Research Output

2020

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

Johnson, J. S., De Veaux, N., Rives, A. W., Lahaye, X., Lucas, S. Y., Perot, B. P., Luka, M., Garcia-Paredes, V., Amon, L. M., Watters, A., Abdessalem, G., Aderem, A., Manel, N., Littman, D. R., Bonneau, R. & Ménager, M. M., Jan 21 2020, In : Cell Reports. 30, 3, p. 914-931.e9

Research output: Contribution to journalArticle

Open Access

An inferred fitness consequence map of the rice genome

Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A. & Purugganan, M. D., Feb 1 2020, In : Nature Plants. 6, 2, p. 119-130 12 p.

Research output: Contribution to journalArticle

A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes

Li, G. X. H., Munro, D., Fermin, D., Vogel, C. & Choi, H., May 1 2020, In : Human Mutation. 41, 5, p. 934-945 12 p.

Research output: Contribution to journalArticle

Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response

Zhang, X., Ménard, R., Li, Y., Coruzzi, G. M., Heitz, T., Shen, W. H. & Berr, A., Mar 11 2020, In : Frontiers in Plant Science. 11, 277.

Research output: Contribution to journalArticle

Open Access

A rapid and label-free platform for virus capture and identification from clinical samples

Yeh, Y. T., Gulino, K., Zhang, Y. H., Sabestien, A., Chou, T. W., Zhou, B., Lin, Z., Albert, I., Lu, H., Swaminathan, V., Ghedin, E. & Terrones, M., Jan 14 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 2, p. 895-901 7 p.

Research output: Contribution to journalArticle

Open Access

Better together: Elements of successful scientific software development in a distributed collaborative community

RosettaCommons Consortium, May 1 2020, In : PLoS computational biology. 16, 5, e1007507.

Research output: Contribution to journalReview article

Open Access

Cannabinoid exposure in rat adolescence reprograms the initial behavioral, molecular, and epigenetic response to cocaine

Scherma, M., Qvist, J. S., Asok, A., Huang, S. S. C., Masia, P., Deidda, M., Wei, Y. B., Soni, R. K., Fratta, W., Fadda, P., Kandel, E. R., Kandel, D. B. & Melas, P. A., May 5 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 18, p. 9991-10002 12 p.

Research output: Contribution to journalArticle

Open Access

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer

Zhang, H., Christensen, C. L., Dries, R., Oser, M. G., Deng, J., Diskin, B., Li, F., Pan, Y., Zhang, X., Yin, Y., Papadopoulos, E., Pyon, V., Thakurdin, C., Kwiatkowski, N., Jani, K., Rabin, A. R., Castro, D. M., Chen, T., Silver, H., Huang, Q. & 29 others, Bulatovic, M., Dowling, C. M., Sundberg, B., Leggett, A., Ranieri, M., Han, H., Li, S., Yang, A., Labbe, K. E., Almonte, C., Sviderskiy, V. O., Quinn, M., Donaghue, J., Wang, E. S., Zhang, T., He, Z., Velcheti, V., Hammerman, P. S., Freeman, G. J., Bonneau, R., Kaelin, W. G., Sutherland, K. D., Kersbergen, A., Aguirre, A. J., Yuan, G. C., Rothenberg, E., Miller, G., Gray, N. S. & Wong, K. K., Jan 13 2020, In : Cancer Cell. 37, 1, p. 37-54.e9

Research output: Contribution to journalArticle

Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection

Wang, C., Forst, C. V., Chou, T. W., Geber, A., Wang, M., Hamou, W., Smith, M., Sebra, R., Zhang, B., Zhou, B. & Ghedin, E., Jan 1 2020, In : mBio. 11, 1, e02880-19.

Research output: Contribution to journalArticle

Open Access

Centering and symmetry breaking in confined contracting actomyosin networks

Ierushalmi, N., Malik-Garbi, M., Manhart, A., Shah, E. A., Goode, B. L., Mogilner, A. & Keren, K., Apr 2020, In : eLife. 9, e55368.

Research output: Contribution to journalArticle

Open Access

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Zhang, L., Forst, C. V., Gordon, A., Gussin, G., Geber, A. B., Fernandez, P. J., Ding, T., Lashua, L., Wang, M., Balmaseda, A., Bonneau, R., Zhang, B. & Ghedin, E., Mar 17 2020, In : Microbiome. 8, 1, 39.

Research output: Contribution to journalArticle

Open Access

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Gabitto, M. I., Rasmussen, A., Wapinski, O., Allaway, K., Carriero, N., Fishell, G. J. & Bonneau, R., Dec 1 2020, In : Nature communications. 11, 1, 747.

Research output: Contribution to journalArticle

Open Access

Chemical chaperones reverse early suppression of regulatory circuits during unfolded protein response in B cells from common variable immunodeficiency patients

Bhatt, D., Stan, R. C., Pinhata, R., Machado, M., Maity, S., Cunningham-Rundles, C., Vogel, C. & de Camargo, M. M., Apr 1 2020, In : Clinical and Experimental Immunology. 200, 1, p. 73-86 14 p.

