Mosialou, I., Ali, A. M., Labella, R., Bisikirska, B., Cuesta-Dominguez, A., Vgenopoulou, P., Reyes, I., Rao, S. M., Wang, A., Luo, N., Galan-Diez, M., Zhao, J., Chernak, B. J., Bewersdorf, J. P., Fukasawa, K., Su, J., Higa, J., Adams, R. A., Corper, A. L., … Kousteni, S. (2025). A niche driven mechanism determines response and a mutation-independent therapeutic approach for myeloid malignancies. Cancer Cell. https://doi.org/10.1016/j.ccell.2025.03.007

Austin, G. I., Brown Kav, A., ElNaggar, S., Park, H., Biermann, J., Uhlemann, A.-C., Pe’er, I., & Korem, T. (2025). Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models. Nature Microbiology. https://doi.org/10.1038/s41564-025-01954-4

Baumeister, T., Proaño-Vasco, A., Metwaly, A., Kleigrewe, K., Kuznetsov, A., Schömig, L., Borgmann, M., Khiat, M., Anand, A., Strangmann, J., Böttcher, K., Haller, D., Dunkel, A., Somoza, V., Reiter, S., Meng, C., Thimme, R., Schmid, R. M., Patil, D. T., … Quante, M. (2025). Loss of FXR or Bile Acid-dependent Inhibition accelerate carcinogenesis of Gastroesophageal Adenocarcinoma. Cellular and Molecular Gastroenterology and Hepatology, 101505. https://doi.org/10.1016/j.jcmgh.2025.101505

Sierant, M. C., Jin, S. C., Bilguvar, K., Morton, S. U., Dong, W., Jiang, W., Lu, Z., Li, B., López-Giráldez, F., Tikhonova, I., Zeng, X., Lu, Q., Choi, J., Zhang, J., Nelson-Williams, C., Knight, J. R., Zhao, H., Cao, J., Mane, S., … Lifton, R. P. (2025). Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes. Proceedings of the National Academy of Sciences, 122(13). https://doi.org/10.1073/pnas.2420343122

Pita-Juarez, Y., Karagkouni, D., Kalavros, N., Melms, J. C., Niezen, S., Delorey, T. M., Essene, A. L., Brook, O. R., Pant, D., Skelton-Badlani, D., Naderi, P., Huang, P., Pan, L., Hether, T., Andrews, T. S., Ziegler, C. G. K., Reeves, J., Myloserdnyy, A., Chen, R., … Vlachos, I. S. (2025). A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. Genome Biology, 26(1). https://doi.org/10.1186/s13059-025-03499-5

Sugimoto, A., Saito, Y., Wang, G., Sun, Q., Yin, C., Lee, K. H., Geng, Y., Rajbhandari, P., Hernandez, C., Steffani, M., Qie, J., Savage, T., Goyal, D. M., Ray, K. C., Neelakantan, T. V., Yin, D., Melms, J., Lehrich, B. M., Yasaka, T. M., … Schwabe, R. F. (2025). Hepatic stellate cells control liver zonation, size and functions via R-spondin 3. Nature. https://doi.org/10.1038/s41586-025-08677-w

Ibarra-Arellano, M. A., Caprio, L. A., Hada, A., Stotzem, N., Cai, L. L., Shah, S. B., Walsh, Z. H., Melms, J. C., Wünneman, F., Bestak, K., Mansaray, I., Izar, B., & Schapiro, D. (2025). micronuclAI enables automated quantification of micronuclei for assessment of chromosomal instability. Communications Biology, 8(1). https://doi.org/10.1038/s42003-025-07796-4

Morano, N. C., Lopez, D. H., Meltzer, H., Sergeeva, A. P., Katsamba, P. S., Rostam, K. D., Gupta, H. P., Becker, J. E., Bornstein, B., Cosmanescu, F., Schuldiner, O., Honig, B., Mann, R. S., & Shapiro, L. (2025). Members of the DIP and Dpr adhesion protein families use cis inhibition to shape neural development in Drosophila. PLOS Biology, 23(3), e3003030. https://doi.org/10.1371/journal.pbio.3003030

