HudsonAlpha Journal Club

The HudsonAlpha Journal Club gives trainees at the Institute an opportunity to present and discuss publications relevant to their research areas. The meetings provide the trainees in HudsonAlpha labs valuable experience with science communication and presentations. Journal Club is hosted by HudsonAlpha faculty investigator Sara Cooper, PhD.

Upcoming Journal Club Meetings

Emily Gordon

Enhancer reprogramming promotes pancreatic cancer metastasis

Michelle Amaral

Topic TBD

Megan Breitbach

Topic TBD

Previous Paper Discussions

  • 2017 Presentations

    Nick Cochran, October 25, 2017

    Shinmyo, Yohei, Yukari Terashita, Tung Anh Dinh Duong, Toshihide Horiike, Muneo Kawasumi, Kazuyoshi Hosomichi, Atsushi Tajima, and Hiroshi Kawasaki. “Folding of the Cerebral Cortex Requires Cdk5 in Upper-Layer Neurons in Gyrencephalic Mammals.” Cell Reports 20, no. 9 (2017): 2131-2143.


    Drew Hardigan, September 20, 2017

    Patel, Shashank J., Neville E. Sanjana, Rigel J. Kishton, Arash Eidizadeh, Suman K. Vodnala, Maggie Cam, Jared J. Gartner et al. “Identification of essential genes for cancer immunotherapy.” Nature 548, no. 7669 (2017): 537-542.


    Jana Whittle, September 13, 2017

    Ezkurdia, Iakes, Jose Manuel Rodriguez, Enrique Carrillo-de Santa Pau, Jesús Vázquez, Alfonso Valencia, and Michael L. Tress. “Most highly expressed protein-coding genes have a single dominant isoform.” Journal of proteome research 14, no. 4 (2015): 1880-1887.


    Ryne Ramaker, August 16, 2017

    Dixit, Atray, Oren Parnas, Biyu Li, Jenny Chen, Charles P. Fulco, Livnat Jerby-Arnon, Nemanja D. Marjanovic et al. “Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens.” Cell 167, no. 7 (2016): 1853-1866.


    Emily Ross, August 2, 2017

    Musah, Samira, Akiko Mammoto, Thomas C. Ferrante, Sauveur SF Jeanty, Mariko Hirano-Kobayashi, Tadanori Mammoto, Kristen Roberts et al. “Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip.” Nature biomedical engineering 1 (2017).


    Timley Watkins, July 19, 2017

    Halpern, Keren Bahar, Rom Shenhav, Orit Matcovitch-Natan, Beáta Tóth, Doron Lemze, Matan Golan, Efi E. Massasa et al. “Single-cell spatial reconstruction reveals global division of labour in the mammalian liver.” Nature 542, no. 7641 (2017): 352-356.


    Matthew Neu, July 5, 2017

    Stessman, H.A., Xiong, B., Coe, B.P., Wang, T., Hoekzema, K., Fenckova, M., Kvarnung, M., Gerdts, J., Trinh, S., Cosemans, N. and Vives, L., 2017. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nature genetics, 49(4), pp.515-526.


    Brian Moyers, June 21, 2017

    Li, S., Alvarez, R.V., Sharan, R., Landsman, D. and Ovcharenko, I., 2016. Quantifying deleterious effects of regulatory variants. Nucleic acids research, 45(5), pp.2307-2317.


    James Lawlor, June 7, 2017

    Zhang, Yu, Lin An, Feng Yue, and Ross C. Hardison. “Jointly characterizing epigenetic dynamics across multiple human cell types.” Nucleic acids research 44, no. 14 (2016): 6721-6731.


    Kimberly Hobbs, May 24, 2017

    Klann, Tyler S., Joshua B. Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B. Hilton, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.” Nature biotechnology (2017).


