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Comment/debate
2019

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

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: 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

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

Isolation of biologically active compounds from mangrove sediments

Solntsev, K. M., Schramm, S., Kremb, S., Gunsalus, K. C. & Amin, S. A., Oct 1 2019, In : Analytical and Bioanalytical Chemistry. 411, 25, p. 6521-6529 9 p.

Research output: Contribution to journalComment/debate

Open Access
2018

Corrigendum: 5-Formylcytosine mediated DNA - Protein cross-links block DNA replication and induce mutations in human cells (Nucleic Acids Research (2018) 46:13 (6455-6469) DOI: 10.1093/nar/gky444)

Ji, S., Fu, I., Naldiga, S., Shao, H., Basu, A. K., Broyde, S. & Tretyakova, N. Y., 2018, In : Nucleic acids research. 46, 18, 1 p.

Research output: Contribution to journalComment/debate

Corrigendum: Landscape of X chromosome inactivation across human tissues

Tukiainen, T., Villani, A. C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., Aguirre, M., Gauthier, L., Fleharty, M., Kirby, A., Cummings, B. B., Castel, S. E., Karczewski, K. J., Aguet, F., Byrnes, A., Consortium, GTE., Lappalainen, T., Regev, A., Ardlie, K. G., Hacohen, N. & 1 others, MacArthur, D. G., Mar 7 2018, In : Nature. 555, 7695, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Erratum: Correction: A sibling method for identifying vQTLs (PloS one (2018) 13 4 (e0194541))

Conley, D., Johnson, R., Domingue, B., Dawes, C., Boardman, J. & Siegal, M. L., 2018, In : PloS one. 13, 5, p. e0196881

Research output: Contribution to journalComment/debate

Open Access

Erratum to: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions (Nature, (2015), 528, 7583, (517-522), 10.1038/nature16193)

Huang, W., Thomas, B., Flynn, R. A., Gavzy, S. J., Wu, L., Kim, S. V., Hall, J. A., Miraldi, E. R., Ng, C. P., Rigo, F., Meadows, S., Montoya, N. R., Herrera, N. G., Domingos, A. I., Rastinejad, F., Myers, R. M., Fuller-Pace, F. V., Bonneau, R., Chang, H. Y., Acuto, O. & 1 others, Littman, D. R., Oct 4 2018, In : Nature. 562, 7725, 1 p.

Research output: Contribution to journalComment/debate

Translating microbiome futures

Taroncher-Oldenburg, G., Jones, S., Blaser, M., Bonneau, R., Christey, P., Clemente, J. C., Elinav, E., Ghedin, E., Huttenhower, C., Kelly, D., Kyle, D., Littman, D., Maiti, A., Maue, A., Olle, B., Segal, L., van Hylckama Vlieg, J. E. T. & Wang, J., Nov 9 2018, In : Nature Biotechnology. 36, 11, p. 1037-1042 6 p.

Research output: Contribution to journalComment/debate

2017

Corrigendum to: CTCF-mediated topological boundaries during development foster appropriate gene regulation (Genes & Development, (2016), 30, (2657–2662), 10.1101/gad.288324.116)

Narendra, V., Bulajić, M., Dekker, J., Mazzoni, E. O. & Reinberg, D., Aug 15 2017, In : Genes and Development. 31, 16, p. 2657-2662 6 p.

Research output: Contribution to journalComment/debate

Molecular genetics: Chaperone protein gets personal

Siegal, M. L., May 4 2017, In : Nature. 545, 7652, p. 36-37 2 p.

Research output: Contribution to journalComment/debate

2016

Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

Huang, W., Thomas, B., Flynn, R. A., Gavzy, S. J., Wu, L., Kim, S. V., Hall, J. A., Miraldi, E. R., Ng, C. P., Rigo, F., Meadows, S., Montoya, N. R., Herrera, N. G., Domingos, A. I., Rastinejad, F., Myers, R. M., Fuller-Pace, F. V., Bonneau, R., Chang, H. Y., Acuto, O. & 1 others, Littman, D. R., May 5 2016, In : Nature. 533, 7601, 1 p.

