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2020

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

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

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., Basanta, B., Bender, B. J., Blacklock, K., Bonet, J., Boyken, S. E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., Correia, B. E. & 88 others, Coventry, B., Das, R., De Jong, R. M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A. S., Frenz, B., Fu, D. Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J. J., Gront, D., Guffy, S., Horowitz, S., Huang, P. S., Huber, T., Jacobs, T. M., Jeliazkov, J. R., Johnson, D. K., Kappel, K., Karanicolas, J., Khakzad, H., Khar, K. R., Khare, S. D., Khatib, F., Khramushin, A., King, I. C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte, J. W., Lai, J. K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J. H., Lyskov, S., Maguire, J., Malmström, L., Marcos, E., Marcu, O., Marze, N. A., Meiler, J., Moretti, R., Mulligan, V. K., Nerli, S., Norn, C., Ó’Conchúir, S., Ollikainen, N., Ovchinnikov, S., Pacella, M. S., Pan, X., Park, H., Pavlovicz, R. E., Pethe, M., Pierce, B. G., Pilla, K. B., Raveh, B., Renfrew, P. D., Burman, S. S. R., Rubenstein, A., Sauer, M. F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A. M., Sgourakis, N. G., Shi, L., Siegel, J. B., Silva, D. A., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F. D., Thyme, S. B., Wang, R. Y. R., Watkins, A., Zimmerman, L. & Bonneau, R., Jul 1 2020, In : Nature methods. 17, 7, p. 665-680 16 p.

Research output: Contribution to journalReview article

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

2019

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

Cell reprogramming: The many roads to success

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

Research output: Contribution to journalReview article

Classical and emerging regulatory mechanisms of cytokinesis in animal cells

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

Research output: Contribution to journalReview article

Open Access

Condensin action and compaction

Paul, M. R., Hochwagen, A. & Ercan, S., Apr 5 2019, In : Current Genetics. 65, 2, p. 407-415 9 p.

Research output: Contribution to journalReview article

Coordination of neural patterning in the Drosophila visual system

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

Research output: Contribution to journalReview article

Copy Number Variation in Domestication

Lye, Z. N. & Purugganan, M. D., Apr 2019, In : Trends in Plant Science. 24, 4, p. 352-365 14 p.

Research output: Contribution to journalReview article

Decanalizing thinking on genetic canalization

Geiler-Samerotte, K., Sartori, F. M. O. & Siegal, M. L., Apr 2019, In : Seminars in Cell and Developmental Biology. 88, p. 54-66 13 p.

Research output: Contribution to journalReview article

Evolutionary Insights into the Nature of Plant Domestication

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

Research output: Contribution to journalReview article

Open Access

Integrative single-cell analysis

Stuart, T. & Satija, R., May 1 2019, In : Nature Reviews Genetics. 20, 5, p. 257-272 16 p.

Research output: Contribution to journalReview article

Toward a Common Coordinate Framework for the Human Body

Rood, J. E., Stuart, T., Ghazanfar, S., Biancalani, T., Fisher, E., Butler, A., Hupalowska, A., Gaffney, L., Mauck, W., Eraslan, G., Marioni, J. C., Regev, A. & Satija, R., Dec 12 2019, In : Cell. 179, 7, p. 1455-1467 13 p.

Research output: Contribution to journalReview article

Towards Building a Plant Cell Atlas

Rhee, S. Y., Birnbaum, K. D. & Ehrhardt, D. W., Apr 2019, In : Trends in Plant Science. 24, 4, p. 303-310 8 p.

Research output: Contribution to journalReview article

2018

Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation

Albritton, S. E. & Ercan, S., Jan 2018, In : Trends in Genetics. 34, 1, p. 41-53 13 p.

Research output: Contribution to journalReview article

Evolution of human malaria

Carlton, J. M., Jun 1 2018, In : Nature Microbiology. 3, 6, p. 642-643 2 p.