Tagore, S., Caprio, L., Amin, A. D., Bestak, K., Luthria, K., D’Souza, E., Barrera, I., Melms, J. C., Wu, S., Abuzaid, S., Wang, Y., Jakubikova, V., Koch, P., Brodtman, D. Z., Bawa, B., Deshmukh, S. K., Ebel, L., Ibarra-Arellano, M. A., Jaiswal, A., … Izar, B. (2025). Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases. Nature Medicine. https://doi.org/10.1038/s41591-025-03530-z

Kars, M. E., Stein, D., Stenson, P. D., Cooper, D. N., Chung, W. K., Gruber, P. J., Seidman, C. E., Shen, Y., Tristani-Firouzi, M., Gelb, B. D., & Itan, Y. (2025). Deciphering the digenic architecture of congenital heart disease using trio exome sequencing data. The American Journal of Human Genetics. https://doi.org/10.1016/j.ajhg.2025.01.024

Zhang, P., Du, Q., Wang, Y., Wei, L., & Wang, X. (2025). Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57031-1

Gejman, R. S., & Izar, B. (2025). Polyguanine microsatellites are robust replication clocks in cancer. Nature Genetics. https://doi.org/10.1038/s41588-025-02098-1

Olsen, T. R., Talla, P., Sagatelian, R. K., Furnari, J., Bruce, J. N., Canoll, P., Zha, S., & Sims, P. A. (2025). Scalable co-sequencing of RNA and DNA from individual nuclei. Nature Methods. https://doi.org/10.1038/s41592-024-02579-x

Linnér, E., Czuba, T., Gidlöf, O., Lundgren, J., Bollano, E., Hellberg, M., Celik, S., Pimpalwar, N., Rentzsch, P., Martorella, M., Gummesson, A., Melander, O., Albinsson, S., Dellgren, G., Borén, J., Jeppsson, A., Lumbers, R. T., Shah, S., Nilsson, J., … Smith, J. G. (2025). Whole genome sequencing in early onset advanced heart failure. Scientific Reports, 15(1). https://doi.org/10.1038/s41598-025-88465-8

Dutta, A., Rodriguez-Calero, A., Ronaldson-Bouchard, K., Offermann, A., Rahman, D., Vhatkar, T. B., Hasson, D., Alshalalfa, M., Davicioni, E., Karnes, R. J., Rubin, M. A., Vunjak-Novakovic, G., Abate-Shen, C., & Arriaga, J. M. (2025). ATAD2 Drives Prostate Cancer Progression to Metastasis. Molecular Cancer Research, OF1–OF12. https://doi.org/10.1158/1541-7786.mcr-24-0544

Bhatt, K. A., Vaynrub, A. J., Cham, J., Iyer, S. G., & Izar, B. (2025). Diagnosis and management of concurrent metastatic melanoma and chronic myelomonocytic leukemia. Melanoma Research. https://doi.org/10.1097/cmr.0000000000001025

Richardson, M., Zhao, S., Lin, L., Sheth, R. U., Qu, Y., Lee, J., Moody, T., Ricaurte, D., Huang, Y., Velez-Cortes, F., Urtecho, G., & Wang, H. H. (2025). SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome. Nature Microbiology, 10(2), 527–540. https://doi.org/10.1038/s41564-024-01914-4

Um, D. H., Knowles, D. A., & Kaiser, G. E. (2025). Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries. Computational Biology and Chemistry, 114, 108251. https://doi.org/10.1016/j.compbiolchem.2024.108251

Doron-Mandel, E., Bokor, B. J., Ma, Y., Street, L. A., Tang, L. C., Abdou, A. A., Shah, N. H., Rosenberger, G., & Jovanovic, M. (2025). SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-56303-0

Fu, X., Mo, S., Buendia, A., Laurent, A. P., Shao, A., Alvarez-Torres, M. del M., Yu, T., Tan, J., Su, J., Sagatelian, R., Ferrando, A. A., Ciccia, A., Lan, Y., Owens, D. M., Palomero, T., Xing, E. P., & Rabadan, R. (2025). A foundation model of transcription across human cell types. Nature, 637(8047), 965–973. https://doi.org/10.1038/s41586-024-08391-z

