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2020

A Bright IDEA

Jackson, C. & Gresham, D., Apr 1 2020, In : Molecular systems biology. 16, 4, p. e9502

Research output: Contribution to journalArticle

Open Access

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

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

Defining symptoms of malaria in India in an era of asymptomatic infections

Van Eijk, A. M., Mannan, A. S., Sullivan, S. A. & Carlton, J. M., Jul 6 2020, In : Malaria Journal. 19, 1, s03310.

Research output: Contribution to journalArticle

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

Effects of malleable kinetochore morphology on measurements of intrakinetochore tension

Renda, F., Magidson, V., Tikhonenko, I., Fisher, R., Miles, C., Mogilner, A. & Khodjakov, A., Jul 1 2020, In : Open Biology. 10, 7, 1 p.

Research output: Contribution to journalArticle

Open Access

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

Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states

Sun, S., Baryshnikova, A., Brandt, N. & Gresham, D., May 1 2020, In : Molecular systems biology. 16, 5, e9167.

Research output: Contribution to journalArticle

Open Access

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., 2020, In : PLoS genetics. 16, 1, e1008571.

Research output: Contribution to journalArticle

Open Access

Genomic history and ecology of the geographic spread of rice

Gutaker, R. M., Groen, S. C., Bellis, E. S., Choi, J. Y., Pires, I. S., Bocinsky, R. K., Slayton, E. R., Wilkins, O., Castillo, C. C., Negrão, S., Oliveira, M. M., Fuller, D. Q., Guedes, J. A. DA., Lasky, J. R. & Purugganan, M. D., May 1 2020, In : Nature Plants. 6, 5, p. 492-502 11 p.

Research output: Contribution to journalArticle

Inference of bacterial small RNA regulatory networks and integration with transcription factor-driven regulatory networks

Arrieta-Ortiz, M. L., Arrieta-Ortiz, M. L., Hafemeister, C., Shuster, B., Baliga, N. S., Bonneau, R., Bonneau, R., Bonneau, R. & Eichenberger, P., Jun 2020, In : mSystems. 5, 3, e00057-20.

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

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

Spealman, P., Burrell, J. & Gresham, D., May 21 2020, In : Nucleic acids research. 48, 9, p. 4940-4945 6 p.

Research output: Contribution to journalArticle

Open Access

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

Wang, L., Lu, Z., delaBastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C. F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H. & 1 others, Gingeras, T. R., Mar 31 2020, In : Frontiers in Plant Science. 11, 289.

Research output: Contribution to journalArticle

Open Access

Mechanics of Multicentrosomal Clustering in Bipolar Mitotic Spindles

Chatterjee, S., Sarkar, A., Zhu, J., Khodjakov, A., Mogilner, A. & Paul, R., Jul 21 2020, In : Biophysical journal. 119, 2, p. 434-447 14 p.

Research output: Contribution to journalArticle

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

Natural variations at the Stay-Green gene promoter control lifespan and yield in rice cultivars

Shin, D., Lee, S., Kim, T. H., Lee, J. H., Park, J., Lee, J., Lee, J. Y., Cho, L. H., Choi, J. Y., Lee, W., Park, J. H., Lee, D. W., Ito, H., Kim, D. H., Tanaka, A., Cho, J. H., Song, Y. C., Hwang, D., Purugganan, M. D., Jeon, J. S. & 2 others, An, G. & Nam, H. G., Dec 1 2020, In : Nature communications. 11, 1, 2819.

Research output: Contribution to journalArticle

Open Access

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

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

Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation

Porcella, S. Y., Koussa, N. C., Tang, C. P., Kramer, D. N., Srivastava, P. & Smith, D. J., May 2020, In : PLoS genetics. 16, 5, e1008755.

Research output: Contribution to journalArticle

Open Access

Sex chromosome evolution in parasitic nematodes of humans

Foster, J. M., Grote, A., Mattick, J., Tracey, A., Tsai, Y. C., Chung, M., Cotton, J. A., Clark, T. A., Geber, A., Holroyd, N., Korlach, J., Li, Y., Libro, S., Lustigman, S., Michalski, M. L., Paulini, M., Rogers, M. B., Teigen, L., Twaddle, A., Welch, L. & 3 others, Berriman, M., Dunning Hotopp, J. C. & Ghedin, E., Dec 1 2020, In : Nature communications. 11, 1, 1964.

Research output: Contribution to journalArticle

Open Access

Simple Method to Quantify Protein Abundances from 1000 Cells

Vitrinel, B., Iannitelli, D. E., Mazzoni, E. O., Christiaen, L. & Vogel, C., 2020, (Accepted/In press) In : ACS Omega.

Research output: Contribution to journalArticle

Open Access

The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-angelensis, a Mexican endangered species

Hinojosa-Alvarez, S., Arias, S., Ferrand, S., Purugganan, M. D., Rozas, J., Rosas, U. & Wegier, A., Jul 2 2020, In : Mitochondrial DNA Part B: Resources. 5, 3, p. 2038-2039 2 p.

Research output: Contribution to journalArticle

Open Access

The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface

Hazzouri, K. M., Sudalaimuthuasari, N., Kundu, B., Nelson, D., Al-Deeb, M. A., Le Mansour, A., Spencer, J. J., Desplan, C. & Amiri, K. M. A., Dec 1 2020, In : Communications Biology. 3, 1, 323.

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

Topoisomerases Modulate the Timing of Meiotic DNA Breakage and Chromosome Morphogenesis in Saccharomyces cerevisiae

Heldrich, J., Sun, X., Vale-Silva, L. A., Markowitz, T. E. & Hochwagen, A., May 2020, In : Genetics. 215, 1, p. 59-73 15 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., Nov 29 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