# Publications Search Within Results Search Within Results search ## 17 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 17 results Download 17 citations download- [BibTeX](/node/730221/export?format=bibtex) - [EndNote X3 XML](/node/730221/export?format=endnote8) - [EndNote 7 XML](/node/730221/export?format=endnote7) - [Endnote tagged](/node/730221/export?format=tagged) - [Marc](/node/730221/export?format=marc) - [PubMedId](/node/730221/export?format=pubmed_id) - [RIS](/node/730221/export?format=ris) ### 2024 Pan, W.; Zhang, W.; Zheng, B.; Camellato, B.; Stern, J.; Lin, Z.; Khodadadi-Jamayran, A.; Kim, J.; Sommer, P.; Khalil, K.; Weldon, E.; Bai, J.; Zhu, Y.; Meyn, P.; Heguy, A.; Mangiola, M.; Griesemer, A.; Keating, B.; Montgomery, R.; Xia, B.; Boeke, J. [Cellular Dynamics in Pig-to-Human Kidney Xenotransplantation](/publications/cellular-dynamics-pig-human-kidney-xenotransplantation). *Med* **2024**. https://doi.org/10.1016/j.medj.2024.05.003. Pan, W.; Zhang, W.; Zheng, B.; Camellato, B.; Stern, J.; Lin, Z.; Khodadadi-Jamayran, A.; Kim, J.; Sommer, P.; Khalil, K.; Weldon, E.; Bai, J.; Zhu, Y.; Meyn, P.; Heguy, A.; Mangiola, M.; Griesemer, A.; Keating, B.; Montgomery, R.; Xia, B.; Boeke, J. [Cellular Dynamics in Pig-to-Human Kidney Xenotransplantation](/publications/cellular-dynamics-pig-human-kidney-xenotransplantation). *Med* **2024**. https://doi.org/10.1016/j.medj.2024.05.003. - add\_circle do\_not\_disturb\_on Abstract BACKGROUND: Xenotransplantation of genetically engineered porcine organs has the potential to address the challenge of organ donor shortage. Two cases of porcine-to-human kidney xenotransplantation were performed, yet the physiological effects on the... Schmauch, E.; Piening, B.; Mohebnasab, M.; Xia, B.; Zhu, C.; Stern, J.; Zhang, W.; Dowdell, A.; Kim, J.; Andrijevic, D.; Khalil, K.; Jaffe, I.; Loza, B.-L.; Gragert, L.; Camellato, B.; Oliveira, M.; O’Brien, D.; Chen, H.; Weldon, E.; Gao, H.; Gandla, D.; Chang, A.; Bhatt, R.; Gao, S.; Lin, X.; Reddy, K.; Kagermazova, L.; Habara, A.; Widawsky, S.; Liang, F.-X.; Sall, J.; Loupy, A.; Heguy, A.; Taylor, S.; Zhu, Y.; Michael, B.; Jiang, L.; Jian, R.; Chong, A.; Fairchild, R.; Linna-Kuosmanen, S.; Kaikkonen, M.; Tatapudi, V.; Lorber, M.; Ayares, D.; Mangiola, M.; Narula, N.; Moazami, N.; Pass, H.; Herati, R.; Griesemer, A.; Kellis, M.; Snyder, M.; Montgomery, R.; Boeke, J.; Keating, B. [Integrative Multi-Omics Profiling in Human Decedents Receiving Pig Heart Xenografts](/publications/integrative-multi-omics-profiling-human-decedents-receiving-pig-heart-xenografts). *Nat Med* **2024**, *30* (5), 1448-1460. https://doi.org/10.1038/s41591-024-02972-1. Schmauch, E.; Piening, B.; Mohebnasab, M.; Xia, B.; Zhu, C.; Stern, J.; Zhang, W.; Dowdell, A.; Kim, J.; Andrijevic, D.; Khalil, K.; Jaffe, I.; Loza, B.-L.; Gragert, L.; Camellato, B.; Oliveira, M.; O’Brien, D.; Chen, H.; Weldon, E.; Gao, H.; Gandla, D.; Chang, A.; Bhatt, R.; Gao, S.; Lin, X.; Reddy, K.; Kagermazova, L.; Habara, A.; Widawsky, S.; Liang, F.