Goldberg, A. R., Dovas, A., Torres, D., Pereira, B., Viswanathan, A., Das Sharma, S., Mela, A., Merricks, E. M., Megino-Luque, C., McInvale, J. J., Olabarria, M., Shokooh, L. A., Zhao, H. T., Chen, C., Kotidis, C., Calvaresi, P., Banu, M. A., Razavilar, A., Sudhakar, T. D., … Canoll, P. (2025). Glioma-induced alterations in excitatory neurons are reversed by mTOR inhibition. Neuron. https://doi.org/10.1016/j.neuron.2024.12.026

Aparicio, L., Crowley, L., Christin, J. R., Laplaca, C. J., Hibshoosh, H., Rabadan, R., & Shen, M. M. (2025). Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer. Genome Medicine, 17(1). https://doi.org/10.1186/s13073-025-01432-w

Shin, A. E., Sugiura, K., Kariuki, S. W., Cohen, D. A., Flashner, S. P., Klein-Szanto, A. J., Nishiwaki, N., De, D., Vasan, N., Gabre, J. T., Lengner, C. J., Sims, P. A., & Rustgi, A. K. (2025). LIN28B-mediated PI3K/AKT pathway activation promotes metastasis in colorectal cancer models. Journal of Clinical Investigation. https://doi.org/10.1172/jci186035

Chen, C., & Wang, H. H. (2025). Diary of a cell in DNA ‘chyrons.’ Nature Chemical Biology. https://doi.org/10.1038/s41589-024-01814-y

Azam, S., Yang, F., & Wu, X. (2025). Finding functional microproteins. Trends in Genetics, 41(2), 107–118. https://doi.org/10.1016/j.tig.2024.12.001

Acitores Cortina, J. M., Fatapour, Y., Brown, K. L., Gisladottir, U., Zietz, M., Bear Don’t Walk IV, O. J., Peter, D., Berkowitz, J. S., Friedrich, N. A., Kivelson, S., Kuchi, A., Liu, H., Srinivasan, A., Tsang, K. K., & Tatonetti, N. P. (2025). Biases in Race and Ethnicity Introduced by Filtering Electronic Health Records for “Complete Data”: Observational Clinical Data Analysis. JMIR Medical Informatics, 13, e67591–e67591. https://doi.org/10.2196/67591

Caron, D. P., Specht, W. L., Chen, D., Wells, S. B., Szabo, P. A., Jensen, I. J., Farber, D. L., & Sims, P. A. (2025). Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. Cell Reports Methods, 5(1), 100938. https://doi.org/10.1016/j.crmeth.2024.100938

Orouji, S., Liu, M. C., Korem, T., & Peters, M. A. K. (2024). Domain adaptation in small-scale and heterogeneous biological datasets. Science Advances, 10(51). https://doi.org/10.1126/sciadv.adp6040

Patiño-Galindo, J., García-Sastre, A., Kuhn, J. H., Rabadan, R., & Palacios, G. (2024). Recombination across distant coronavirid species and genera is a rare event with distinct genomic features. Journal of Virology, 98(12). https://doi.org/10.1128/jvi.01100-24

Hung, L. Y., Alves, N. D., Del Colle, A., Talati, A., Najjar, S. A., Bouchard, V., Gillet, V., Tong, Y., Huang, Z., Browning, K. N., Hua, J., Liu, Y., Woodruff, J. O., Juarez, D., Medina, M., Posner, J., Tonello, R., Yalcinkaya, N., Israelyan, N., … Margolis, K. G. (2024). Intestinal Epithelial Serotonin as a Novel Target for Treating Disorders of Gut-Brain Interaction and Mood. Gastroenterology. https://doi.org/10.1053/j.gastro.2024.11.012

Ryan, C. P., Corcoran, D. L., Banskota, N., Eckstein Indik, C., Floratos, A., Friedman, R., Kobor, M. S., Kraus, V. B., Kraus, W. E., MacIsaac, J. L., Orenduff, M. C., Pieper, C. F., White, J. P., Ferrucci, L., Horvath, S., Huffman, K. M., & Belsky, D. W. (2024). The CALERIE Genomic Data Resource. Nature Aging. https://doi.org/10.1038/s43587-024-00775-0

