bioRxiv Channel: Arc Institute https://biorxiv.org This feed contains articles for bioRxiv Channel "Arc Institute" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Accurate isoform quantification by joint short- and long-read RNA-sequencing ]]> https://biorxiv.org/cgi/content/short/2024.07.11.603067v1?rss=1" Apostolides, M. Choi, B. Navickas, A. Saberi, A. Soto, L. M. Goodarzi, H. Najafabadi, H. S. 2024-07-13 doi:10.1101/2024.07.11.603067 Cold Spring Harbor Laboratory Press 2024-07-13 <![CDATA[ Blocking oligomerization is the most viable strategy to inhibit STING ]]> https://biorxiv.org/cgi/content/short/2023.08.11.553045v1?rss=1" Chan, R. J. M. Cao, X. Ergun, S. L. Njomen, E. Lynch, S. R. Cravatt, B. F. Li, L. 2023-08-12 doi:10.1101/2023.08.11.553045 Cold Spring Harbor Laboratory Press 2023-08-12 <![CDATA[ Rewriting endogenous human transcripts with trans-splicing ]]> https://biorxiv.org/cgi/content/short/2024.01.29.577779v1?rss=1" Chandrasekaran, S. S. Tau, C. Nemeth, M. Pawluk, A. Konermann, S. Hsu, P. D. 2024-01-30 doi:10.1101/2024.01.29.577779 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs ]]> https://biorxiv.org/cgi/content/short/2025.01.25.634869v1?rss=1" Choi, B. Sobti, S. Soto, L. M. Charbonneau, T. Sababi, A. Navickas, A. Najafabadi, H. S. Goodarzi, H. 2025-01-27 doi:10.1101/2025.01.25.634869 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Site-specific DNA insertion into the human genome with engineered recombinases ]]> https://biorxiv.org/cgi/content/short/2024.11.01.621560v1?rss=1" Fanton, A. Bartie, L. J. Martins, J. Q. Tran, V. Q. Goudy, L. Durrant, M. G. Wei, J. Pawluk, A. Konermann, S. Marson, A. Gilbert, L. A. Hsu, P. D. 2024-11-03 doi:10.1101/2024.11.01.621560 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Environmental challenge rewires functional connections among human genes ]]> https://biorxiv.org/cgi/content/short/2023.08.09.552346v1?rss=1" Herken, B. W. Wong, G. Norman, T. Gilbert, L. 2023-08-09 doi:10.1101/2023.08.09.552346 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ A generative framework for enhanced cell-type specificity in rationally designed mRNAs ]]> https://biorxiv.org/cgi/content/short/2024.12.31.630783v1?rss=1" Khoroshkin, M. S. Zinkevich, A. Aristova, E. Yousefi, H. Lee, S. B. Mittmann, T. Manegold, K. Penzar, D. Raleigh, D. R. Kulakovskiy, I. V. Goodarzi, H. 2024-12-31 doi:10.1101/2024.12.31.630783 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ Semantic mining of functional de novo genes from a genomic language model ]]> https://biorxiv.org/cgi/content/short/2024.12.17.628962v1?rss=1" Merchant, A. T. King, S. H. Nguyen, E. Hie, B. L. 2024-12-18 doi:10.1101/2024.12.17.628962 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ A combinatorial domain screening platform reveals epigenetic effector interactions for transcriptional perturbation ]]> https://biorxiv.org/cgi/content/short/2024.10.28.620683v1?rss=1" Moon, H. C. Herschl, M. H. Pawluk, A. Konermann, S. Hsu, P. D. 2024-10-30 doi:10.1101/2024.10.28.620683 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ A Suite of Foundation Models Captures the Contextual Interplay Between Codons ]]> https://biorxiv.org/cgi/content/short/2024.10.10.617568v1?rss=1" Naghipourfar, M. Chen, S. Howard, M. Macdonald, C. Saberi, A. Hagen, T. Mofrad, M. Coyote-Maestas, W. Goodarzi, H. 2024-10-13 doi:10.1101/2024.10.10.617568 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ A long context RNA foundation model for predicting transcriptome architecture ]]> https://biorxiv.org/cgi/content/short/2024.08.26.609813v1?rss=1" Goodarzi, H. Najafabadi, H. S. Ramani, V. Emad, A. Namini, A. Naghipourfar, M. Wang, S. Choi, B. Saberi, A. 2024-08-27 doi:10.1101/2024.08.26.609813 Cold Spring Harbor Laboratory Press 2024-08-27 <![CDATA[ Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers ]]> https://biorxiv.org/cgi/content/short/2025.01.17.633622v1?rss=1" 85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortion in vivo. Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elements in vivo. Our work suggests extreme--but regulated--plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts. ]]> Yang, M. G. Richter, H. J. Wang, S. McNally, C. P. Harris, N. Dhillon, S. Maresca, M. de Wit, E. Willenbring, H. Maher, J. Goodarzi, H. Ramani, V. 2025-01-22 doi:10.1101/2025.01.17.633622 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations ]]> https://biorxiv.org/cgi/content/short/2024.12.13.628239v1?rss=1" Yu, J. X. Suh, J. M. Popova, K. D. Garcia, K. Joshi, T. Culbertson, B. Spinelli, J. B. Subramanyam, V. Lou, K. Shokat, K. M. Weissman, J. Goodarzi, H. 2024-12-16 doi:10.1101/2024.12.13.628239 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Dietary manipulation of intestinal microbes prolongs survival in a mouse model of Hirschsprung disease ]]> https://biorxiv.org/cgi/content/short/2025.02.10.637436v1?rss=1" View larger version (15K): org.highwire.dtl.DTLVardef@d95251org.highwire.dtl.DTLVardef@1ab58caorg.highwire.dtl.DTLVardef@5260b0org.highwire.dtl.DTLVardef@49ce42_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Tjaden, N. E. B. Liou, M. J. Sax, S. Lassoued, N. Lou, M. Schneider, S. Beigel, K. Eisenberg, J. D. Loeffler, E. Anderson, S. E. Yan, G. Litichevskiy, L. Dohnalova, L. Zhu, Y. Jin, D. M. J. C. Raab, J. Furth, E. E. Thompson, Z. Rubenstein, R. C. Pilon, N. Thaiss, C. A. Heuckeroth, R. 2025-02-11 doi:10.1101/2025.02.10.637436 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics ]]> https://biorxiv.org/cgi/content/short/2025.02.05.636714v1?rss=1" Wang, C. X. Cui, H. Zhang, A. H. Xie, R. Goodarzi, H. Wang, B. 2025-02-08 doi:10.1101/2025.02.05.636714 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Learning single-cell spatial context through integrated spatial multiomics with CORAL ]]> https://biorxiv.org/cgi/content/short/2025.02.01.636038v1?rss=1" He, S. Bieniosek, M. Song, D. Zhou, J. Chidester, B. Wu, Z. Boen, J. Sharma, P. Trevino, A. E. Zou, J. 2025-02-06 doi:10.1101/2025.02.01.636038 Cold Spring Harbor Laboratory Press 2025-02-06 <![CDATA[ Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers ]]> https://biorxiv.org/cgi/content/short/2024.03.19.585748v1?rss=1" Wang, J. Suh, J. M. Woo, B. J. Navickas, A. Garcia, K. Yin, K. Fish, L. Cavazos, T. Hanisch, B. Markett, D. Yu, S. Hirst, G. Brown-Swigart, L. Esserman, L. J. van 't Veer, L. J. Goodarzi, H. 2024-03-21 doi:10.1101/2024.03.19.585748 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ Genome modeling and design across all domains of life with Evo 2 ]]> https://biorxiv.org/cgi/content/short/2025.02.18.638918v1?rss=1" Brixi, G. Durrant, M. G. Ku, J. Poli, M. Brockman, G. Chang, D. Gonzalez, G. A. King, S. H. Li, D. B. Merchant, A. T. Naghipourfar, M. Nguyen, E. Ricci-Tam, C. Romero, D. W. Sun, G. Taghibakshi, A. Vorontsov, A. Yang, B. Deng, M. Gorton, L. Nguyen, N. Wang, N. K. Adams, E. Baccus, S. A. Dillmann, S. Ermon, S. Guo, D. Ilango, R. Janik, K. Lu, A. X. Mehta, R. Mofrad, M. R. K. Ng, M. Y. Pannu, J. Re, C. Schmok, J. C. St. John, J. Sullivan, J. Zhu, K. Zynda, G. Balsam, D. Collison, P. Costa, A. B. Hernandez-Boussard, T. Ho, E. Liu, M.