Research output: Contribution to journalComment/debate

Erratum: An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses (Cell (2015) 163 (381-393))

Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., Lee, J. Y., Ziel, J. W., Miraldi, E. R., Domingos, A. I., Bonneau, R. & Littman, D. R., Jan 14 2016, In : Cell. 164, 1-2, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (Cell (2016) 165(5) (1280–1292))

O'Malley, R. C., Huang, S. S. C., Song, L., Lewsey, M. G., Bartlett, A., Nery, J. R., Galli, M., Gallavotti, A. & Ecker, J. R., Sep 8 2016, In : Cell. 166, 6, 1 p.

Research output: Contribution to journalComment/debate

Erratum to: MINE: Module Identification in Networks[BMC Bioinformatics. (2011);12:192.]

Rhrissorrakrai, K. & Gunsalus, K. C., Feb 17 2016, In : BMC bioinformatics. 17, 1, 89.

Research output: Contribution to journalComment/debate

Evolution of plant phenotypes, from genomes to traits

Casacuberta, J. M., Jackson, S., Panaud, O., Purugganan, M. & Wendel, J., 2016, In : G3: Genes, Genomes, Genetics. 6, 4, p. 775-778 4 p.

Research output: Contribution to journalComment/debate

Systems genetics of plant adaptation to environmental stresses

Groen, S. C. & Purugganan, M. D., 2016, In : Applications in Plant Sciences. 103, 12, p. 2019-2021 3 p.

Research output: Contribution to journalComment/debate

2015

Breaking TADs: Insights into hierarchical genome organization

Rocha, P. P., Raviram, R., Bonneau, R. & Skok, J. A., Jun 1 2015, In : Epigenomics. 7, 4, p. 523-526 4 p.

Research output: Contribution to journalComment/debate

Erratum: Pathogen cell-to-cell variability drives heterogeneity in host immune responses ((Cell (2015) 162 (1309-1321))

Avraham, R., Haseley, N., Brown, D., Penaranda, C., Jijon, H. B., Trombetta, J. J., Satija, R., Shalek, A. K., Xavier, R. J., Regev, A. & Hung, D. T., Oct 8 2015, In : Cell. 163, 2, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (Cell Systems (2015) 1 (72-87) )

Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., Gandara, D. & 26 others, Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O'Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O'halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S. & Mason, C. E., Jul 29 2015, In : Cell Systems. 1, 1, p. 97-97.e3 13.

Research output: Contribution to journalComment/debate

Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells (Nature (2014) 516 (5661) DOI:10.1038/nature13920)

Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., DaleyKeyser, A. J., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., Ferrante, T. C., Regev, A., Daley, G. Q. & Collins, J. J., Mar 5 2015, In : Nature. 519, 7541, 1 p.

Research output: Contribution to journalComment/debate

The Expendables: Natural selection driving reduced gene function (Comment on DOI 10.1002/bies.201500083)

Bernstein, M. R. & Rockman, M. V., Nov 2015, In : BioEssays. 37, 11, 1 p.

Research output: Contribution to journalComment/debate

2014

Corrigendum to 3D arrays for high throughput assay of cell migration and electrotaxis [Cell Biol Int 37, 995-1002]

Zhao, S., Gao, R., Devreotes, P. N., Mogilner, A. & Zhao, M., Aug 2014, In : Cell Biology International. 38, 8, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Comparative analysis of RNA sequencing methods for degraded or low-input samples (Nature Methods (2013) 10 (623-629 )

Adiconis, X., Borges-Rivera, D., Satija, R., DeLuca, D. S., Busby, M. A., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., Gnirke, A., Pochet, N., Regev, A. & Levin, J. Z., 2014, In : Nature Protocols. 9, 4, 1 p.

Research output: Contribution to journalComment/debate

Erratum: Comparative analysis of RNA sequencing methods for degraded or low-input samples (Nature Methods (2013) 10 (623-629))

Adiconis, X., Borges-Rivera, D., Satija, R., Deluca, D. S., Busby, M. A., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., Gnirke, A., Pochet, N., Regev, A. & Levin, J. Z., Feb 2014, In : Nature methods. 11, 2, 1 p.

Research output: Contribution to journalComment/debate

Interpreting 4C-Seq data: How far can we go?

Raviram, R., Rocha, P. P., Bonneau, R. & Skok, J. A., Oct 1 2014, In : Epigenomics. 6, 5, p. 455-457 3 p.

Research output: Contribution to journalComment/debate

The genetics of sex: Exploring differences

Arbeitman, M. N., Kopp, A., Siegal, M. L. & Van Doren, M., Jun 2014, In : Genetics. 197, 2, p. 527-529 3 p.

