Research Output 1961 2019

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

An evolving view of copy number variants

Lauer, S. & Gresham, D., Jan 1 2019, In : Current Genetics.

Research output: Contribution to journalReview article

Inverted Repeat Sequences
Archaea
DNA Replication
Population
Saccharomyces cerevisiae

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

Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (Nature, (2018), 554, 7692, (373-377), 10.1038/nature25500)

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R. & Littman, D. R., Feb 21 2019, In : Nature. 566, 7744, p. E7

Research output: Contribution to journalComment/debate

Regulatory T-Lymphocytes

Author Correction: Testing the key assumption of heritability estimates based on genome-wide genetic relatedness (Journal of Human Genetics, (2014), 59, 6, (342-345), 10.1038/jhg.2014.14)

Conley, D., Siegal, M., Domingue, B. W., Harris, K. M., McQueen, M. B. & Boardman, J. D., Jan 1 2019, In : Journal of Human Genetics.

Research output: Contribution to journalComment/debate

Open Access
Medical Genetics
Genome
Surveys and Questionnaires

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

Cell reprogramming: The many roads to success

Aydin, B. & Mazzoni, E., Jan 1 2019, In : Annual Review of Cell and Developmental Biology. 35, p. 433-452 20 p.

Research output: Contribution to journalReview article

Transcription Factors
Cellular Reprogramming

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

Classical and emerging regulatory mechanisms of cytokinesis in animal cells

Verma, V., Mogilner, A. & Maresca, T. J., Sep 1 2019, In : Biology. 8, 3, 55.

Research output: Contribution to journalReview article

Open Access
Myosin Type II
Actomyosin
Cytokinesis
cytokinesis
Chromosomes

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

Coordination of neural patterning in the Drosophila visual system

Courgeon, M. & Desplan, C., Jun 1 2019, In : Current Opinion in Neurobiology. 56, p. 153-159 7 p.

Research output: Contribution to journalReview article

Neuropil
Drosophila
Gene Expression

Copy Number Variation in Domestication

Lye, Z. N. & Purugganan, M., Jan 1 2019, In : Trends in Plant Science.

Research output: Contribution to journalReview article

domestication
mutation
genetic variation
animals
genes

Correction: Transmission bottleneck size estimation from pathogen deep-sequencing data, with an application to human influenza A virus (Journal of Virology (2017) 91:14 (e00171-17) DOI: 10.1128/JVI.00171-17)

Leonard, A. S., Weissman, D. B., Greenbaum, B., Ghedin, E. & Koelle, K., Sep 1 2019, In : Journal of virology. 93, 17, e00936-19.

Research output: Contribution to journalComment/debate

Open Access
human influenza
High-Throughput Nucleotide Sequencing
virology
Virology
Influenza A virus

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
Open Access
human influenza
High-Throughput Nucleotide Sequencing
virology
Virology
Influenza A virus

Evolutionary Insights into the Nature of Plant Domestication

Purugganan, M., Jul 22 2019, In : Current Biology. 29, 14, p. R705-R714

Research output: Contribution to journalReview article

Open Access
domestication
Crops
crops
Genomics
genomics

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

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

Vitrinel, B., Koh, H. W. L., Mujgan Kar, F., Maity, S., Rendleman, J., Choi, H. & Vogel, C., Aug 9 2019, In : Molecular & cellular proteomics : MCP. 18, 8, p. S5-S14

Research output: Contribution to journalReview article

Open Access
Proteomics
Messenger RNA
Molecules
Data integration
Mass spectrometry

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

iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community

Falter-Braun, P., Brady, S., Gutiérrez, R. A., Coruzzi, G. & Krouk, G., Jun 3 2019, In : Molecular Plant. 12, 6, p. 727-730 4 p.

Research output: Contribution to journalEditorial

Open Access
Systems Biology
plant communities
Biological Sciences

Isolation of biologically active compounds from mangrove sediments

Solntsev, K. M., Schramm, S., Kremb, S., Gunsalus, K. & Amin, S., Jan 1 2019, In : Analytical and Bioanalytical Chemistry.

Research output: Contribution to journalComment/debate

Open Access
Sediments

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