-Y. McGrath, T. P 2025-02-21 doi:10.1101/2025.02.18.638918 Cold Spring Harbor Laboratory Press 2025-02-21 <![CDATA[ Toxicity of extracellular cGAMP and its analogs to T cells is due to SLC7A1-mediated import ]]> https://biorxiv.org/cgi/content/short/2024.09.21.614248v1?rss=1" Sudaryo, V. R. Carvalho, D. Lee, J. M. Carozza, J. A. Cao, X. Cordova, A. F. Li, L. 2024-09-24 doi:10.1101/2024.09.21.614248 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling ]]> https://biorxiv.org/cgi/content/short/2025.02.20.639398v1?rss=1" Zhang, J. Ubas, A. A. de Borja, R. Svensson, V. Thomas, N. Thakar, N. Lai, I. Winters, A. Khan, U. Jones, M. G. Tran, V. Pangallo, J. Papalexi, E. Sapre, A. Nguyen, H. Sanderson, O. Nigos, M. Kaplan, O. Schroeder, S. Hariadi, B. Marrujo, S. Salvino, C. C. A. Gallareta Olivares, G. Koehler, R. Geiss, G. Rosenberg, A. Roco, C. Merico, D. Alidoust, N. Goodarzi, H. Yu, J. 2025-02-24 doi:10.1101/2025.02.20.639398 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Combinatorial effector targeting (COMET) for transcriptional modulation and locus-specific biochemistry ]]> https://biorxiv.org/cgi/content/short/2024.10.28.620517v1?rss=1" Wilson, C. M. Pommier, G. C. Richman, D. D. Sambold, N. Hussmann, J. A. Weissman, J. S. Gilbert, L. A. 2024-10-28 doi:10.1101/2024.10.28.620517 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ scBaseCamp: An AI agent-curated, uniformly processed, and continually expanding single cell data repository ]]> https://biorxiv.org/cgi/content/short/2025.02.27.640494v1?rss=1" Youngblut, N. D. Carpenter, C. Prashar, J. Ricci-Tam, C. Ilango, R. Teyssier, N. Konermann, S. Hsu, P. Dobin, A. Burke, D. P. Goodarzi, H. Roohani, Y. H. 2025-03-04 doi:10.1101/2025.02.27.640494 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Megabase-scale human genome rearrangement with programmable bridge recombinases ]]> https://biorxiv.org/cgi/content/short/2025.05.14.653916v1?rss=1" Perry, N. T. Bartie, L. J. Katrekar, D. Gonzalez, G. A. Durrant, M. G. Pai, J. J. Fanton, A. Hiraizumi, M. Ricci-Tam, C. Nishimasu, H. Konermann, S. Hsu, P. D. 2025-05-14 doi:10.1101/2025.05.14.653916 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences ]]> https://biorxiv.org/cgi/content/short/2025.04.08.647863v1?rss=1" Teyssier, N. Dobin, A. 2025-04-15 doi:10.1101/2025.04.08.647863 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis ]]> https://biorxiv.org/cgi/content/short/2025.04.26.650725v1?rss=1" Chen, S. Markett, D. Karimzadeh, M. Luo, Y. Khoroshkin, M. S. Boyraz, B. Lee, S. Carpenter, C. Nguyen, P. Garcia, K. Joshi, T. Martin, C. Hanisch, B. Molina, H. Tavazoie, S. Ramani, V. Navickas, A. Goodarzi, H. 2025-04-29 doi:10.1101/2025.04.26.650725 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Red Blood Cells Serve as a Primary Glucose Sink to Improve Glucose Tolerance at Altitude ]]> https://biorxiv.org/cgi/content/short/2025.04.24.650365v1?rss=1" View larger version (51K): org.highwire.dtl.DTLVardef@b6e505org.highwire.dtl.DTLVardef@175e720org.highwire.dtl.DTLVardef@198efdborg.highwire.dtl.DTLVardef@1ab2418_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Marti-Mateos, Y. Midha, A. D. Huynh, H. Flanigan, W. R. Blume, S. Y. Jain, I. H. 2025-04-26 doi:10.1101/2025.04.24.650365 Cold Spring Harbor Laboratory Press 2025-04-26 <![CDATA[ Predicting cellular responses to perturbation across diverse contexts with STATE ]]> https://biorxiv.org/cgi/content/short/2025.06.26.661135v1?rss=1" Adduri, A. Gautam, D. Bevilacqua, B. Imran, A. Shah, R. Naghipourfar, M. Teyssier, N. Ilango, R. Nagaraj, S. Ricci-Tam, C. Carpenter, C. Subramanyam, V. Winters, A. Dong, M. Tirukkovalur, S. Sullivan, J. Plosky, B. Eraslan, B. Youngblut, N. D. Leskovec, J. Gilbert, L. A. Konermann, S. Hsu, P. D. Dobin, A. Burke, D. P. Goodarzi, H. Goodarzi, H. Roohani, Y. H. 2025-06-27 doi:10.1101/2025.06.26.661135 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Generative design of novel bacteriophages with genome language models ]]> https://biorxiv.org/cgi/content/short/2025.09.12.675911v1?rss=1" King, S. H. Driscoll, C. L. Li, D. B. Guo, D. Merchant, A. T. Brixi, G. Wilkinson, M. E. Hie, B. L. 