Library Menu

Cold Spring Harbor Laboratory Research Papers Published in 2022*

Print Friendly, PDF & Email

*List under construction: More to be added soon!

CSHL-affiliated author names are in bold.

Caught in a Web: Emerging Roles of Neutrophil Extracellular Traps in Cancer.
He, X.-Y., Ng, D., & Egeblad, M.
(2022). Annual Review of Cancer Biology, 6(1), 223–243. https://doi.org/10.1146/annurev-cancerbio-080421-015537

Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention.
Bhattacharya, N., Thomas, N., Rao, R., Dauparas, J., Koo, P. K., Baker, D., Song, Y. S., Ovchinnikov, S.
(2022). Pacific Symposium on Biocomputing, 27, 34-45. https://doi.org/10.1142/9789811250477_0004

SciApps: An automated platform for processing and distribution of plant genomics data.
Wang, L., Lu, Z., Van Buren, P., & Ware, D.
(2022) In D. Edwards (Ed.), Plant bioinformatics: Methods and protocols. (Vol. 2443, pp. 197-209). Humana. https://doi.org/10.1007/978-1-0716-2067-0_10

Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways
Tello-Ruiz M. K., Jaiswal, P., Ware, D.
In Edwards, D. (Ed.) (2022) Plant Bioinformatics. Methods in Molecular Biology (Vol. 2443, pp. 101-131). Humana. https://doi.org/10.1007/978-1-0716-2067-0_5

Phase 1 Clinical Trial of Trametinib and Ponatinib in Patients With NSCLC Harboring KRAS Mutations.
Arbour, K. C., Manchado, E., Bott, M. J., Ahn, L., Tobi, Y., Ni, A. A., Yu, H. A., Shannon, A., Ladanyi, M., Perron, V., Ginsberg, M. S., Johnson, A., Holodny, A., Kris, M. G., Rudin, C. M., Lito, P., Rosen, N., Lowe, S., & Riely, G. J.
(2022, January). JTO Clinical and Research Reports, 3(1), 100256. https://doi.org/10.1016/j.jtocrr.2021.100256

Longitudinal Intravital Imaging Through Clear Silicone Windows.
Maiorino, L., Shevik, M., Adrover, J. M., Han, X., Georgas, E., Wilkinson, J. E., Seidner, H., Foerschner, L., Tuveson, D. A., Qin, Y. X., Egeblad, M.
(2022, January 5). Journal of Visual Experiments (JoVE), (179), e62757. https://dx.doi.org/10.3791/62757

SorghumBase: a web-based portal for sorghum genetic information and community advancement.
Gladman, N., Olson, A., Wei, S., Chougule, K., Lu, Z., Tello-Ruiz, M., Meijs, I., Van Buren, P., Jiao, Y., Wang, B., Kumar, V., Kumari, S., Zhang, L., Burke, J., Chen, J., Burow, G., Hayes, C., Emendack, Y., Xin, Z., Ware, D. 
(2022, January 11). Planta, 255(2), 35. https://doi.org/10.1007/s00425-022-03821-6

Exon-skipping antisense oligonucleotides for cystic fibrosis therapy
Kim. Y. J., Sivetz. N., Layne, J., Voss, D. M., Yang, L., Zhang, Q., Krainer, A. R.
(2022, January 18). Proceedings of the National Academy of Sciences, 119(3), e2114858118. https://doi.org/10.1073/pnas.2114858118

Hot ‘n cold: Applying the cis-regulatory code to predict heat and cold stress response in maize.
Benoit M.
(2022, January 20). The Plant Cell. 34(1), 497-498. https://doi.org/10.1093/plcell/koab269

Carcinomas assemble a filamentous CXCL12–keratin-19 coating that suppresses T cell–mediated immune attack
Wang, Z., Moresco, P., Yan, R., Li, J., Gao, Y., Biasci, D., Yao, M., Pearson, J., Hechtman, J. F., Janowitz, T., Zaidi, R. M., Weiss, M. J., Fearon. D. T.
(2022, January 25). Proceedings of the National Academy of Sciences, 119(4), e2119463119. https://doi.org/10.1073/pnas.2119463119

CyVerse for Reproducible Research: RNA-Seq Analysis
Williams, J.
(2022). In: Edwards, D. (Ed.), Plant Bioinformatics. Methods in molecular biology, (Vol. 2443. pp 57–79). Humana. https://doi.org/10.1007/978-1-0716-2067-0_3

Interrupting the nitrosative stress fuels tumor-specific cytotoxic T lymphocytes in pancreatic cancer.
De Sanctis, F., Lamolinara, A., Boschi, F., Musiu, C., Caligola, S., Trovato, R., Fiore, A., Frusteri, C., Anselmi, C., Poffe, O., Cestari, T., Canè .S., Sartoris, S., Giugno, R., Del Rosario, G., Zappacosta, B., Del Pizzo, F., Fassan, M., Dugnani, E., Piemonti, L., Bottani, E., Decimo, I., Paiella, S., Salvia, R., Lawlor, R. T., Corbo, V., Park, Y., Tuveson, D. A., Bassi, C., Scarpa, A., Iezzi, M., Ugel, S., Bronte, V.
(2022, January). Journal for ImmunoTherapy of Cancer, 10(1): e003549. http://10.1136/jitc-2021-003549

SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia
Polyanskaya, S. A., Moreno, R. Y., Lu, B., Feng, R., Yao, Y., Irani, S., Klingbeil, O., Yang, Z., Wei, Y., Demerdash, O. E., Benjamin, L. A., Weiss, M. J., Zhang, Y. J., Vakoc, C. R.
(2022, January 11). Cell Reports, 38(2), 110233. doi: https://doi.org/10.1016/j.celrep.2021.110233

Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA.
Gao,. Y., Lin, K. T., Jiang, T., Yang, Y., Rahman, M. A., Gong, S., Bai, J., Wang, L., Sun, J., Sheng, L., Krainer, A. R., Hua, Y.
(2022, January 25). Nucleic Acids Research, 50(2), 731-749. https://doi.org/10.1093/nar/gkab1280

Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung.
Concepcion, C. P., Ma, S., LaFave, L. M., Bhutkar, A., Liu, M., DeAngelo, L. P., Kim, J. Y., Del Priore, I., Schoenfeld, A. J., Miller, M., Kartha, V. K., Westcott, P. M. K., Sánchez-Rivera, F. J., Meli, K,. Gupta, M., Bronson, R. T., Riely,  G. J., Rekhtman, N., Rudin, C. M., Kim, C. F., Regev, A., Buenrostro, J. D., Jacks, T.
(2022, February 1). Cancer Discovery, 12(2): 562-585. https://doi.org/10.1158/2159-8290.CD-21-0248

Aromatase inhibitors versus tamoxifen in premenopausal women with oestrogen receptor-positive early-stage breast cancer treated with ovarian suppression: A patient-level meta-analysis of 7030 women from four randomised trials.
Early Breast Cancer Trialists’ Collaborative Group (EBCTCG).
Epub: (2022, February 3). The Lancet Oncology, 23(3), 382–392. https://doi.org/10.1016/S1470-2045(21)00758-0

Mutation bias shapes the spectrum of adaptive substitutions.
Cano, A.V., Rozhoňová, H., Stoltzfus, A., McCandlish, D. M., Payne, J. L.
(2022, February 15). Proceedings of the National Academy of Sciences119(7), e2119720119. https://doi.org/10.1073/pnas.2119720119

Development and characterization of functional antibodies targeting NMDA receptors.
Tajima, N., Simorowski, N., Yovanno, R. A., Regan, M. C.,, Michalski, K., Gómez, R., Lau, A. Y., Furukawa, H.
(2022, February 17 ). Nature Communications, 13(1), 923. https://doi.org/10.1038/s41467-022-28559-3

Bone mineral density in women newly diagnosed with breast cancer: a prospective cohort study.
Fraenkel, M., Novack, V., Mizrakli, Y., Koretz, M., Siris, E., Norton, L., Shafat, T., Geffen, D. B.
(2022, February 17). NPJ Breast Cancer, 8(1), 21. https://doi.org/10.1038/s41523-022-00388-z

Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4.
Gutbrod, M. J., Roche, B., Steinberg, J. I., Lakhani, A. A., Chang, K., Schorn, A. J., & Martienssen, R. A.
(2022, February 22). Nature Communications, 13(1), 1001. https://doi.org/10.1038/s41467-022-28554-8

SMARCA4 biology in alveolar rhabdomyosarcoma.
Bharathy, N., Cleary, M. M., Kim, J.-A., Nagamori, K., Crawford, K. A., Wang, E., Saha, D., Settelmeyer, T. P., Purohit, R., Skopelitis, D., Chang, K., Doran, J. A., Kirschbaum, C. W., Bharathy, S., Crews, D. W., Randolph, M. E., Karnezis, A. N., Hudson-Price, L., Dhawan, J., Michalek, J. E., Ciulli, A., Vakoc, C. R., Keller, C.
(2022, March 10). Oncogene, 41(11), 1647–1656. https://doi.org/10.1038/s41388-022-02205-0

Spatiotemporal 3D image registration for mesoscale studies of brain development.
Shuvaev, S., Lazutkin, A., Kiryanov, R., Anokhin, K., Enikolopov, G., & Koulakov, A. A.
(2022, March 7). Scientific Reports, 12(1), 3648. https://doi.org/10.1038/s41598-022-06871-8

Disulfiram inhibits neutrophil extracellular trap formation and protects rodents from acute lung injury and SARS-CoV-2 infection.
Adrover, J. M., Carrau, L., Daßler-Plenker, J., Bram, Y., Chandar, V., Houghton, S., Redmond, D., Merrill, J. R., Shevik, M., tenOever, B. R., Lyons, S. K., Schwartz, R. E., Egeblad, M.
(2022, March 8). JCI Insight, 7(5), e157342. https://doi.org/10.1172/jci.insight.157342.