Research output: Contribution to journalArticle

Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter

Salazar, M. D., Zelt, N. B., Saldivar, R., Kuntz, C. P., Chen, S., Penn, W. D., Bonneau, R., Koehler Leman, J. & Schlebach, J. P., Apr 7 2020, In : Biochemistry. 59, 13, p. 1367-1377 11 p.

Research output: Contribution to journalArticle

Clinical and epidemiological characterization of severe Plasmodium vivax malaria in Gujarat, India

Anvikar, A. R., van Eijk, A. M., Shah, A., Upadhyay, K. J., Sullivan, S. A., Patel, A. J., Joshi, J. M., Tyagi, S., Singh, R., Carlton, J. M., Gupta, H. & Wassmer, S. C., Jan 1 2020, In : Virulence. 11, 1, p. 730-738 9 p.

Research output: Contribution to journalArticle

Open Access

Compatibility of Site-Specific Recombination Units between Mobile Genetic Elements

Suzuki, S., Yoshikawa, M., Imamura, D., Abe, K., Eichenberger, P. & Sato, T., Jan 24 2020, In : iScience. 23, 1, 100805.

Research output: Contribution to journalArticle

Open Access

Coronavirus Pandemic

Reiss, C. S., Jun 1 2020, In : DNA and cell biology. 39, 6, 1 p.

Research output: Contribution to journalEditorial

Open Access

Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

Choi, J. Y., Purugganan, M. & Stacy, E. A., Mar 1 2020, In : Molecular Biology and Evolution. 37, 3, p. 695-710 16 p.

Research output: Contribution to journalArticle

Open Access

Evolution, developmental expression and function of odorant receptors in insects

Yan, H., Jafari, S., Pask, G., Zhou, X., Reinberg, D. & Desplan, C., Feb 7 2020, In : The Journal of experimental biology. 223, Pt

Research output: Contribution to journalReview article

Open Access

Evolution of serotonin: sunlight to suicide

Azmitia, E. C., 2020, Handbook of Behavioral Neuroscience. Elsevier B.V., p. 3-22 20 p. (Handbook of Behavioral Neuroscience; vol. 31).

Research output: Chapter in Book/Report/Conference proceedingChapter

Experiment, theory, and the keratocyte: An ode to a simple model for cell motility

Mogilner, A., Barnhart, E. L. & Keren, K., Apr 2020, In : Seminars in Cell and Developmental Biology. 100, p. 143-151 9 p.

Research output: Contribution to journalReview article

Gene regulatory network reconstruction using single-cell rna sequencing of barcoded genotypes in diverse environments

Jackson, C. A., Castro, D. M., Saldi, G. A., Bonneau, R. & Gresham, D., Jan 2020, In : eLife. 9, e51254.

Research output: Contribution to journalArticle

Open Access

Gene regulatory networks during the development of the Drosophila visual system

Chen, Y. C. & Desplan, C., 2020, Current Topics in Developmental Biology. Academic Press Inc., p. 89-125 37 p. (Current Topics in Developmental Biology; vol. 139).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Read, A. C., Moscou, M. J., Zimin, A. V., Pertea, G., Meyer, R. S., Purugganan, M. D., Leach, J. E., Triplett, L. R., Salzberg, S. L. & Bogdanove, A. J., Jan 1 2020, In : PLoS genetics. 16, 1, e1008571.

Research output: Contribution to journalArticle

Open Access

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25–Driven Intestinal Inflammation

Manasson, J., Wallach, D. S., Guggino, G., Stapylton, M., Badri, M. H., Solomon, G., Reddy, S. M., Coras, R., Aksenov, A. A., Jones, D. R., Girija, P. V., Neimann, A. L., Heguy, A., Segal, L. N., Dorrestein, P. C., Bonneau, R., Guma, M., Ciccia, F., Ubeda, C., Clemente, J. C. & 1 others, Scher, J. U., Apr 1 2020, In : Arthritis and Rheumatology. 72, 4, p. 645-657 13 p.

Research output: Contribution to journalArticle

Just passing through: The auxin gradient of the root meristem

Guillotin, B. & Birnbaum, K. D., 2020, Current Topics in Developmental Biology. Small, S. & Briscoe, J. (eds.). Academic Press Inc., p. 433-454 22 p. (Current Topics in Developmental Biology; vol. 137).

Research output: Chapter in Book/Report/Conference proceedingChapter

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Choi, J. Y., Lye, Z. N., Groen, S. C., Dai, X., Rughani, P., Zaaijer, S., Harrington, E. D., Juul, S. & Purugganan, M. D., Feb 5 2020, In : Genome biology. 21, 1, 21.

Research output: Contribution to journalArticle

Open Access

New Journal Section and Section Editor

Reiss, C. S., Jan 2020, In : DNA and Cell Biology. 39, 1, 1 p.

Research output: Contribution to journalEditorial

Nutrient dose-responsive transcriptome changes driven by Michaelis–Menten kinetics underlie plant growth rates

Swift, J., Alvarez, J. M., Araus, V., Gutiérrez, R. A. & Coruzzi, G. M., Jun 9 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 23, p. 12531-12540 10 p.