2025-09-17 doi:10.1101/2025.09.12.675911 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Efficient generation of epitope-targeted de novo antibodies with Germinal ]]> https://biorxiv.org/cgi/content/short/2025.09.19.677421v1?rss=1" Mille-Fragoso, L. S. Wang, J. N. Driscoll, C. L. Dai, H. Widatalla, T. M. Zhang, X. Hie, B. L. Gao, X. J. 2025-09-24 doi:10.1101/2025.09.19.677421 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates ]]> https://biorxiv.org/cgi/content/short/2025.09.21.676939v1?rss=1" Wong, M. M.-K. Zhou, S. Carpenter, C. Valbuena, R. Priyadarshini, M. Arya, A. Rizvi, A. Carswell-Crumpton, C. Wileveau, A. Lopez-Lopez, G. Tycko, J. Yao, D. Spees, K. Maynard, J. Bassik, M. C. Goodarzi, H. Sanulli, S. 2025-09-21 doi:10.1101/2025.09.21.676939 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Stack: In-Context Learning of Single-Cell Biology ]]> https://biorxiv.org/cgi/content/short/2026.01.09.698608v1?rss=1" Dong, M. Adduri, A. Gautam, D. Carpenter, C. Shah, R. Ricci-Tam, C. Kluger, Y. Burke, D. P. Roohani, Y. H. 2026-01-09 doi:10.64898/2026.01.09.698608 Cold Spring Harbor Laboratory Press 2026-01-09 <![CDATA[ cyto: ultra high-throughput processing of 10x-flex single cell sequencing ]]> https://biorxiv.org/cgi/content/short/2026.01.21.700936v1?rss=1" Teyssier, N. Dobin, A. 2026-01-22 doi:10.64898/2026.01.21.700936 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ Genome-wide CRISPRi screen identifies basigin loss as protective in cardiac hypoxia ]]> https://biorxiv.org/cgi/content/short/2026.01.26.701810v1?rss=1" Flanigan, W. R. Midha, A. D. Blume, S. Y. Marti-Mateos, Y. Costa, M. W. Huang, Y. Baik, A. H. Huynh, H. Susarla, G. Bennett, N. K. Nowak, R. A. Srivastava, D. Nakamura, K. Jain, I. H. 2026-01-27 doi:10.64898/2026.01.26.701810 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Structure-guided design of a targeted autoantibody degrader for neurologic disease ]]> https://biorxiv.org/cgi/content/short/2026.02.01.703132v1?rss=1" Zimanyi, M. Dayao, M. Asencor, A. I. Kondapavulur, S. Asaki, J. McCutcheon, K. Dabaco, C. Bodansky, A. Craik, C. Pleasure, S. DeRisi, J. L. Cheng, Y. Wilson, M. Pluvinage, J. V. 2026-02-03 doi:10.64898/2026.02.01.703132 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Systemic hypoxia suppresses solid tumor growth ]]> https://biorxiv.org/cgi/content/short/2026.02.09.704975v1?rss=1" Midha, A. D. Chew, B. T. L. Choi, B. M. H. Suh, J. M. Carpenter, C. Baik, A. H. Joshi, T. Blume, S. Y. Haribowo, A. G. Ruivo, P. Flanigan, W. R. Garg, A. Zhang, D. D. Subramanyam, V. Shuere, R. Seo, Y. VanBrocklin, H. Goodarzi, H. Jain, I. H. 2026-02-10 doi:10.64898/2026.02.09.704975 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning ]]> https://biorxiv.org/cgi/content/short/2026.03.19.712954v1?rss=1" Fallahpour, A. Seyed-Ahmadi, A. Idehpour, P. Ibrahim, O. Gupta, P. Naimer, J. Zhu, K. Shah, A. Ma, S. Adduri, A. Güloglu, T. Liu, N. Cui, H. Jain, A. de Castro, M. Fallahpour, A. Cembellin-Prieto, A. Stiles, J. S. Nemcko, F. Nevue, A. A. Moon, H. C. Sosnick, L. Markham, O. Duan, H. Lee, M. Y. Y. Salvador, A. F. M. Maddison, C. J. Thaiss, C. A. Ricci-Tam, C. Plosky, B. S. Burke, D. P. Hsu, P. D. Goodarzi, H. Wang, B. 2026-03-20 doi:10.64898/2026.03.19.712954 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ ENPP1 buffers extracellular cGAMP in brown adipose tissue to limit insulin resistance ]]> https://biorxiv.org/cgi/content/short/2026.04.12.718013v1?rss=1" Wang, S. Guo, Y. An, W. Lee, M. Li, Y. Sudaryo, V. Grenot, G. Skariah, G. Reghupaty, S. C. Young, S. Bai, X. Svensson, K. J. Li, L. 2026-04-14 doi:10.64898/2026.04.12.718013 Cold Spring Harbor Laboratory Press 2026-04-14