CVG Journal Club History

September 26, 2024

• Monthly Theme: How AI Gives US Wings?!
• Science Topic: AI for Genomics Discovery
  Michelle Liu (Weiss Lab)
  Majima, Koichiro, et al. "LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors." Bioinformatics (2024): btae520. Article
• DEI Topic: How Scientists Leveral AI
  Fred Fazan (Pugh Lab)
  Huang, Jonathan, et al. "Generative artificial intelligence for chest radiograph interpretation in the emergency department." JAMA network open 6.10 (2023): e2336100-e2336100. Article

October 31, 2024

• Monthly Theme: Feeding Your Genes
• Science Topic: Nutrition and Metabolism
  Kathyani Parasram (Buchon Lab)
  Fan, Yun, et al. "Caloric restriction remodels the hepatic chromatin landscape and bile acid metabolism by modulating the gut microbiota." Genome Biology 24.1 (2023): 98. Article
• DEI Topic: Sustaining STEM Talent in Academia
  Deepthi Mahishi (Yapici Lab)
  Spoon, Katie, et al. "Gender and retention patterns among US faculty." Science advances 9.42 (2023): eadi2205. Article

December 5, 2024

• Monthly Theme: Stars Within and Beyond
• Science Topic: Astrobiology and Genomics
  Akshayakeerthi Arthanarisami (Grimson and Rudd Labs)
  Garrett-Bakelman, Francine E., et al. "The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight." Science 364.6436 (2019): eaau8650. Article
• DEI Topic: Ethics of Gene Therapies
  Jenna Todero (Sethupathy Lab)
  Kratzer, Kateryna, et al. "Addressing the dark matter of gene therapy: technical and ethical barriers to clinical application." Human genetics 141.6 (2022): 1175-1193.. Article

September 28, 2023

• Science Discussion: AI and Genomics
  Adam He (Danko Lab)
  Linder, Johannes, et al. "Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation." bioRxiv (2023): 2023-08. Article
• DEI & Ethics in Science: Mental Health in STEM
  Jingyi Chen (White Lab)
  Jachim, Sarah K., et al. "A single-center assessment of mental health and well-being in a biomedical sciences graduate program." Nature biotechnology 41.5 (2023): 728-733. Article

October 26, 2023

• Science Discussion: Conservation Genomics
  Connor Kean (Grimson & Rudd Labs)
  Guhlin, J., Le Lec, M.F., Wold, J. et al. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 7, 1693–1705 (2023). Article
• DEI & Ethics in Science: Tenure Discrimination
  Daryl Phuong (Schimenti Lab)
  Gender and Race Differences in Faculty Assessment of Tenure Clarity: The Influence of Departmental Relationships and Practices - Rodica Lisnic, Anna Zajicek, Shauna Morimoto, 2019. Article

December 7, 2023

• Science Discussion: Synthetic Biology
  Yannis Ntekas (De Vlaminck Lab)
  Stranford DM, Simons LM, Berman KE, Cheng L, DiBiase BN, Hung ME, Lucks JB, Hultquist JF, Leonard JN. Genetically encoding multiple functionalities into extracellular vesicles for the targeted delivery of biologics to T cells. Nature Biomedical Engineering. 2023 Nov 27:1-8. Article
• DEI & Ethics in Science: Having a difficult conversation with a PI
  Sarah Saddoris (Parrish Lab)
  Griffin KA, Stone J, Dissassa DT, Hall TN, Clarke A. Surviving or flourishing: how relationships with principal investigators influence science graduate students’ wellness. Studies in Graduate and Postdoctoral Education. 2023 Jan 2;14(1):47-62. Article

January 25, 2024

• Science Discussion: Tissue Regeneration
  Kuang-Tse Wang (Adler Lab)
  Sun, Q., Lee, W., Hu, H. et al. Dedifferentiation maintains melanocyte stem cells in a dynamic niche. Nature 616, 774–782 (2023). Article
• DEI & Ethics in Science: Neurodiversity in STEM
  Chloe Cheng (Barrow Lab)
  Syharat, Connie Mosher, Alexandra Hain, Arash E. Zaghi, Rachael Gabriel, and Catherine GP Berdanier. "Experiences of neurodivergent students in graduate STEM programs." Frontiers in Psychology 14 (2023): 1149068. Article