Characterization of intrinsically disordered regions in proteins informed by human genetic diversity.
Ahmed, S. S., Rifat, Z. T., Lohia, R., Campbell, A. J., Dunker, A. K., Rahman, M. S., Iqbal, S.
(2022, March 11). PLoS Computational Biology, 18(3), e1009911. https://doi.org/10.1371/journal.pcbi.1009911

Convergent selection of a WD40 protein that enhances grain yield in maize and rice.
Chen, W., Chen, L., Zhang, X., Yang, N., Guo, J., Wang, M., Ji, S., Zhao, X., Yin, P., Cai, L., Xu, J., Zhang, L., Han, Y., Xiao, Y., Xu, G., Wang, Y., Wang, S., Wu, S., Yang, F., Jackson, D., Cheng, J., Chen, S., Sun, C., Qin, F., Tian, F., Fernie, A. R., Li, J., Yan, J., & Yang, X.
(2022, March 25). Science, 375(6587), eabg7985. https://doi.org/10.1126/science.abg7985

A Forward Genetic Approach to Identify Plasmodesmal Trafficking Regulators Based on Trichome Rescue.
Kitagawa, M., & Jackson, D.
(2022, March 30). In: Benitez-Alfonso, Y., & Heinlein, M. (Eds.) Plasmodesmata. Methods in Molecular Biology, (Vol. 2457, pp. 393–407). Humana. https://doi.org/10.1007/978-1-0716-2132-5_27

Mapping odorant receptors to their glomeruli.
Bast, W. G., Albeanu, D. F. 
(2022, April). Nature Neuroscience, 25(4), 405-407. https://doi.org/10.1038/s41593-022-01045-1

Lead identification using 3D models of pancreatic cancer.
Fernandez-Vega, V., Hou, S., Plenker, D., Tiriac, H., Baillargeon, P., Shumate, J., Scampavia, L., Seldin, J., Souza, G. R., Tuveson, D. A., & Spicer, T. P.
(2022, April). SLAS Discovery, 27(3), 159–166. https://doi.org/10.1016/j.slasd.2022.03.002

Four to the floor: Active DNA demethylation defines somatic epigenetic patterns and impacts quantitative traits.
Benoit, M.
(2022, April).  The Plant Cell, 34(4), 1149–1150. https://doi.org/10.1093/plcell/koac003

Dynamic evolution of small signalling peptide compensation in plant stem cell control.
Kwon, C. T., Tang, L., Wang, X., Gentile, I., Hendelman, A., Robitaille, G., Van Eck. J., Xu, C., & Lippman, Z. B.
(2022, April). Nature Plants, 8(4), 346–355. https://doi.org/10.1038/s41477-022-01118-w

Convergent behavioral strategies and neural computations during vocal turn-taking across diverse species.
Banerjee, A., & Vallentin, D.
(2022, April). Current Opinion Neurobiology, 73, 102529. https://doi.org/10.1016/j.conb.2022.102529

Bayes and Darwin: How replicator populations implement Bayesian computations.
Czégel, D., Giaffar, H., Tenenbaum, J. B., & Szathmáry, E.
(2022, April). BioEssays, 44(4), e2100255. https://doi.org/10.1002/bies.202100255

Special Issue: Biological Distributed Algorithms 2021.
Emek, Y., & Navlakha, S.
(2022, April). Journal of Computational Biology, 29(4), 305–305. https://doi.org/10.1089/cmb.2022.29060.ye

Patient-Derived Triple-Negative Breast Cancer Organoids Provide Robust Model Systems That Recapitulate Tumor Intrinsic Characteristics.
Bhatia, S., Kramer, M., Russo, S., Naik, P., Arun, G., Brophy, K., Andrews, P., Fan, C., Perou, C. M., Preall, J., Ha, T., Plenker, D., Tuveson, D. A., Rishi, A., Wilkinson, J. E., McCombie, W. R., Kostroff, K., & Spector, D. L.
(2022, April 1). Cancer Research, 82(7), 1174–1192. https://doi.org/10.1158/0008-5472.CAN-21-2807

A complete reference genome improves analysis of human genetic variation.
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Rhie, A., Meredith, M., Martin, S., Lee, J., Koren, S., Rosenfeld, J. A., Paten, B., Layer, R., Chin, C. S., Sedlazeck, F. J., Hansen, N. F., Miller, D. E., Phillippy, A. M., Miga, K. H., McCoy, R. C., Dennis, M. Y., Zook, J. M., & Schatz, M. C.
(2022, April 1). Science, 376(6588), eabl3533. https://doi.org/10.1126/science.abl3533

Complete genomic and epigenetic maps of human centromeres.
Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., Sauria, M. E. G., Borchers, M., Gershman, A., Mikheenko, A., Shepelev, V. A., Dvorkina, T., Kunyavskaya, O., Vollger, M. R., Rhie, A., McCartney, A. M., Asri, M., Lorig-Roach, R., Shafin, K., Lucas, J. K., Aganezov, S., Olson, D., de Lima, L. G., Potapova, T., Hartley, G. A., Haukness, M., Kerpedjiev, P., Gusev, F., Tigyi, K., Brooks, S., Young, A., Nurk, S., Koren, S., Salama, S. R., Paten, B., Rogaev, E. I., Streets, A., Karpen, G. H., Dernburg, A. F., Sullivan, B. A., Straight, A. F., Wheeler, T. J., Gerton, J. L., Eichler, E. E., Phillippy, A. M., Timp, W., Dennis, M. Y., O’Neill, R. J., Zook, J. M., Schatz, M. C., Pevzner, P. A., Diekhans, M., Langley, C. H., Alexandrov, I. A., & Miga, K. H.
(2022, April 1). Science, 376(6588), eabl4178. https://doi.org/10.1126/science.abl4178