Research output: Contribution to journalArticle

Open Access

OutPredict: multiple datasets can improve prediction of expression and inference of causality

Cirrone, J., Brooks, M. D., Bonneau, R., Coruzzi, G. M. & Shasha, D. E., Dec 1 2020, In : Scientific reports. 10, 1, 6804.

Research output: Contribution to journalArticle

Open Access

Political psycholinguistics: A comprehensive analysis of the language habits of liberal and conservative social media users

Sterling, J., Jost, J. T. & Bonneau, R., Apr 2020, In : Journal of personality and social psychology. 118, 4, p. 805-834 30 p.

Research output: Contribution to journalArticle

Relationship between impact-crater size and severity of related extinction episodes

Rampino, M. R., Feb 2020, In : Earth-Science Reviews. 201, 102990.

Research output: Contribution to journalReview article

SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling

Li, Y., Brooks, M., Yeoh-Wang, J., McCoy, R. M., Rock, T. M., Pasquino, A., Moon, C. I., Patrick, R. M., Tanurdzic, M., Ruffel, S., Widhalm, J. R., McCombie, W. R. & Coruzzi, G. M., Jan 2020, In : Plant physiology. 182, 1, p. 215-227 13 p.

Research output: Contribution to journalArticle

Open Access

The strength and pattern of natural selection on gene expression in rice

Groen, S. C., Ćalić, I., Joly-Lopez, Z., Platts, A. E., Choi, J. Y., Natividad, M., Dorph, K., Mauck, W. M., Bracken, B., Cabral, C. L. U., Kumar, A., Torres, R. O., Satija, R., Vergara, G., Henry, A., Franks, S. J. & Purugganan, M. D., Feb 27 2020, In : Nature. 578, 7796, p. 572-576 5 p.

Research output: Contribution to journalArticle

Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Alvarez, J. M., Schinke, A. L., Brooks, M. D., Pasquino, A., Leonelli, L., Varala, K., Safi, A., Krouk, G., Krapp, A. & Coruzzi, G. M., Dec 1 2020, In : Nature communications. 11, 1, 1157.

Research output: Contribution to journalArticle

Open Access
2019

5-Formylcytosine-induced DNA–peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells

Ji, S., Park, D., Kropachev, K., Kolbanovskiy, M., Fu, I., Broyde, S., Essawy, M., Geacintov, N. E. & Tretyakova, N. Y., Jan 1 2019, In : Journal of Biological Chemistry. 294, 48, p. 18387-18397 11 p.

Research output: Contribution to journalArticle

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 2019, In : PLoS computational biology. 15, 3, e1006794.

Research output: Contribution to journalArticle

Open Access

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

Age-Related Pathology Associated with H1N1 A/California/07/2009 Influenza Virus Infection

Bissel, S. J., Carter, C. E., Wang, G., Johnson, S. K., Lashua, L. P., Kelvin, A. A., Wiley, C. A., Ghedin, E. & Ross, T. M., Dec 2019, In : American Journal of Pathology. 189, 12, p. 2389-2399 11 p.

Research output: Contribution to journalArticle

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., Dec 1 2019, In : Current Genetics. 65, 6, p. 1287-1295 9 p.

Research output: Contribution to journalReview article

Antibody responses within two leading Plasmodium vivax vaccine candidate antigens in three geographically diverse malaria-endemic regions of India

Kale, S., Yadav, C. P., Rao, P. N., Shalini, S., Eapen, A., Srivasatava, H. C., Sharma, S. K., Pande, V., Carlton, J. M., Singh, O. P. & Mallick, P. K., Dec 16 2019, In : Malaria Journal. 18, 1, 425.

Research output: Contribution to journalArticle

Open Access

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

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. L., Toda, M. J., Rebeiz, M., Courtier-Orgogozo, V. & Yassin, A., Oct 2 2019, In : Fly. 13, 1-4, p. 51-64 14 p.

Research output: Contribution to journalArticle

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. L., Domingue, B. W., Harris, K. M., McQueen, M. B. & Boardman, J. D., Jun 1 2019, In : Journal of Human Genetics. 64, 6, p. 597-598 2 p.

Research output: Contribution to journalComment/debate

Open Access

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

Author Correction: The bone marrow microenvironment at single-cell resolution (Nature, (2019), 569, 7755, (222-228), 10.1038/s41586-019-1104-8)

Tikhonova, A. N., Dolgalev, I., Hu, H., Sivaraj, K. K., Hoxha, E., Cuesta-Domínguez, Á., Pinho, S., Akhmetzyanova, I., Gao, J., Witkowski, M., Guillamot, M., Gutkin, M. C., Zhang, Y., Marier, C., Diefenbach, C., Kousteni, S., Heguy, A., Zhong, H., Fooksman, D. R., Butler, J. M. & 6 others, Economides, A., Frenette, P. S., Adams, R. H., Satija, R., Tsirigos, A. & Aifantis, I., Aug 1 2019, In : Nature. 572, 7767, p. E6

Research output: Contribution to journalComment/debate