February 29, 2024

• Science Discussion: Transgenerational epigenetic memory
  Satyam Srivastav (Feschotte and Clark Labs)
  Beltran T, Shahrezaei V, Katju V, Sarkies P. Epimutations driven by small RNAs arise frequently but most have limited duration in Caenorhabditis elegans. Nature Ecology & Evolution. 2020 Nov;4(11):1539-48. Article
• DEI & Ethics in Science: Difficulties faced by the global south in publishing
  Jessica Noll (Diel Lab)
  Rodríguez Mega E. Latin America’s bird scientists issue manifesto to end marginalization. Science. 2023;379:527. Article
  Ortega RP. Rare dinosaur heads home as Germany agrees to return Brazilian fossil. Science website [acessado em 22/07/2022]. doi. 2022;10. Article

March 28, 2024

• Science Discussion: Genomics and climate change
  Arielle Fogel(Clark Lab)
  Oliver Kersten et al. ,Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change.Sci. Adv.9,eadh1407(2023).DOI:10.1126/sciadv.adh1407 Article
• DEI & Ethics in Science: Difficulties faced by first gen students
  Dan Sprockett (Moeller Lab)
  Wofford, A.M., Griffin, K.A. & Roksa, J. Unequal expectations: First-generation and continuing-generation students’ anticipated relationships with doctoral advisors in STEM. High Educ 82, 1013–1029 (2021). https://doi.org/10.1007/s10734-021-00713-8 Article

May 2, 2024

• Science Discussion: Novel methods and model organisms in genomics studies
  Jonathon Tomalla (Wolfner and Schimenti Labs)
  Lu MW, Beh LY, Yerlici VT, Fang W, Kulej K, Garcia BA, Landweber LF. Exploration of the Nuclear Proteomes in the Ciliate Oxytricha trifallax. Microorganisms. 2023; 11(2):343. Article
• DEI & Ethics in Science: Ethics of Peer Review
  Meihong Shi (Duan Lab)
  Tennant, J.P., Ross-Hellauer, T. The limitations to our understanding of peer review. Res Integr Peer Rev 5, 6 (2020). Article

September 29, 2022

• Discussion Topics: Ethical Issues in Genomics and DEI in Science: LGBTQ+ in STEM
• Alexx Shumway (Sethupathy Lab)
  Gonsalves GS, Mayer K, Beyrer C. Déjà vu All Over Again? Emergent Monkeypox, Delayed Responses, and Stigmatized Populations. Journal of Urban Health. 2022 Aug;99(4):603-6. Article
• Renna Costa (Crickard Lab)
  Tarazi S, Aguilera-Castrejon A, Joubran C, Ghanem N, Ashouokhi S, Roncato F, Wildschutz E, Haddad M, Oldak B, Gomez-Cesar E, Livnat N. Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs. Cell. 2022 Sep 1;185(18):3290-306. Article

October 27, 2022

• Brian Aguilera (Kurpios Lab)
  DEI in Science: Lack of Diversity in Biobanks
  Fatumo S, Chikowore T, Choudhury A, Ayub M, Martin AR, Kuchenbaecker K. A roadmap to increase diversity in genomic studies. Nature Medicine. 2022 Feb;28(2):243-50. Article
• Heesoo Jeong (Vacanti Lab)
  Computational Modeling Techniques for Genomics
  Katzir R, Polat IH, Harel M, Katz S, Foguet C, Selivanov VA, Sabatier P, Cascante M, Geiger T, Ruppin E. The landscape of tiered regulation of breast cancer cell metabolism. Scientific reports. 2019 Nov 28;9(1):1-2. Article

December 1, 2022

• Sagar R. Shah (Lis and Yu Labs)
  DEI in Science: Scientific Communication & Social Media
  Habibi, Sarah A., and Lidya Salim. "Static vs. dynamic methods of delivery for science communication: A critical analysis of user engagement with science on social media." PLoS One 16.3 (2021): e0248507. Article
• Chloe Cheng (Barrow Lab)
  Li VL, He Y, Contrepois K, Liu H, Kim JT, Wiggenhorn AL, Tanzo JT, Tung AS, Lyu X, Zushin PJ, Jansen RS. An exercise-inducible metabolite that suppresses feeding and obesity. Nature. 2022 Jun;606(7915):785-90. Article