-X.; Sall, J.; Loupy, A.; Heguy, A.; Taylor, S.; Zhu, Y.; Michael, B.; Jiang, L.; Jian, R.; Chong, A.; Fairchild, R.; Linna-Kuosmanen, S.; Kaikkonen, M.; Tatapudi, V.; Lorber, M.; Ayares, D.; Mangiola, M.; Narula, N.; Moazami, N.; Pass, H.; Herati, R.; Griesemer, A.; Kellis, M.; Snyder, M.; Montgomery, R.; Boeke, J.; Keating, B. [Integrative Multi-Omics Profiling in Human Decedents Receiving Pig Heart Xenografts](/publications/integrative-multi-omics-profiling-human-decedents-receiving-pig-heart-xenografts). *Nat Med* **2024**, *30* (5), 1448-1460. https://doi.org/10.1038/s41591-024-02972-1. - add\_circle do\_not\_disturb\_on Abstract In a previous study, heart xenografts from 10-gene-edited pigs transplanted into two human decedents did not show evidence of acute-onset cellular- or antibody-mediated rejection. Here, to better understand the detailed molecular landscape following... Xia, B.; Zhang, W.; Zhao, G.; Zhang, X.; Bai, J.; Brosh, R.; Wudzinska, A.; Huang, E.; Ashe, H.; Ellis, G.; Pour, M.; Zhao, Y.; Coelho, C.; Zhu, Y.; Miller, A.; Dasen, J.; Maurano, M.; Kim, S.; Boeke, J.; Yanai, I. [On the Genetic Basis of Tail-Loss Evolution in Humans and Apes](/publications/genetic-basis-tail-loss-evolution-humans-and-apes-0). *Nature* **2024**, *626* (8001), 1042-1048. https://doi.org/10.1038/s41586-024-07095-8. Xia, B.; Zhang, W.; Zhao, G.; Zhang, X.; Bai, J.; Brosh, R.; Wudzinska, A.; Huang, E.; Ashe, H.; Ellis, G.; Pour, M.; Zhao, Y.; Coelho, C.; Zhu, Y.; Miller, A.; Dasen, J.; Maurano, M.; Kim, S.; Boeke, J.; Yanai, I. [On the Genetic Basis of Tail-Loss Evolution in Humans and Apes](/publications/genetic-basis-tail-loss-evolution-humans-and-apes-0). *Nature* **2024**, *626* (8001), 1042-1048. https://doi.org/10.1038/s41586-024-07095-8. - add\_circle do\_not\_disturb\_on Abstract The loss of the tail is among the most notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the 'anthropomorphous apes'1-3, with a proposed role in contributing to human bipedalism4-6. Yet, the genetic... ### 2023 Tan, J.; Shenker-Tauris, N.; Rodriguez-Hernaez, J.; Wang, E.; Sakellaropoulos, T.; Boccalatte, F.; Thandapani, P.; Skok, J.; Aifantis, I.; Fenyö, D.; Xia, B.; Tsirigos, A. [Cell-Type-Specific Prediction of 3D Chromatin Organization Enables High-Throughput in Silico Genetic Screening](/publications/cell-type-specific-prediction-3d-chromatin-organization-enables-high-throughput). *Nat Biotechnol* **2023**, *41* (8), 1140-1150. https://doi.org/10.1038/s41587-022-01612-8. Tan, J.; Shenker-Tauris, N.; Rodriguez-Hernaez, J.; Wang, E.; Sakellaropoulos, T.; Boccalatte, F.; Thandapani, P.; Skok, J.; Aifantis, I.; Fenyö, D.; Xia, B.; Tsirigos, A. [Cell-Type-Specific Prediction of 3D Chromatin Organization Enables High-Throughput in Silico Genetic Screening](/publications/cell-type-specific-prediction-3d-chromatin-organization-enables-high-throughput). *Nat Biotechnol* **2023**, *41* (8), 1140-1150. https://doi.org/10.1038/s41587-022-01612-8. - add\_circle do\_not\_disturb\_on Abstract Investigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting... ### 2022 Barkley, D.; Moncada, R.; Pour, M.; Liberman, D.; Dryg, I.; Werba, G.; Wang, W.; Baron, M.; Rao, A.; Xia, B.; França, G.; Weil, A.; Delair, D.; Hajdu, C.; Lund, A.; Osman, I.; Yanai, I. [Cancer Cell States Recur across Tumor Types and Form Specific Interactions With the Tumor Microenvironment](/publications/cancer-cell-states-recur-across-tumor-types-and-form-specific-interactions-tumor). *Nat Genet* **2022**, *54* (8), 1192-1201. https://doi.org/10.1038/s41588-022-01141-9. Barkley, D.; Moncada, R.; Pour, M.; Liberman, D.; Dryg, I.; Werba, G.; Wang, W.; Baron, M.; Rao, A.; Xia, B.; França, G.; Weil, A.; Delair, D.; Hajdu, C.; Lund, A.; Osman, I.; Yanai, I. [Cancer Cell States Recur across Tumor Types and Form Specific Interactions With the Tumor Microenvironment](/publications/cancer-cell-states-recur-across-tumor-types-and-form-specific-interactions-tumor). *Nat Genet* **2022**, *54* (8), 1192-1201. https://doi.org/10.1038/s41588-022-01141-9. - add\_circle