Building an embryo: An auxin gene toolkit for zygotic and somatic embryogenesis in Brazilian pine.
Elbl, P. M., Souza, D. T. de, Rosado, D., Oliveira, L. F. de, Navarro, B. V., Matioli, S. R., & Floh, E.
(2022, April 5). Gene, 817, 146168. https://doi.org/10.1016/j.gene.2021.146168

Precise and pervasive phasic bursting in locus coeruleus during maternal behavior in mice.
Dvorkin, R., & Shea, S. D.
(2022, April 6). Journal of Neuroscience, 42(14), 2986-2999. https://doi.org/10.1523/JNEUROSCI.0938-21.2022

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect.</strong
Tareen, A., Kooshkbaghi, M., Posfai, A.,
Ireland, W. T., McCandlish, D. M., & Kinney, J. B.
(2022, April 15). Genome Biology, 23(1), 98. https://doi.org/10.1186/s13059-022-02661-7

β-Hydroxybutyrate suppresses colorectal cancer.
Dmitrieva-Posocco, O., Wong, A. C., Lundgren, P., Golos, A. M., Descamps, H. C., Dohnalová, L., Cramer, Z., Tian, Y., Yueh, B., Eskiocak, O., Egervari, G., Lan, Y., Liu, J., Fan, J., Kim, J., Madhu, B., Schneider, K. M., Khoziainova, S., Andreeva, N., Wang, Q., Li, N., Furth, E. E., Bailis, W., Kelsen, J. R., Hamilton, K. E., Kaestner, K. H., Berger, S. L., Epstein, J. A., Jain, R., Li, M., Beyaz, S., Lengner , C. J., Katona, B. W., Grivennikov, S. I., Thaiss, C. A., & Levy, M.
(2022, May). Nature. 605(7908). 160-165. https://doi.org/10.1038/s41586-022-04649-6

Oral famotidine versus placebo in non-hospitalised patients with COVID-19: a randomised, double-blind, data-intense, phase 2 clinical trial.
Brennan, C. M., Nadella, S., Zhao, X., Dima, R. J., Jordan-Martin, N., Demestichas, B. R., Kleeman, S. O., Ferrer, M., von Gablenz, E. C., Mourikis, N., Rubin, M. E., Adnani, H., Lee, H., Ha, T., Prum, S., Schleicher, C. B., Fox, S. S., Ryan, M. G., Pili, C., Goldberg, G., Crawford, J. M., Goodwin, S., Zhang, X., Preall, J. B., Costa, A. S. H., Conigliaro, J., Masci, J. R., Yang, J., Tuveson, D. A., Tracey, K. J., Janowitz, T.
(2022, May). Gut, 71(5): 879-888. http://10.1136/gutjnl-2022-326952

Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms.
Crow, M., Suresh, H., Lee, J., & Gillis, J.
(2022, May 6). Nucleic Acids Research, 50(8), 4302–4314. https://doi.org/10.1093/nar/gkac276

Sizing up whole-brain neuronal tracing.
Ascoli, G. A., Huo, B. X., Mitra, P. P.
(2022, May 15). Science Bulletin, 67(9): 883-884. https://doi.org/10.1016/j.scib.2022.01.018

Sleep Disruption and Cancer: Chicken or the Egg?
Berisha, A., Shutkind, K., & Borniger, J. C.
(2022, May 19). Frontiers in Neuroscience, 16. https://doi.org/10.3389/fnins.2022.856235

In Vivo Imaging of Circadian NET Formation During Lung Injury by Four-Dimensional Intravital Microscopy
Aroca-Crevillén, A., Hidalgo, A., & Adrover, J. M.
(2022, May 25). In: Solanas, G., Welz, P. S. (Eds.), Circadian Regulation. Methods in Molecular Biology, (Vol. 2482, pp. 285–300). Humana. https://doi.org/10.1007/978-1-0716-2249-0_19

Measuring Circadian Neutrophil Infiltration in Tissues by Paired Whole-Mount Tissue Clearing and Flow Cytometry.
Vicanolo, T., Hidalgo, A., & Adrover, J. M.
(2022, May 25). In: Solanas, G., Welz, P. S. (Eds.), Circadian Regulation. Methods in Molecular Biology, (Vol. 2482, pp. 265–284 ). Humana. https://doi.org/10.1007/978-1-0716-2249-0_18

Correction: γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans.
Chu, T. H., Khairallah, C., Shieh, J., Cho, R., Qiu, Z., Zhang, Y., Eskiocak, O., Thanassi, D. G., Kaplan, M. H., Beyaz, S., Yang, V. W., Bliska, J. B., & Sheridan, B. S.
(2022, May 25). PLOS Pathogens, 18(5), 1–1. https://doi.org/10.1371/journal.ppat.1010586

HMGB1-mediated restriction of EPO signaling contributes to anemia of inflammation.
Dulmovits, B. M., Tang, Y., Papoin, J., He, M., Li, J., Yang, H., Addorisio, M. E., Kennedy, L., Khan, M., Brindley, E., Ashley, R. J., Ackert-Bicknell, C., Hale, J., Kurita, R., Nakamura, Y., Diamond, B., Barnes, B. J., Hermine, O., Gallagher, P. G., Steiner, L. A., Lipton, J. M., Taylor, N., Mohandas, N., Andersson, U., Al-Abed, Y., Tracey, K. J., & Blanc, L.
(2022, May 26). Blood, 139(21), 3181–3193. https://doi.org/10.1182/blood.2021012048

Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy.
Kim, Y. J., Nomakuchi, T., Papaleonidopoulou, F., Yang, L., Zhang, Q., Krainer, & A. R.
(2022, May 27). Nature Communications, 13(1), 2978. https://doi.org/10.1038/s41467-022-30668-y

Internally-controlled and dynamic optical measures of functional tumor biology.
Chung, T., Garcia, L., Swamynathan, M. M., Froeling, F. E. M., Trotman, L. C., Tuveson, D. A., & Lyons, S. K.
(2022, May 31). BioRxiv. https://doi.org/10.1101/2022.05.30.493733

Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release.
Bibel, B., Elkayam, E., Silletti, S., Komives, E. A., & Joshua-Tor, L.
(2022, May 31). ELife, 11, e76908. https://doi.org/10.7554/eLife.76908

Stimulation of the hepatoportal nerve plexus with focused ultrasound restores glucose homoeostasis in diabetic mice, rats and swine.
Cotero, V., Graf, J., Miwa, H., Hirschstein, Z., Qanud, K., Huerta, T. S., Tai, N., Ding, Y., Jimenez-Cowell, K., Tomaio, J. N., Song, W., Devarajan, A., Tsaava, T., Madhavan, R., Wallace, K., Loghin, E., Morton, C., Fan, Y., Kao, T.-J., Akhtar, K., Damaraju, M., Barenboim, L., Maietta, T., Ashe, J., Tracey, K. J., Coleman, T. R., Di Carlo, D., Shin, D., Zanos, S., Chavan, S. S., Herzog, R. I., & Puleo, C.
(2022, June). Nature Biomedical Engineering, 6(6), 683–705. https://doi.org/10.1038/s41551-022-00870-w

Gene regulation by gonadal hormone receptors underlies brain sex differences.
Gegenhuber, B., Wu, M.V., Bronstein, R., Tollkuhn, J.
(2022, June). Nature, 606(7912), 153-159.  https://doi.org/10.1038/s41586-022-04686-1

Structural insights into binding of therapeutic channel blockers in NMDA receptors.
Chou, T. H., Epstein, M., Michalski, K., Fine, E., Biggin, P. C., & Furukawa, H.
(2022, June). Nature Structural & Molecular Biology, 29(6), 507-518. https://doi.org/10.1038/s41594-022-00772-0

Genome-wide association analysis and replication in 810,625 individuals with varicose veins.
Ahmed, WUR., Kleeman, S., Ng, M., Wang, W., Auton, A.; 23andMe Research Team; Lee, R., Handa, A., Zondervan, K. T., Wiberg, A.,  & Furniss, D.
(2022, June 2). Nature Communications, 13(1), 3065. https://doi.org/10.1038/s41467-022-30765-y

Evaluating the differential expression of TAM family receptors and efferocytosis activities in differentiated and polarized THP-1 macrophage.
Chamberland, M., Farrell, B., & Yeh, J.
(2022, June 21). BioRxiv, 2022.06.21.497076. https://doi.org/10.1101/2022.06.21.497076

PKR Binds Enterovirus IRESs, Displaces Host Translation Factors, and Impairs Viral Translation to Enable Innate Antiviral Signaling.
Dobrikov, M. I., Dobrikova, E. Y., McKay, Z. P., Kastan, J. P., Brown, M. C., & Gromeier, M.
(2022, June 28). MBio, 13(3), e00854-22. https://doi.org/10.1128/mbio.00854-22

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time.
Barnes, A. C., Rodríguez-Zapata, F., Juárez-Núñez, K. A., Gates, D. J., Janzen, G. M., Kur, A., Wang, L., Jensen, S. E., Estévez-Palmas, J. M., Crow, T. M., Kavi, H. S., Pil, H. D., Stokes, R. L., Knizner, K. T., Aguilar-Rangel, M. R., Demesa-Arévalo, E., Skopelitis, T., Pérez-Limón, S., Stutts, W. L., Thompson, P., Chiu, Y. C., Jackson, D., Muddiman, D. C., Fiehn, O., Runcie, D., Buckler, E. S., Ross-Ibarra, J., Hufford, M. B., Sawers, R. J. H., Rellán-Álvarez, R.
(2022, June 30). Proceedings of the National Academy of Sciences, 119(27), e2100036119. https://doi.org/10.1073/pnas.2100036119

OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage
Wu, X. S., He, X. Y., Ipsaro, J. J., Huang, Y. H., Preall, J. B., Ng, D., Shue, Y. T., Sage, J., Egeblad, M., Joshua-Tor, L., Vakoc, C. R.
(2022, July). Nature, 607(7917): 169-175. http://10.1136/gutjnl-2022-326952

Training the host organism to enhance anti-cancer immunity.
Ferrer, M., & Janowitz, T.
(2022, July 11). Cancer Cell, 40(7), 703-705. https://doi.org/10.1016/j.ccell.2022.06.003

The application of artificial intelligence to biology and neuroscience.
Richards, B., Tsao, D., & Zador, A.
(2022, July 21). Cell, 185(15), 2640-2643. https://doi.org/10.1016/j.cell.2022.06.04