Research output: Contribution to journalReview article

Integration of large-scale multi-omic datasets: A protein-centric view

Rendleman, J., Choi, H. & Vogel, C., Oct 2018, In : Current Opinion in Systems Biology. 11, p. 74-81 8 p.

Research output: Contribution to journalReview article

Intracellular Fluid Mechanics: Coupling Cytoplasmic Flow with Active Cytoskeletal Gel

Mogilner, A. & Manhart, A., Jan 5 2018, In : Annual Review of Fluid Mechanics. 50, p. 347-370 24 p.

Research output: Contribution to journalReview article

Malaria parasite evolution in a test tube

Carlton, J. M., Jan 12 2018, In : Science. 359, 6372, p. 159-160 2 p.

Research output: Contribution to journalReview article

Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair

Mu, H., Geacintov, N. E., Broyde, S., Yeo, J. E. & Schärer, O. D., Nov 2018, In : DNA Repair. 71, p. 33-42 10 p.

Research output: Contribution to journalReview article

Neuro-evo-devo in the single cell sequencing era

Konstantinides, N., Degabriel, S. & Desplan, C., Oct 2018, In : Current Opinion in Systems Biology. 11, p. 32-40 9 p.

Research output: Contribution to journalReview article

Neuronal specification in space and time

Holguera, I. & Desplan, C., Oct 12 2018, In : Science. 362, 6411, p. 176-180 5 p.

Research output: Contribution to journalReview article

Piecing together cis-regulatory networks: insights from epigenomics studies in plants

Huang, S. S. C. & Ecker, J. R., May 1 2018, In : Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 10, 3, e1411.

Research output: Contribution to journalReview article

Power in numbers: Single-cell RNA-seq strategies to dissect complex tissues

Birnbaum, K. D., Nov 23 2018, In : Annual Review of Genetics. 52, p. 203-221 19 p.

Research output: Contribution to journalReview article

Recent advances in behavioral (epi)genetics in eusocial insects

Opachaloemphan, C., Yan, H., Leibholz, A., Desplan, C. & Reinberg, D., Nov 23 2018, In : Annual Review of Genetics. 52, p. 489-510 22 p.

Research output: Contribution to journalReview article

Single-cell RNA sequencing to explore immune cell heterogeneity

Papalexi, E. & Satija, R., Jan 1 2018, In : Nature Reviews Immunology. 18, 1, p. 35-45 11 p.

Research output: Contribution to journalReview article

The metabolic axis of macrophage and immune cell polarization

Hobson-Gutierrez, S. A. & Carmona-Fontaine, C., Aug 2018, In : DMM Disease Models and Mechanisms. 11, 8, dmm034462.

Research output: Contribution to journalReview article

The rice genome revolution: From an ancient grain to Green Super Rice

Wing, R. A., Purugganan, M. D. & Zhang, Q., Aug 1 2018, In : Nature Reviews Genetics. 19, 8, p. 505-517 13 p.

Research output: Contribution to journalReview article

Why are there hotspot mutations in the TP53 gene in human cancers?

Baugh, E. H., Ke, H., Levine, A. J., Bonneau, R. A. & Chan, C. S., 2018, In : Cell Death and Differentiation. 25, 1, p. 154-160 7 p.

Research output: Contribution to journalReview article

2017

Are all repeats created equal? Understanding DNA repeats at an individual level

Yang, J. & Li, F., Feb 1 2017, In : Current Genetics. 63, 1, p. 57-63 7 p.

Research output: Contribution to journalReview article

Biophysically motivated regulatory network inference: Progress and prospects

Äijö, T. & Bonneau, R., Jan 1 2017, In : Human Heredity. 81, 2, p. 62-77 16 p.

Research output: Contribution to journalReview article

Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System

Perry, M., Konstantinides, N., Pinto-Teixeira, F. & Desplan, C., Nov 27 2017, In : Annual Review of Genetics. 51, p. 501-577 77 p.