January 26, 2023

• DEI & Ethics in Science: Pregnancy Discrimination in Higher Education
  Sarah Saddoris (Schang Lab)
  Morgan, Allison C., et al. "The unequal impact of parenthood in academia." Science Advances 7.9 (2021): eabd1996. Article
• Science Discussion: Spatial Genomics Technologies
  Julien Morival (Lammerding Lab)
  Rao, Anjali, et al. "Exploring tissue architecture using spatial transcriptomics." Nature 596.7871 (2021): 211-220. Article

February 23, 2023

• DEI & Ethics in Science: Lack of Diversity in Biobanks
  Daryl Phuong (Schimenti Lab)
  Manolio TA. Using the data we have: improving diversity in genomic research. The American Journal of Human Genetics. 2019 Aug 1;105(2):233-6. Article
• Science Discussion: Cancer Immunotherapy
  Leanne Donahue (White Lab)
  Tichet, Mélanie, et al. "Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8+ T cells and reprogramming macrophages." Immunity 56.1 (2023): 162-179. Article

March 30, 2023

• DEI & Ethics in Science: Current topics in DEI
  Mercedes Carro (Cohen Lab)
  Kaiser R, White R. What happens on the ice, stays on the ice: transgression and layered silence in Antarctica. Current Issues in Criminal Justice. 2022 Jul 3;34(3):239-54. Article
• Science Discussion: Genomics of marine organisms
  Mitch Lokey (Clark and Messer Labs)
  Stanhope MJ, Ceres KM, Sun Q, Wang M, Zehr JD, Marra NJ, Wilder AP, Zou C, Bernard AM, Pavinski-Bitar P, Lokey MG. Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead. Iscience. 2023 Jan 20;26(1):105815. Article

May 4, 2023

• DEI & Ethics in Science: Ethics of direct to consumer genetic testing
  Yiqin Wang (O'Brien and Clark Labs)
  KLewis AC, Green RC. Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues. Genome Medicine. 2021 Dec;13:1-0. Article
• Science Discussion: Visualization Methods for Genomics Data
  Madhav Mantri (De Vlaminck Lab)
  Chari T, Banerjee J, Pachter L. The specious art of single-cell genomics. BioRxiv. 2021 Aug 26:2021-08. Article

May 5, 2022
  DEI in Science: AAPI Heritage Month

• Elena Panizza (Cerione lab)
  Pensky J, Richardson C, Serrano A, Gorski G, Price AN, Zimmer M. Disrupt and demystify the unwritten rules of graduate school. Nature Geoscience. 2021 Aug;14(8):538-9. Article
• Blake Mitchell (Aydemir lab)
  Laudisi F, Stolfi C, Bevivino G, Maresca C, Franzè E, Troncone E, Lolli E, Marafini I, Pietrucci D, Teofani A, Di Grazia A, Di Fusco D, Colantoni A, Ortenzi A, Desideri A, Monteleone I, Monteleone G. GATA6 Deficiency Leads to Epithelial Barrier Dysfunction and Enhances Susceptibility to Gut Inflammation. J Crohns Colitis. 2022 Feb 23;16(2):301-311. doi: 10.1093/ecco-jcc/jjab145. PMID: 34374415. pdf

March 31, 2022
  DEI in Science: Women's History Month

• Anusha Shankar (Lovette and Vitousek labs)
  Responses to 10 Common Criticisms of Anti-Racism Action in STEM
• Matt Edwards (Koren lab)
  Nakatani T, Lin J, Ji F, Ettinger A, Pontabry J, Tokoro M, Altamirano-Pacheco L, Fiorentino J, Mahammadov E, Hatano Y, Van Rechem C. DNA replication fork speed underlies cell fate changes and promotes reprogramming. Nature Genetics. 2022 Mar 7:1-0. Article

January 27, 2022
  DEI in Science: Mentorship of Minorities in STEM

• Madhav Mantri (De Vlaminck lab)
  The Role of Mentoring in Promoting Diversity, Equity, and Inclusion in STEM Education and Research Andrea G. Marshall, Zer Vue, Caroline B. Palavicino-Maggio, Elsie C. Spencer, Heather K. Beasley, Edgar Garza-Lopez, Zachary Conley, Kit Neikirk, Sandra A. Murray, Denise Martinez, Jamaine Davis, Lillian Brady, Haysetta D. Shuler, Derrick Morton, Antentor Hinton Jr. doi: https://doi.org/10.1101/2021.12.08.471502 Preprint
• Carolline Ascencao (Smolka lab)
  Phosphoproteomics of ATR signaling in mouse testes. Sims JR, Faca VM, Periera C, Ascencao C, Comstock W, Bada J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. eLife. In Press.