Extreme purifying selection against point mutations in the human genome.
Dukler, N., Mughal, M. R., Ramani, R., Huang ,Y. F, & Siepel, A.
(2022, July 25). Nature Communications, 13(1), 4312. https://doi.org/10.1038/s41467-022-31872-6

Transcriptomic diversity in human medullary thymic epithelial cells.
Carter, J. A., Strömich, L., Peacey, M., Chapin, S. R., Velten, L., Steinmetz, L. M., Brors, B., Pinto, S., & Meyer, H. V.
(2022, August 2). Nature Communications, 13(1), 4296. https://doi.org/10.1038/s41467-022-31750-1

UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth.
Lindbäck, L. N., Hu, Y., Ackermann, A., Artz, O., & Pedmale, U. V.
(2022, August 8). Current Biology, 32(15, 3221-3231.e6. https://doi.org/10.1016/j.cub.2022.05.046

When the levee of sympathetic outflow breaks.
Ferro, A., & Cheadle, L.
(2022, August 9). Immunity, 55(8), 1334-1336. https://doi.org/10.1016/j.immuni.2022.07.009

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription.
Abuhashem, A., Chivu, A. G., Zhao, Y., Rice, E. J., Siepel, A., Danko, C. G., & Hadjantonakis, A. K.
(2022, August 18). Genes & Development, 36(13-14), 770-789. http://www.genesdev.org/cgi/doi/10.1101/gad.349565.122.

Ordered and deterministic cancer genome evolution after p53 loss.
Baslan, T., Morris, J. P., Zhao, Z., Reyes, J., Ho, Y.-J., Tsanov, K. M., Bermeo, J., Tian, S., Zhang, S., Askan, G., Yavas, A., Lecomte, N., Erakky, A., Varghese, A. M., Zhang, A., Kendall, J., Ghiban, E., Chorbadjiev, L., Wu, J., Dimitrova, N., Chadalavada, K., Nanjangud, G. J., Bandlamudi, C., Gong, Y., Donoghue, M. T. A., Socci, N. D., Krasnitz, A., Notta, F., Leach, S. D., Iacobuzio-Donahue, C. A., Lowe, S. W.
(2022, August 25). Nature, 608(7924), 795–802. https://doi.org/10.1038/s41586-022-05082-5

EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma.
Balinth, S., Fisher, M.L., Hwangbo, Y., Wu, C., Ballon, C., Sun, X., & Mills, A. A.
(2022, August 26). Oncogene, 41(35), 4130–4144. https://doi.org/10.1038/s41388-022-02417-4

On the parameter combinations that matter and on those that do not: Data-driven studies of parameter (non)identifiability.
Evangelou, N., Wichrowski, N. J., Kevrekidis, G. A., Dietrich, F., Kooshkbaghi, M., McFann, S., & Kevrekidis, I. G.
(2022, September). PNAS Nexus, 1(4), pgac154. https://doi.org/10.1093/pnasnexus/pgac154

A synthetic KLHL20 ligand to validate CUL3KLHL20 as a potent E3 ligase for targeted protein degradation.
Farrell, B. M., Gerth, F., Yang, C.-H. R., & Yeh, J. T.-H.
(2022, September 1). Genes & Development, 36(17–18), 1031–1042. https://doi.org/10.1101/gad.349717.122

Pancreatic Cancer Patient-derived Organoids Can Predict Response to Neoadjuvant Chemotherapy.
Demyan, L., Habowski, A. N., Plenker, D., King, D. A., Standring, O. J., Tsang, C., St. Surin, L., Rishi, A., Crawford, J. M., Boyd, J., Pasha, S. A., Patel, H., Galluzzo, Z., Metz, C., Gregersen, P. K., Fox, S., Valente, C., Abadali, S., Matadial-Ragoo, S., DePeralta, D. K., Deutsch, G. B., Herman, J. M., Talamini, M. A., Tuveson, D. A., & Weiss,, M. J.
(2022, September 1). Annals of Surgery, 276(3).  https://journals.lww.com/annalsofsurgery/Fulltext/2022/09000/Pancreatic_Cancer_Patient_derived_Organoids_Can.5.aspx

Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling.
Doepner, M., Lee, I., Natale, C. A., Brathwaite, R., Venkat, S., Kim, S. H., Wei, Y., Vakoc, C. R., Capell, B. C., Katzenellenbogen, J. A., Katzenellenbogen, B. S., Feigin, M. E., & Ridky, T. W.
(2022, September 2). Science Advances, 8(35), eabn4007.https://doi.org/10.1126/sciadv.abn4007

Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors.
Cheng, Y., Li, G., Smedley, C. J., Giel, M.-C., Kitamura, S., Woehl, J. L., Bianco, G., Forli, S., Homer, J. A., Cappiello, J. R., Wolan, D. W., Moses, J. E., & Sharpless, K. B.
(2022, September 7). Proceedings of the National Academy of Sciences, 119(37), e2208540119. https://doi.org/10.1073/pnas.2208540119

ΔNp63α in cancer: importance and therapeutic opportunities.
Fisher, M. L., Balinth, S., Mills, A. A.
(2022, September 14). Trends Cell Biology, S0962-8924(22), 00194-5. (Online ahead of print). https://doi.org/10.1016/j.tcb.2022.08.003

Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time.
Corcoran, E. T., LeBlanc, C., Huang, Y.-C., Arias Tsang, M., Sarkiss, A., Hu, Y., Pedmale, U. V., & Jacob, Y.
(2022, October). The Plant Cell, 34(10), 3611–3631. https://doi.org/10.1093/plcell/koac211

Oligodendrocyte precursor cells engulf synapses during circuit remodeling in mice.
Auguste, Y. S. S., Ferro, A., Kahng, J. A., Xavier, A. M., Dixon, J. R., Vrudhula, U., Nichitiu, A. S., Rosado, D., Wee, T. L., Pedmale, U. V., & Cheadle, L.
(2022, October). Nature Neuroscience, 25(10), 1273-1278. https://doi.org/10.1038/s41593-022-01170-x

A neural theory for counting memories.
Dasgupta, S., Hattori, D. & Navlakha, S.
(2022, October 10). Nature Communications, 13(1), 5961. https://doi.org/10.1038/s41467-022-33577-2

Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage.
Balasooriya, G. I., & Spector, D. L.
(2022, October 10). Nature Communications, 13(1), 5984. https://doi.org/10.1038/s41467-022-33722-x

High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex.
Chen, Y., Chen, X., Baserdem, B., Zhan, H., Li, Y., Davis, M. B., Kebschull, J. M., Zador, A. M., Koulakov, A. A., & Albeanu, D. F.
(2022, October 27). Cell, 185(22), 4117-4134.e28. https://doi.org/10.1016/j.cell.2022.09.038

Split-GFP Reassembly Assay: Strengths and Caveats from a Multiparametric Analysis.
Bignon, C., Gruet, A., & Longhi, S.
(2022, October 29). International Journal of Molecular Sciences, 23(21). https://doi.org/10.3390/ijms232113167

Associations between circulating interferon and kynurenine/tryptophan pathway metabolites: support for a novel potential mechanism for cognitive dysfunction in SLE
Anderson, E. W., Jin, Y., Shih, A., Arazi, A., Goodwin, S., Roeser, J., Furie, R. A., Aranow, C., Volpe, B., Diamond, B., Mackay, M..
(2022, November). Lupus Science & Medicine, 9(1), e000808. http://dx.doi.org/10.1136/lupus-2022-000808

Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species
Leonardo Campagna, Ziyi Mo, Adam Siepel, J. Albert C. Uy
(2022, November 1). PLoS Genetics,  18(11), e1010474. https://doi.org/10.1371/journal.pgen.1010474.

Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model
Chatterjee, D., Costa, C. A. M., Wang, XF., Jevitt, A., Huang, Y.-C., Deng, W.-M.
(2022, November 2). Elife,11, e80956. https://doi.org/10.7554/eLife.80956

Platr4 is an early embryonic lncRNA that exerts its function downstream on cardiogenic mesodermal lineage commitment
Hazra, R., Brine, L., Garcia, L., Benz, B., Chirathivat, N., Shen, M. M., Wilkinson, J. E., Lyons, S. K., Spector, D. L.
(2022, November 7 ). Developmental Cell, 57(21), 2450-2468.e7. https://doi.org/10.1016/j.devcel.2022.10.002

Recent Advances at the Interface of Neuroscience and Artificial Neural Networks
Cohen ,Y., Engel, T. A., Langdon, C., Lindsay, G. W., Ott, T., Peters, M. A. K., Shine, J. M., Breton-Provencher, V., Ramaswamy, S.
(2022, November 9 ). Journal of Neuroscience, 42(45), 8514-8523. DOI: https://doi.org/10.1523/JNEUROSCI.1503-22.2022.

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships
Ruchi Lohia, Nathan Fox, Jesse Gillis
(2022, November 9). Genome Biology, 23(1), 238. https://doi.org/10.1186/s13059-022-02790-z

Clinical applications of 3D normal and breast cancer organoids: A review of concepts and methods
Steven M. Lewis, Mackenzie K. Callaway, Camila O. dos Santos
(2022, November 19). Experimental Biology and Medicine, 247(2), 2176-2183. (Online ahead of print). https://doi.org/10.1177/15353702221131877

Phosphorylation of the smooth muscle master splicing regulator RBPMS regulates its splicing activity.
Barnhart, M. D., Yang, Y., Nakagaki-Silva, E. E., Hammond, T. H., Pizzinga, M., Gooding, C., Stott, K., & Smith, C. W. J.
(2022, November 21). Nucleic Acids Research, 50(20), 11895–11915. https://doi.org/10.1093/nar/gkac1048

Cortex-wide response mode of VIP-expressing inhibitory neurons by reward and punishment.
Szadai, Z., Pi, H.-J., Chevy, Q., Ócsai, K., Albeanu, D. F., Chiovini, B., Szalay, G., Katona, G., Kepecs, A., & Rózsa, B.
(2022, November 23). ELife, 11, e78815. https://doi.org/10.7554/eLife.78815

Non-symmetric pinning of topological defects in living liquid crystals
Figueroa-Morales, N., Genkin, M. M.,  Sokolov, A. & Aranson, I. S.
(2022, November 24). Communications Physics, 5, 301. https://doi.org/10.1038/s42005-022-01077-w