Bunne, C., Roohani, Y., Rosen, Y., Gupta, A., Zhang, X., Roed, M., Alexandrov, T., AlQuraishi, M., Brennan, P., Burkhardt, D. B., Califano, A., Cool, J., Dernburg, A. F., Ewing, K., Fox, E. B., Haury, M., Herr, A. E., Horvitz, E., Hsu, P. D., … Quake, S. R. (2024). How to build the virtual cell with artificial intelligence: Priorities and opportunities. Cell, 187(25), 7045–7063. https://doi.org/10.1016/j.cell.2024.11.015

Ke, X., van Soldt, B., Vlahos, L., Zhou, Y., Qian, J., George, J., Capdevila, C., Glass, I., Yan, K., Califano, A., & Cardoso, W. V. (2024). Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate. Developmental Cell. https://doi.org/10.1016/j.devcel.2024.11.017

Blattman, S. B., Jiang, W., McGarrigle, E. R., Liu, M., Oikonomou, P., & Tavazoie, S. (2024). Identification and genetic dissection of convergent persister cell states. Nature, 636(8042), 438–446. https://doi.org/10.1038/s41586-024-08124-2

De Felice, D., Alaimo, A., Bressan, D., Genovesi, S., Marmocchi, E., Annesi, N., Beccaceci, G., Dalfovo, D., Cutrupi, F., Medaglia, S., Foletto, V., Lorenzoni, M., Gandolfi, F., Kannan, S., Verma, C. S., Vasciaveo, A., Shen, M. M., Romanel, A., Chiacchiera, F., … Lunardi, A. (2024). Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer. EMBO Reports. https://doi.org/10.1038/s44319-024-00335-y

Wang, Q., Guo, Y., Schwanz, L. T., Mellis, I. A., Sun, Y., Qu, Y., Urtecho, G., Valdez, R., Stoneman, E., Gordon, A., Wang, H. H., Ho, D. D., & Liu, L. (2024). SARS-CoV-2 omicron BA.2.87.1 exhibits higher susceptibility to serum neutralization than EG.5.1 and JN.1. Emerging Microbes & Infections, 13(1). https://doi.org/10.1080/22221751.2024.2359004

Nishiwaki, N., Sugiura, K., Suzuki, K., Li, A. L., Contreras, C. T., Efe, G., Shin, A. E., Sadeghian, D., Zhao, J., Maitra, A., Pitarresi, J. R., Sims, P. A., Chandwani, R., & Rustgi, A. K. (2024). PRRX1 has functional roles in pancreatic acinar to ductal metaplasia and carcinogenesis. Cellular and Molecular Gastroenterology and Hepatology, 101442. https://doi.org/10.1016/j.jcmgh.2024.101442

Henick, B. S., Koch, P. D., Gainor, J. F., Awad, M. M., Chiuzan, C., Izard, S., Georgis, Y., Mallick, S., Garofano, R. F., Wong, C. V., Saqi, A., Grindheim, J., Schulze, K., Sonett, J. R., Rizvi, N. A., Izar, B., Taylor, A. M., & Shu, C. A. (2024). Neoadjuvant atezolizumab + chemotherapy for resectable NSCLC: 3-year clinical update of phase II clinical trial results and translational findings. Journal for ImmunoTherapy of Cancer, 12(12), e009301. https://doi.org/10.1136/jitc-2024-009301

Mavros, C. F., Bongers, M., Neergaard, F. B. F., Cusimano, F., Sun, Y., Kaufman, A., Richardson, M., Kammler, S., Kristensen, M., Sommer, M. O. A., & Wang, H. H. (2024). Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.4c00453

Zahr, T., Li, T., Bhansali, D., Wan, Q., Leong, K. W., & Qiang, L. (2024). Targeted delivery of a cationic dendrimer with a plaque-homing peptide for the treatment of atherosclerosis. Life Medicine. https://doi.org/10.1093/lifemedi/lnae039