do\_not\_disturb\_on Abstract Transcriptional heterogeneity among malignant cells of a tumor has been studied in individual cancer types and shown to be organized into cancer cell states; however, it remains unclear to what extent these states span tumor types, constituting general... Xia, B.; Yanai, I. [Gene Expression Levels Modulate Germline Mutation Rates through the Compound Effects of Transcription-Coupled Repair and Damage](/publications/gene-expression-levels-modulate-germline-mutation-rates-through-compound-effects). *Hum Genet* **2022**, *141* (6), 1211-1222. https://doi.org/10.1007/s00439-021-02355-3. Xia, B.; Yanai, I. [Gene Expression Levels Modulate Germline Mutation Rates through the Compound Effects of Transcription-Coupled Repair and Damage](/publications/gene-expression-levels-modulate-germline-mutation-rates-through-compound-effects). *Hum Genet* **2022**, *141* (6), 1211-1222. https://doi.org/10.1007/s00439-021-02355-3. - add\_circle do\_not\_disturb\_on Abstract Of all mammalian organs, the testis has long been observed to have the most diverse gene expression profile. To account for this widespread gene expression, we have proposed a mechanism termed 'transcriptional scanning', which reduces germline mutation... ### 2020 Xia, B.; YunYan; Baron, M.; Wagner, F.; Barkley, D.; Chiodin, M.; Kim, S. Y.; Keefe, D. L.; Alukal, J. P.; Boeke, J. D.; Yanai, I. [Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates](/publication/widespread-transcriptional-scanning-testis-modulates-gene-evolution-rates). *Cell* **2020**, *180* (2), 248-262. Xia, B.; YunYan; Baron, M.; Wagner, F.; Barkley, D.; Chiodin, M.; Kim, S. Y.; Keefe, D. L.; Alukal, J. P.; Boeke, J. D.; Yanai, I. [Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates](/publication/widespread-transcriptional-scanning-testis-modulates-gene-evolution-rates). *Cell* **2020**, *180* (2), 248-262. - add\_circle do\_not\_disturb\_on Abstract The [testis](https://www.sciencedirect.com/topics/immunology-and-microbiology/testis) expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Our single-cell [transcriptomic](https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/transcriptomics) data of human and mouse [spermatogenesis](https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/spermatogenesis) provide evidence that this widespread transcription... Yi, C.; Zhu, C.; Xia, B. [Method for Marking 5-Formyl Cytosine and Use Thereof in Single Base Resolution Sequencing](/publications/method-marking-5-formyl-cytosine-and-use-thereof-single-base-resolution), 2020. Yi, C.; Zhu, C.; Xia, B. [Method for Marking 5-Formyl Cytosine and Use Thereof in Single Base Resolution Sequencing](/publications/method-marking-5-formyl-cytosine-and-use-thereof-single-base-resolution), 2020. - [ descriptionPublisher's Version](https://patents.google.com/patent/US11293050B2/en) - [ descriptionPublisher's Version](https://patents.google.com/patent/US11293050B2/en) ### 2019 Xia, B.; Yanai, I. [A Periodic Table of Cell Types](/publications/periodic-table-cell-types). *Development* **2019**, *146* (12). https://doi.org/10.1242/dev.169854. Xia, B.; Yanai, I. [A Periodic Table of Cell Types](/publications/periodic-table-cell-types). *Development* **2019**, *146* (12). https://doi.org/10.1242/dev.169854. - add\_circle do\_not\_disturb\_on Abstract Single cell biology is currently revolutionizing developmental and evolutionary biology, revealing new cell types and states in an impressive range of biological systems. With the