littman, D. R. & Bonneau, R., Mar 1 2019, In : Genome Research. 29, 3, p. 449-463 15 p.

Research output: Contribution to journalArticle

Open Access
Th17 Cells
Gene Regulatory Networks
Transposases
Chromatin
Transcription Factors

Longitudinal comparison of bacterial diversity and antibiotic resistance genes in New York City sewage

Joseph, S. M., Battaglia, T., Maritz, J. M., Carlton, J. & Blaser, M. J., Jan 1 2019, In : mSystems. 4, 4, e00327-19.

Research output: Contribution to journalArticle

Open Access
Bacterial Drug Resistance
antibiotic resistance
Antibiotics
Sewage
sewage

Meeting report: Experimental and evolutionary approaches to yeast and other organisms 2018

Gresham, D. & Rancati, G., Mar 1 2019, In : G3: Genes, Genomes, Genetics. 9, 3, p. 635-638 4 p.

Research output: Contribution to journalArticle

Systems Biology
Molecular Biology
Yeasts
Research Personnel

Metabolic Regulation of Developmental Cell Cycles and Zygotic Transcription

Djabrayan, N. J. V., Smits, C. M., Krajnc, M., Stern, T., Yamada, S., Lemon, W. C., Keller, P. J., Rushlow, C. & Shvartsman, S. Y., Apr 1 2019, In : Current Biology. 29, 7, p. 1193-1198.e5

Research output: Contribution to journalArticle

Transcription
cell cycle
Cell Cycle
embryo (animal)
Embryonic Structures

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status

Ding, T., Song, T., Zhou, B., Geber, A., Ma, Y., Zhang, L., Volk, M., Kapadia, S. N., Jenkins, S. G., Salvatore, M. & Ghedin, E., Jul 2 2019, In : mBio. 10, 4

Research output: Contribution to journalArticle

Open Access
Nasopharynx
Orthomyxoviridae
Human Influenza
Vaccination
Microbiota

miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5' terminus

Chahal, J., Gebert, L. F. R., Gan, H. H., Camacho, E., Gunsalus, K., MacRae, I. J. & Sagan, S. M., Jun 4 2019, In : Nucleic acids research. 47, 10, p. 5307-5324 18 p.

Research output: Contribution to journalArticle

Open Access
Viral Structures
Hepacivirus
Genome
5' Untranslated Regions
Acylation

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

Mimitou, E. P., Cheng, A., Montalbano, A., Hao, S., Stoeckius, M., Legut, M., Roush, T., Herrera, A., Papalexi, E., Ouyang, Z., Satija, R., Sanjana, N. E., Koralov, S. B. & Smibert, P., May 1 2019, In : Nature Methods. 16, 5, p. 409-412 4 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Transcriptome
Epitopes
Guide RNA
Proteins

Multi-study inference of regulatory networks for more accurate models of gene regulation

Castro, D. M., de Veaux, N. R., Miraldi, E. R. & Bonneau, R., Jan 1 2019, In : PLoS Computational Biology. 15, 1, e1006591.

Research output: Contribution to journalArticle

Gene Regulation
Regulatory Networks
Gene expression
gene
Genes

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

Brooks, M. D., Cirrone, J., Pasquino, A. V., Alvarez, J. M., Swift, J., Mittal, S., Juang, C. L., Varala, K., Gutiérrez, R. A., Krouk, G., Shasha, D. & Coruzzi, G., Dec 1 2019, In : Nature Communications. 10, 1, 1569.

Research output: Contribution to journalArticle

Open Access
walking
genome
charts
Walking
Transcription Factors

Nuclear Scaling Is Coordinated among Individual Nuclei in Multinucleated Muscle Fibers

Windner, S. E., Manhart, A., Brown, A., Mogilner, A. & Baylies, M. K., Apr 8 2019, In : Developmental Cell. 49, 1, p. 48-62.e3

Research output: Contribution to journalArticle

Muscle
Muscles
Fibers
Cell Size
Muscle Cells

Nucleotide Excision Repair and Impact of Site-Specific 5′,8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes

Shafirovich, V., Kolbanovskiy, M., Kropachev, K., Liu, Z., Cai, Y., Terzidis, M. A., Masi, A., Chatgilialoglu, C., Amin, S., Dadali, A., Broyde, S. & Geacintov, N., Jan 1 2019, (Accepted/In press) In : Biochemistry.

Research output: Contribution to journalArticle

Nucleosomes
DNA Repair
Repair
Nucleotides
Physical properties

Patterns of protist diversity associated with raw sewage in New York City

Maritz, J. M., Ten Eyck, T. A., Elizabeth Alter, S. & Carlton, J., Jan 1 2019, In : ISME Journal.

Research output: Contribution to journalArticle

Open Access
protist
Sewage
sewage
Metagenome
animal

Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on short chromosomes

Subramanian, V. V., Zhu, X., Markowitz, T. E., Vale-Silva, L. A., San-Segundo, P. A., Hollingsworth, N. M., Keeney, S. & Hochwagen, A., Dec 1 2019, In : Nature Communications. 10, 1, 970.

Research output: Contribution to journalArticle

Open Access
telomeres
DNA Breaks
chromosomes
Telomere
Chromosomes

Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo

Kahli, M., Osmundson, J. S., Yeung, R. & Smith, D., Feb 28 2019, In : Nucleic acids research. 47, 4, p. 1814-1822 9 p.

Research output: Contribution to journalArticle

Open Access
DNA Replication
Ligation
DNA Polymerase III
Deoxyribonucleases
Eukaryota

Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes

Aydin, B., Kakumanu, A., Rossillo, M., Moreno-Estellés, M., Garipler, G., Ringstad, N., Flames, N., Mahony, S. & Mazzoni, E., Jan 1 2019, In : Nature Neuroscience.

Research output: Contribution to journalArticle

Chromatin
Transcription Factors
E-Box Elements
Embryonic Stem Cells
Nervous System

Quantitative regulation of the dynamic steady state of actin networks

Manhart, A., Icheva, T. A., Guerin, C., Klar, T., Boujemaa-Paterski, R., Thery, M., Blanchoin, L. & Mogilner, A., Mar 14 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
Actin Depolymerizing Factors
Actins
Physiological Feedback
Heterogeneous networks
Computer Simulation

Scaling behaviour in steady-state contracting actomyosin networks

Malik-Garbi, M., Ierushalmi, N., Jansen, S., Abu-Shah, E., Goode, B. L., Mogilner, A. & Keren, K., Jan 1 2019, In : Nature Physics.

Research output: Contribution to journalArticle

scaling
contraction
cell division
myosins
encapsulating

SNP-ChIP: A versatile and tag-free method to quantify changes in protein binding across the genome

Vale-Silva, L. A., Markowitz, T. E. & Hochwagen, A., Jan 17 2019, In : BMC Genomics. 20, 1, 54.

Research output: Contribution to journalArticle

Protein Binding
Single Nucleotide Polymorphism
Genome
Chromatin Immunoprecipitation
Histone Code

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., Cuevas, M., Watters, A., Lundeberg, J., Bonneau, R. & Phatnani, H., Apr 5 2019, In : Science. 364, 6435, p. 89-93 5 p.

Research output: Contribution to journalArticle

Molecular Pathology
Amyotrophic Lateral Sclerosis
Motor Neurons
Spinal Cord
Nerve Degeneration