Urtecho, G., Moody, T., Huang, Y., Sheth, R. U., Richardson, M., Descamps, H. C., Kaufman, A., Lekan, O., Zhang, Z., Velez-Cortes, F., Qu, Y., Cohen, L., Ricaurte, D., Gibson, T. E., Gerber, G. K., Thaiss, C. A., & Wang, H. H. (2024). Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut. Cell Systems, 15(11), 1002-1017.e4. https://doi.org/10.1016/j.cels.2024.10.007

Cheng, X., Sui, H., Chen, F., Li, C., Du, M., Zhang, S., Chen, J., Dou, J., Huang, Y., Xie, X., Cheng, C., Yang, R., Yang, C., Shi, B., Shao, D., Leong, K. W., & Huang, H. (2024). Nanomaterial‐Mediated Reprogramming of Macrophages to Inhibit Refractory Muscle Fibrosis. Advanced Materials. Portico. https://doi.org/10.1002/adma.202410368

Izar, B., & Kim, M. (2024). Peritumoral Venous Vessels: Autobahn and Portal for T cells to Melanoma Brain Metastasis. Cancer Research. https://doi.org/10.1158/0008-5472.can-24-4054

Windemuth, S., Hahn, J., You, J., Wang, Z., Ding, S., Tarrab, S., Coker, C., Leong, K. W., & Danino, T. (2024). Iron-Tannin Coating Reduces Clearance and Increases Tumor Colonization of Systemically Delivered Bacteria. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.4c00333

Davis-Porada, J., George, A. B., Lam, N., Caron, D. P., Gray, J. I., Huang, J., Hwu, J., Wells, S. B., Matsumoto, R., Kubota, M., Lee, Y., Morrison-Colvin, R., Jensen, I. J., Ural, B. B., Shaabani, N., Weiskopf, D., Grifoni, A., Sette, A., Szabo, P. A., … Farber, D. L. (2024). Maintenance and functional regulation of immune memory to COVID-19 vaccines in tissues. Immunity, 57(12), 2895-2913.e8. https://doi.org/10.1016/j.immuni.2024.10.003

Zarco, N., Dovas, A., de Araujo Farias, V., Nagaiah, N. K. H., Haddock, A., Sims, P. A., Hambardzumyan, D., Meyer, C. T., Canoll, P., Rosenfeld, S. S., & Kenchappa, R. S. (2024). Resistance to spindle inhibitors in glioblastoma depends on STAT3 and therapy induced senescence. IScience, 27(12), 111311. https://doi.org/10.1016/j.isci.2024.111311

Davar, D., Williams, A., Lopez, J., Olson, D., Sato, T., Shaw, H., Friedman, C. F., Thistlethwaite, F., Middleton, M., Lebbe, C., Ma, V. T., Izar, B., Lau, P., Bechter, O., Kirk, P., Yuan, Y., Marshall, S., & Hamid, O. (2024). 694 Phase 1 safety and efficacy of brenetafusp, a PRAME × CD3 ImmTAC bispecific, in post-checkpoint cutaneous melanoma (CM). Regular and Young Investigator Award Abstracts, A796–A796. https://doi.org/10.1136/jitc-2024-sitc2024.0694

Ager, C. R., Jugler, C., Zhu, Y., Chen, D., Athar, M., Izar, B., Bickers, D., & Kim, A. (2024). 791 Immunological correlates of response to vismodegib and PD-1 blockade in an autochthonous model of basal cell nevus (Gorlin-Goltz) syndrome. Regular and Young Investigator Award Abstracts, A896–A896. https://doi.org/10.1136/jitc-2024-sitc2024.0791

Schoenfeld, A. J., Izar, B., Spira, A., Zamarin, D., Spigel, D. R., Hoimes, C., McDermott, D. F., Sehgal, K., Najjar, Y. G., Garon, E. B., Sullivan, R. J., Henick, B., Leal, T. A., Hurwitz, M., McKay, R., Gong, X., Rokade, S., Stager, A. M., Bach, K., … Oft, M. (2024). 1325 T cell and immune activation from a phase 1 study of STK-012, a first-in-class IL-2R α/β selective partial agonist in advanced solid tumors. Regular and Young Investigator Award Abstracts, A1484–A1484. https://doi.org/10.1136/jitc-2024-sitc2024.1325

Li, X., Melo, L. A. N., & Bussemaker, H. J. (2024). Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03424-2