December 2, 2021
  Genomics & the Gut Microbiome
  DEI in Science: Native American Heritage Month

• Rosanna Ma (Sethupathy lab)
  Burns AR, Miller E, Agarwal M, Rolig AS, Milligan-Myhre K, Seredick S, Guillemin K, Bohannan BJ. Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model. Proceedings of the National Academy of Sciences. 2017 Oct 17;114(42):11181-6. pdf
• Min-Ting Lee (E. Johnson lab)
  Javdan B, Lopez JG, Chankhamjon P, Lee YC, Hull R, Wu Q, Wang X, Chatterjee S, Donia MS. Personalized mapping of drug metabolism by the human gut microbiome. Cell. 2020 Jun 25;181(7):1661-79. Article
• Kaydine Edwards (Barrow lab)
  Bjursell MK, Martens EC, Gordon JI. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. Journal of biological chemistry. 2006 Nov 24;281(47):36269-79. Article

October 28, 2021
  Cancer Genomics (Breast Cancer Awareness Month)
  DEI in Science: Disparities in Health Care

• Austin Hovland (Simoes-Costa lab)
  Vrdoljak E, Gligorov J, Wierinck L, Conte P, De Grève J, Meunier F, Palmieri C, Travado L, Walker A, Wiseman T, Wuerstlein R. Addressing disparities and challenges in underserved patient populations with metastatic breast cancer in Europe. The Breast. 2020 Dec 13. Article
• Madhav Mantri (De Vlaminck lab)
  Oren Y, Tsabar M, Cuoco MS, Amir-Zilberstein L, Cabanos HF, Hütter JC, Hu B, Thakore PI, Tabaka M, Fulco CP, Colgan W. Cycling cancer persister cells arise from lineages with distinct programs. Nature. 2021 Aug;596(7873):576-82. Article
• Adam He (Danko lab)
  Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS, Nimmakayalu M. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nature Genetics. 2020 Nov;52(11):1178-88. Article

September 30, 2021
  Genomics of Companion Animals
  DEI in Science: Hispanic / Latinx Heritage Month

• Hector Loyola Irizarry (Brito lab)
  Danila MI, Allison JJ, Goins KV, Chiriboga G, Fischer M, Puliafico M, Mudano AS, Rahn EJ, Merchant J, Lawrence CE, Dunkel L. Development of a multi-component intervention to promote participation of Black and Latinx individuals in biomedical research. Journal of Clinical and Translational Science. 2021;5(1). Article
• Tatiane Kanno (Simoes-Costa lab)
  Bannasch DL, Kaelin CB, Letko A, Loechel R, Hug P, Jagannathan V, Henkel J, Roosje P, Hytönen MK, Lohi H, Arumilli M. Dog colour patterns explained by modular promoters of ancient canid origin. Nature ecology & evolution. 2021 Aug 12:1-9. Article
• Sylvia Chang (Feschotte lab)
  Kwon Y, Vranken N, Hoge C, Lichak MR, Francis KX, Camacho-Garcia J, Bista I, Wood J, McCarthy S, Chow W, Tan HH. Genomic consequences of domestication of the Siamese fighting fish. bioRxiv. 2021 Jan 1. Article

May 27, 2021

• Viviana Maymi (Rudd Lab)
  Temba GS, Kullaya V, Pecht T, Mmbaga BT, Aschenbrenner AC, Ulas T, Kibiki G, Lyamuya F, Boahen CK, Kumar V, Joosten LA. Urban living in healthy Tanzanians is associated with an inflammatory status driven by dietary and metabolic changes. Nature Immunology. 2021 Mar;22(3):287-300. Article
• Josh Jones (Brito Lab)
  Cheng S, Li Z, Gao R, Xing B, Gao Y, Yang Y, Qin S, Zhang L, Ouyang H, Du P, Jiang L. A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. Cell. 2021 Feb 4;184(3):792-809. Article