Neurotensin neurons in the extended amygdala control dietary choice and energy homeostasis
Furlan, A., Corona, A., Boyle, S., Sharma, R., Rubino, R., Habel, J., Gablenz, E. C., Giovanniello, J., Beyaz, S., Janowitz, T., Shea, S.D., & Li, B.
(2022, November). Nature Neuroscience, 25(11), 1470-1480. https://doi.org/10.1038/s41593-022-01178-3

Centering the Needs of Transgender, Nonbinary, and Gender-Diverse Populations in Neuroendocrine Models of Gender-Affirming Hormone Therapy
Aghi, K., Goetz, T. G., Pfau, D. R., Sun, S. E. D., Roepke, T. A., & Guthman, E. M.
(2022, December). Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 7(12), 1268-1279.  https://doi.org/10.1016/j.bpsc.2022.07.002

Machine-learning-based data-driven discovery of nonlinear phase-field dynamics
Elham Kiyani, Steven Silber, Mahdi Kooshkbaghi, and Mikko Karttunen
(2022, December). Physical Review E, 106(6), 065303. https://doi.org/10.1103/PhysRevE.106.065303

Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs.
Chou, T. H., Kang, H., Simorowski, N., Traynelis, S. F., & Furukawa, H.
(2022, December 1). Molecular Cell, 82(23), 4548-4563.e4. https://doi.org/10.1016/j.molcel.2022.10.008

PP2A methylesterase PME-1 suppresses anoikis and is associated with therapy relapse of PTEN-deficient prostate cancers.
Aakula, A., Isomursu, A., Rupp, C., Erickson, A., Gupta, N., Kauko, O., Shah, P., Padzik, A., Pokharel, Y. R., Kaur, A., Li. S.-P., Trotman, L., Taimen, P., Rannikko, A., Lammerding, J., Paatero, I., Mirtti, T., Ivaska, J., Westermarck, J.
(2022, December 3). Molecular Oncology, (Online ahead of print).  https://doi.org/10.1002/1878-0261.13353

Evaluating deep learning for predicting epigenomic profiles
Shushan Toneyan, Ziqi Tang, Peter K. Koo 
(2022, December 5). Nature Machine Intelligence, 4(12), 1088-1100. https://doi.org/10.1038/s42256-022-00570-9

Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. 
Jiří C. Moravec, Robert Lanfear, David L. Spector, Sarah D. Diermeier, and Alex Gavryushkin
(2022, December 6). Journal of Computational Biology, (Online ahead of print). https://doi.org/10.1089/cmb.2022.0357.

Long-range functional loops in the mouse olfactory system and their roles in computing odor identity.
Chae, H., Banerjee, A., Dussauze, M., & Albeanu, D. F.
(2022, December 7). Neuron, 110(23), 3970-3985.e7. https://doi.org/10.1016/j.neuron.2022.09.005

The effects of microglia on tauopathy progression can be quantified using Nexopathy in silico (Nexis) models
Anand. C., Maia, P. D., Torok, J., Mezias, C., Raj, A.
(2022, December 7). Scientific Reports, 12(1), 21170. https://doi.org/10.1038/s41598-022-25131-3

A path to translation: How 3D patient tumor avatars enable next generation precision oncology.
Barroso, M., Chheda, M. G., Clevers, H., Elez, E., Kaochar, S., Kopetz, S. E., Li, X.-N., Meric-Bernstam, F., Meyer, C. A., Mou, H., Naegle, K. M., Pera, M. F., Perova, Z., Politi, K. A., Raphael, B. J., Robson, P., Sears, R. C., Tabernero, J., Tuveson, D. A., Welm, A. L., Welm,  B. E., Willey, C. D., Salnikow, K., Chuang, J. H., & Shen, X.
(2022, December 12). Cancer Cell, 40(12), 1448–1453. https://doi.org/10.1016/j.ccell.2022.09.017

A dopaminergic reward prediction error signal shapes maternal behavior in mice
Yunyao Xie, Longwen Huang, Alberto Corona, Alexa H. Pagliaro, Stephen D. Shea
(2022, December 13). Neuron, 11(4), 557-570.e7. (Online ahead of print). https://doi.org/10.1016/j.neuron.2022.11.019

Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.
Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S., Wang, X., Lippman, Z. B., Schatz, M. C., Soyk, S.
(2022, December 15). Genome Biology, 23(1), 258. https://doi.org/10.1186/s13059-022-02823-7

Isolation of mouse mammary carcinoma-derived macrophages and cancer cells for co-culture assays
Lijuan Sun, Xiao Han, & Mikala Egeblad
(2022, December 16). STAR Protocols, 3(4), 101833. https://doi.org/10.1016/j.xpro.2022.10183

Metabolism in acute myeloid leukemia: mechanistic insights and therapeutic targets
Mishra, S. K., Millman, S. E., Zhang, L.
(2022, December 22). Blood, blood.2022018092. (Online ahead of print).  https://doi.org/10.1182/blood.2022018092.

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes
Kawaguchi, K. R., Tang, Z., Fischer, S., Rajesh, C., Tripathy, R., Koo, P. K., Gillis, J.
(2022, December 22). Briefings in Bioinformatics, 24(1), bbac541. (Online ahead of print). https://doi.org/10.1093/bib/bbac541