Research output: Contribution to journalReview article

Getting the flu: 5 key facts about influenza virus evolution

Johnson, K. E. E., Song, T., Greenbaum, B. & Ghedin, E., Aug 2017, In : PLoS Pathogens. 13, 8, e1006450.

Research output: Contribution to journalReview article

Quantifying protein (dis)order: A study of bacteria, yeast, and mammalian cells maps the melting behavior of cellular proteins

Vogel, C., Feb 24 2017, In : Science. 355, 6327, p. 794-795 2 p.

Research output: Contribution to journalReview article

Repair-Resistant DNA Lesions

Geacintov, N. E. & Broyde, S., Aug 21 2017, In : Chemical research in toxicology. 30, 8, p. 1517-1548 32 p.

Research output: Contribution to journalReview article

Retinal perception and ecological significance of color vision in insects

Lebhardt, F. & Desplan, C., Dec 2017, In : Current Opinion in Insect Science. 24, p. 75-83 9 p.

Research output: Contribution to journalReview article

The lung mycobiome in the next-generation sequencing era

Tipton, L., Ghedin, E. & Morris, A., Apr 3 2017, In : Virulence. 8, 3, p. 334-341 8 p.

Research output: Contribution to journalReview article

The role of 'omics' in the quest to eliminate human filariasis

Lustigman, S., Grote, A. & Ghedin, E., Apr 20 2017, In : PLoS neglected tropical diseases. 11, 4, e0005464.

Research output: Contribution to journalReview article

Timing temporal transitions during brain development

Rossi, A. M., Fernandes, V. M. & Desplan, C., Feb 1 2017, In : Current Opinion in Neurobiology. 42, p. 84-92 9 p.

Research output: Contribution to journalReview article

2016

A Case for Distributed Control of Local Stem Cell Behavior in Plants

Rahni, R., Efroni, I. & Birnbaum, K. D., Sep 26 2016, In : Developmental Cell. 38, 6, p. 635-642 8 p.

Research output: Contribution to journalReview article

Agent-based modeling: Case study in cleavage furrow models

Mogilner, A. & Manhart, A., Nov 7 2016, In : Molecular biology of the cell. 27, 22, p. 3379-3384 6 p.

Research output: Contribution to journalReview article

A synopsis on aging—Theories, mechanisms and future prospects

da Costa, J. P., Vitorino, R., Silva, G. M., Vogel, C., Duarte, A. C. & Rocha-Santos, T., Aug 1 2016, In : Ageing Research Reviews. 29, p. 90-112 23 p.

Research output: Contribution to journalReview article

Developing maps of fitness consequences for plant genomes

Joly-Lopez, Z., Flowers, J. M. & Purugganan, M. D., Apr 1 2016, In : Current Opinion in Plant Biology. 30, p. 101-107 7 p.

Research output: Contribution to journalReview article

How many ways are there to make a root?

Birnbaum, K. D., Dec 1 2016, In : Current Opinion in Plant Biology. 34, p. 61-67 7 p.

Research output: Contribution to journalReview article

Network inference from multimodal data: A review of approaches from infectious disease transmission

Ray, B., Ghedin, E. & Chunara, R., Dec 1 2016, In : Journal of Biomedical Informatics. 64, p. 44-54 11 p.

Research output: Contribution to journalReview article

Nitrate Transport, Sensing, and Responses in Plants

O'Brien, JA. A., Vega, A., Bouguyon, E., Krouk, G., Gojon, A., Coruzzi, G. & Gutiérrez, RA. A., 2016, In : Molecular Plant. 9, 6, p. 837-856 20 p.

Research output: Contribution to journalReview article

Programmed cell death acts at different stages of Drosophila neurodevelopment to shape the central nervous system

Pinto-Teixeira, F., Konstantinides, N. & Desplan, C., Aug 1 2016, In : FEBS Letters. p. 2435-2453 19 p.

Research output: Contribution to journalReview article