April 29, 2021

• Alexandra Chivu (Danko Lab) and Ethan Sanford (Smolka Lab)
  Mahdessian D, Cesnik AJ, Gnann C, Danielsson F, Stenström L, Arif M, Zhang C, Le T, Johansson F, Shutten R, Bäckström A. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. Nature. 2021 Feb;590(7847):649-54. Article
• Mauricio Paramo (H. Yu Lab)
  Lee JD, Paulo JA, Posey RR, Mugoni V, Kong NR, Cheloni G, Lee YR, Slack FJ, Tenen DG, Clohessy JG, Gygi SP. Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. Nature Methods. 2021 Mar;18(3):293-302. Article

March 25, 2021 4:00 - 4:30 pm

• Divya Ganapathi Sankaran (Grimson Lab)
  Coyle SM, Flaum EM, Li H, Krishnamurthy D, Prakash M. Coupled active systems encode an emergent hunting behavior in the unicellular predator Lacrymaria olor. Current Biology. 2019 Nov 18;29(22):3838-50. Article
• Watch a video of hunting behavior! video

February 25, 2021

• Lauren Walter (Cosgrove Lab)
  Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE. Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome biology. 2020 Dec;21(1):1-21. Article
• Adriana Alexander (Cohen & Danko Labs)
  Maxwell KG, Augsornworawat P, Velazco-Cruz L, Kim MH, Asada R, Hogrebe NJ, Morikawa S, Urano F, Millman JR. Gene-edited human stem cell–derived β cells from a patient with monogenic diabetes reverse preexisting diabetes in mice. Science translational medicine. 2020 Apr 22;12(540). Article
• Sangeeta Ghuwalewala (Tumbar Lab)
  Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma. Cell. 2020 Jul 23;182(2):497-514. Article

January 28, 2021

• Austin Hovland (Simoes-Costa lab)
  da Silveira WA, Fazelinia H, Rosenthal SB, Laiakis EC, Kim MS, Meydan C, Kidane Y, Rathi KS, Smith SM, Stear B, Ying Y. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. Cell. 2020 Nov 25;183(5):1185-201. Article
• Kieran Koch-Laskowski (Sethupathy Lab)
  Malkani S, Chin CR, Cekanaviciute E, Mortreux M, Okinula H, Tarbier M, Schreurs AS, Shirazi-Fard Y, Tahimic CG, Rodriguez DN, Sexton BS. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. Cell Reports. 2020 Dec 8;33(10):108448. Article

December 3, 2020

• Albert Vill (Brito Lab)
  Ignacio-Espinoza JC, Laperriere S, Yeh YC, Weissman J, Hou S, Long A, Fuhrman JA. Ribosome-linked mRNA-rRNA chimeras reveal active novel virus-host associations. bioRxiv. 2020 Oct 30. Article

October 29, 2020

• R. Nicolas Lou (Therkildsen lab)
  Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T. Population genomics of the Viking world. Nature. 2020 Sep;585(7825):390-6. Article
• Seoyeon Lee(Soloway lab)
  Oguri Y, Shinoda K, Kim H, Alba DL, Bolus WR, Wang Q, Brown Z, Pradhan RN, Tajima K, Yoneshiro T, Ikeda K. CD81 controls beige fat progenitor cell growth and energy balance via FAK signaling. Cell. 2020 Aug 6;182(3):563-77. Article
• Luye An (White lab)
  Shwartz Y, Gonzalez-Celeiro M, Chen CL, Pasolli HA, Sheu SH, Fan SM, Shamsi F, Assaad S, Lin ET, Zhang B, Tsai PC. Cell Types Promoting Goosebumps Form a Niche to Regulate Hair Follicle Stem Cells. Cell. 2020 Aug 6;182(3):578-93. Article

September 24, 2020

• Bhargav Sanketi (Kurpios lab)
  Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Granillo AO, Wang Y, Robb S, Schnittker R, Zhang S. Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates. Science. 2020 Sep 4;369(6508). Article
• Ky'ara Carr (Cohen lab)
  He W, Rao HP, Tang S, Bhagwat N, Kulkarni DS, Ma Y, Chang MA, Hall C, Bragg JW, Manasca HS, Baker C. Regulated proteolysis of MutSγ controls meiotic crossing over. Molecular cell. 2020 Apr 2. Article