accumulation of data, however, the field is grappling with a central... Zeng, H.; Mondal, M.; Song, R.; Zhang, J.; Xia, B.; Liu, M.; Zhu, C.; He, B.; Gao, Y. Q.; Yi, C. [Unnatural Cytosine Bases Recognized As Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry](/publications/unnatural-cytosine-bases-recognized-thymines-dna-polymerases-formation-watson). *Angew Chem Int Ed Engl* **2019**, *58* (1), 130-133. https://doi.org/10.1002/anie.201807845. Zeng, H.; Mondal, M.; Song, R.; Zhang, J.; Xia, B.; Liu, M.; Zhu, C.; He, B.; Gao, Y. Q.; Yi, C. [Unnatural Cytosine Bases Recognized As Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry](/publications/unnatural-cytosine-bases-recognized-thymines-dna-polymerases-formation-watson). *Angew Chem Int Ed Engl* **2019**, *58* (1), 130-133. https://doi.org/10.1002/anie.201807845. - add\_circle do\_not\_disturb\_on Abstract The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which DNA polymerases faithfully decode chemical information on the template. It was previously shown that two unnatural cytosine bases (termed "M-fC" and "I-fC")... ### 2018 Zeng, H.; He, B.; Xia, B.; Bai, D.; Lu, X.; Cai, J.; Chen, L.; Zhou, A.; Zhu, C.; Meng, H.; Gao, Y.; Guo, H.; He, C.; Dai, Q.; Yi, C. [Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution](/publications/bisulfite-free-nanoscale-analysis-5-hydroxymethylcytosine-single-base-resolution). *J Am Chem Soc* **2018**, *140* (41), 13190-13194. https://doi.org/10.1021/jacs.8b08297. Zeng, H.; He, B.; Xia, B.; Bai, D.; Lu, X.; Cai, J.; Chen, L.; Zhou, A.; Zhu, C.; Meng, H.; Gao, Y.; Guo, H.; He, C.; Dai, Q.; Yi, C. [Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution](/publications/bisulfite-free-nanoscale-analysis-5-hydroxymethylcytosine-single-base-resolution). *J Am Chem Soc* **2018**, *140* (41), 13190-13194. https://doi.org/10.1021/jacs.8b08297. - add\_circle do\_not\_disturb\_on Abstract High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on... ### 2017 Cimmino, L.; Dolgalev, I.; Wang, Y.; Yoshimi, A.; Martin, G.; Wang, J.; Ng, V.; Xia, B.; Witkowski, M.; Mitchell-Flack, M.; Grillo, I.; Bakogianni, S.; Ndiaye-Lobry, D.; Martín, M. T.; Guillamot, M.; Banh, R.; Xu, M.; Figueroa, M.; Dickins, R.; Abdel-Wahab, O.; Park, C.; Tsirigos, A.; Neel, B.; Aifantis, I. [Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression](/publications/restoration-tet2-function-blocks-aberrant-self-renewal-and-leukemia-progression). *Cell* **2017**, *170* (6), 1079-1095.e20. https://doi.org/10.1016/j.cell.2017.07.032. Cimmino, L.; Dolgalev, I.; Wang, Y.; Yoshimi, A.; Martin, G.; Wang, J.; Ng, V.; Xia, B.; Witkowski, M.; Mitchell-Flack, M.; Grillo, I.; Bakogianni, S.; Ndiaye-Lobry, D.; Martín, M. T.; Guillamot, M.; Banh, R.; Xu, M.; Figueroa, M.; Dickins, R.; Abdel-Wahab, O.; Park, C.; Tsirigos, A.; Neel, B.; Aifantis, I. [Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression](/publications/restoration-tet2-function-blocks-aberrant-self-renewal-and-leukemia-progression). *Cell* **2017**, *170* (6), 1079-1095.e20. https://doi.org/10.1016/j.cell.2017.07.032. - add\_circle do\_not\_disturb\_on Abstract Loss-of-function mutations in TET2 occur frequently in patients with clonal hematopoiesis, myelodysplastic syndrome (MDS), and acute myeloid leukemia (AML) and are associated with a DNA hypermethylation phenotype. To determine the role of TET2 deficiency... - Previous page chevron\_left - [1](?page=0 "Current page") - [2](?page=1 "Go to page 2") - [ Next page chevron\_right ](?page=1 "Go to next page")