    Kevin Bowling, May 3, 2017

    Saleheen, Danish, Pradeep Natarajan, Irina M. Armean, Wei Zhao, Asif Rasheed, Sumeet A. Khetarpal, Hong-Hee Won et al. “Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity.” Nature 544, no. 7649 (2017): 235-239.


    Jaimie Richards, April 19, 2017

    Yusuf, Rafeek A., Deevakar Rogith, Shelly RA Hovick, Susan K. Peterson, Allison M. Burton‐Chase, Bryan M. Fellman, Yisheng Li, Carolyn McKinney, Elmer V. Bernstam, and Funda Meric‐Bernstam. “Attitudes toward molecular testing for personalized cancer therapy.” Cancer 121, no. 2 (2015): 243-250.


    Megan Breitbach, April 5, 2017

    Erikson, Galina A., Dale L. Bodian, Manuel Rueda, Bhuvan Molparia, Erick R. Scott, Ashley A. Scott-Van Zeeland, Sarah E. Topol et al. “Whole-genome sequencing of a healthy aging cohort.” Cell 165, no. 4 (2016): 1002-1011.


    Michelle Amaral, March 15, 2017

    Sambandan, S., Akbalik, G., Kochen, L., Rinne, J., Kahlstatt, J., Glock, C., … & Schuman, E. M. (2017). Activity-dependent spatially localized miRNA maturation in neuronal dendrites. Science, 355(6325), 634-637.


    Emily Gordon, March 1, 2017

    Verissimo, C. S., Overmeer, R. M., Ponsioen, B., Drost, J., Mertens, S., Verlaan-Klink, I., … & Bernards, R. (2016). Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening. eLife, 5, e18489.


    Krysta Engel, February 15, 2017

    Jagannathan, S., & Bradley, R. K. (2016). Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Research, 26(12), 1639-1650.


    Nick Cochran, January 25, 2017

    Chailangkarn, T., Trujillo, C. A., Freitas, B. C., Hrvoj-Mihic, B., Herai, R. H., Diana, X. Y., … & Stefanacci, L. (2016). A human neurodevelopmental model for Williams syndrome. Nature, 536(7616), 338-343.


    Surya Chhetri, January 13, 2016

    Domcke, S., Bardet, A. F., Ginno, P. A., Hartl, D., Burger, L., & Schübeler, D. (2015). Competition between DNA methylation and transcription factors determines binding of NRF1. Nature.

  • 2016 Presentations

    Drew Hardigan, December 7, 2016

    Javierre, Biola M., Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns et al. “Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.” Cell 167, no. 5 (2016): 1369-1384.


    Brittany Lasseigne, November 16, 2016

    Hause, R. J., Pritchard, C. C., Shendure, J., & Salipante, S. J. (2016). Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine.


    Ryan Ramaker, November 2, 2016

    Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Välimäki, N., … & Kondelin, J. (2015). CTCF/cohesin-binding sites are frequently mutated in cancer. Nature genetics, 47(7), 818-821.


    Jaimie Richards, October 19, 2016

    Ewing, A., Thompson, N., & Ricks-Santi, L. (2015). Strategies for enrollment of African Americans into cancer genetic studies. Journal of Cancer Education, 30(1), 108-115.

    Keenan, T., Moy, B., Mroz, E. A., Ross, K., Niemierko, A., Rocco, J. W., … & Bardia, A. (2015). Comparison of the genomic landscape between primary breast cancer in African American versus white women and the association of racial differences with tumor recurrence. Journal of Clinical Oncology, JCO-2015.


    Timley Watkins, October 5, 2016

    Chew, W. L., Tabebordbar, M., Cheng, J. K., Mali, P., Wu, E. Y., Ng, A. H., … & Church, G. M. (2016). A multifunctional AAV-CRISPR-Cas9 and its host response. Nature Methods, 13(10), 868-874.


    Matthew Neu, September 15, 2016

    Krishnan, A., Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., … & Troyanskaya, O. G. (2016). Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nature Neuroscience.