Research output: Contribution to journalComment/debate

2012

Altruistic cell death and collective drug resistance

Carmona-Fontaine, C. & Xavier, J. B., 2012, In : Molecular systems biology. 8, 627.

Research output: Contribution to journalComment/debate

Balance of Activity between LN vs and Glutamatergic Dorsal Clock Neurons Promotes Robust Circadian Rhythms in Drosophila

Collins, B., Kane, E. A., Reeves, D. C., Akabas, M. H. & Blau, J., Jun 21 2012, In : Neuron. 74, 6, 1 p.

Research output: Contribution to journalComment/debate

Did the great dying of life take 700 k.y.? Evidence from global astronomical correlation of the Permian-Triassic boundary interval

Rampino, M. R. & Kaiho, K., May 2012, In : Geology. 40, 5, p. e267

Research output: Contribution to journalComment/debate

Erratum: A protein domain-based interactome network for C. elegans early embryogenesis (Cell (2008) 134 (534-545))

Boxem, M., Maliga, Z., Klitgord, N., Li, N., Lemmens, I., Mana, M., De Lichtervelde, L., Mul, J. D., Van De Peut, D., Devos, M., Simonis, N., Yildirim, M. A., Cokol, M., Kao, H. L., De Smet, A. S., Wang, H., Schlaitz, A. L., Hao, T., Milstein, S., Fan, C. & 17 others, Tipsword, M., Drew, K., Galli, M., Rhrissorrakrai, K., Drechsel, D., Koller, D., Roth, F. P., Iakoucheva, L. M., Dunker, A. K., Bonneau, R., Gunsalus, K. C., Hill, D. E., Piano, F., Tavernier, J., Van Den Heuvel, S., Hyman, A. A. & Vidal, M., Dec 21 2012, In : Cell. 151, 7, 1 p.

Research output: Contribution to journalComment/debate

Hsp90 depletion goes wild

Siegal, M. L. & Masel, J., Feb 27 2012, In : BMC Biology. 10, 14.

Research output: Contribution to journalComment/debate

The QTN program and the alleles that matter for evolution: All that's gold does not glitter

Rockman, M. V., Jan 2012, In : Evolution. 66, 1, p. 1-17 17 p.

Research output: Contribution to journalComment/debate

2011

Comment on "atmospheric PCO2perturbations associated with the central atlantic magmatic province"

Rampino, M. R. & Caldeira, K., Nov 4 2011, In : Science. 334, 6056, p. 594-b

Research output: Contribution to journalComment/debate

Erratum: Centromere clustering: Where synapsis begins ((Current Biology (2011) 21 (R920-R922))

Subramanian, V. V. & Hochwagen, A., Dec 20 2011, In : Current Biology. 21, 24, 1 p.

Research output: Contribution to journalComment/debate

2010

David fitch

Fitch, D., Oct 26 2010, In : Current Biology. 20, 20, p. R869-R871

Research output: Contribution to journalComment/debate

Mass extinctions of life and catastrophic flood basalt volcanism

Rampino, M. R., Apr 13 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 15, p. 6555-6556 2 p.

Research output: Contribution to journalComment/debate

Serotonergic mechanisms in human allergic contact dermatitis (Acta Dermato-Venereologica (2007) 87, (390-396))

El-Nour, H., Lundeberg, L., Abdelmagid, N., Lonne-Rahm, S. B., Azmitia, E. C. & Nordlind, K., 2010, In : Acta Dermato-Venereologica. 90, 5, 1 p.

Research output: Contribution to journalComment/debate

Towards a quantitative understanding of mitotic spindle assembly and mechanics

Mogilner, A. & Craig, E., Oct 15 2010, In : Journal of Cell Science. 123, 20, p. 3435-3445 11 p.

Research output: Contribution to journalComment/debate

2009

Draft genome of the filarial nematode parasite Brugia malayi (Science (2007) (1756))

Ghedin, E., Anton, B. P. & White, O., Jan 2 2009, In : Science. 323, 5910, 1 p.

Research output: Contribution to journalComment/debate

Erratum: The fifth sentence under "Protoplast Isolation and Transfection (Materials and Methods (2009)149: (1231-1239))

Bargmann, B. O. R. & Birnbaum, K. D., Jun 2009, In : Plant physiology. 150, 2, 1 p.

Research output: Contribution to journalComment/debate