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| 1. | Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana [RESOURCES] | Denyer, T., Wu, P.-J., Colt, K., Abramson, B. W., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J. R., Lam, E., Michael, T. P., Timmermans, M. C. P. | |
| 2. | Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs [METHODS] | Kuronen, J., Horsfield, S. T., Pöntinen, A. K., Mallawaarachchi, S., Arredondo-Alonso, S., Thorpe, H., Gladstone, R. A., Willems, R. J. L., Bentley, S. D., Croucher, N. J., Pensar, J., Lees, J. A., Tonkin-Hill, G., Corander, J. | |
| 3. | Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [RESOURCES] | Xiang, G., He, X., Giardine, B. M., Isaac, K. J., Taylor, D. J., McCoy, R. C., Jansen, C., Keller, C. A., Wixom, A. Q., Cockburn, A., Miller, A., Qi, Q., He, Y., Li, Y., Lichtenberg, J., Heuston, E. F., Anderson, S. M., Luan, J., Vermunt, M. W., Yue, F., Sauria, M. E. G., Schatz, M. C., Taylor, J., Göttgens, B., Hughes, J. R., Higgs, D. R., Weiss, M. J., Cheng, Y., Blobel, G. A., Bodine, D. M., Zhang, Y., Li, Q., Mahony, S., Hardison, R. C. | |
| 4. | Delineating yeast cleavage and polyadenylation signals using deep learning [METHODS] | Stroup, E. K., Ji, Z. | |
| 5. | Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences [METHODS] | Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T., Zhang, C. | |
| 6. | A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data [METHODS] | Zhao, M., Li, J., Liu, X., Ma, K., Tang, J., Guo, F. | |
| 7. | CodonBERT large language model for mRNA vaccines [METHODS] | Li, S., Moayedpour, S., Li, R., Bailey, M., Riahi, S., Kogler-Anele, L., Miladi, M., Miner, J., Pertuy, F., Zheng, D., Wang, J., Balsubramani, A., Tran, K., Zacharia, M., Wu, M., Gu, X., Clinton, R., Asquith, C., Skaleski, J., Boeglin, L., Chivukula, S., Dias, A., Strugnell, T., Montoya, F. U., Agarwal, V., Bar-Joseph, Z., Jager, S. | |
| 8. | High-fidelity, large-scale targeted profiling of microsatellites [METHODS] | Loh, C. A., Shields, D. A., Schwing, A., Evrony, G. D. | |
| 9. | The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution [RESEARCH] | Li, X., Mank, J. E., Ban, L. | |
| 10. | The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores [RESEARCH] | Liu, Y., Zhai, G., Su, J., Gong, Y., Yang, B., Lu, Q., Xi, L., Zheng, Y., Cao, J., Liu, H., Jin, J., Zhang, Z., Yang, Y., Zhu, X., Wang, Z., Gong, G., Mei, J., Yin, Z., Gozlan, R. E., Xie, S., Han, D. | |
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| 2024-08-21 | Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana [RESOURCES] | Denyer, T., Wu, P.-J., Colt, K., Abramson, B. W., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J. R., Lam, E., Michael, T. P., Timmermans, M. C. P. | |
| 2024-08-21 | Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs [METHODS] | Kuronen, J., Horsfield, S. T., Pöntinen, A. K., Mallawaarachchi, S., Arredondo-Alonso, S., Thorpe, H., Gladstone, R. A., Willems, R. J. L., Bentley, S. D., Croucher, N. J., Pensar, J., Lees, J. A., Tonkin-Hill, G., Corander, J. | |
| 2024-08-21 | Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [RESOURCES] | Xiang, G., He, X., Giardine, B. M., Isaac, K. J., Taylor, D. J., McCoy, R. C., Jansen, C., Keller, C. A., Wixom, A. Q., Cockburn, A., Miller, A., Qi, Q., He, Y., Li, Y., Lichtenberg, J., Heuston, E. F., Anderson, S. M., Luan, J., Vermunt, M. W., Yue, F., | |
| 2024-08-21 | Delineating yeast cleavage and polyadenylation signals using deep learning [METHODS] | Stroup, E. K., Ji, Z. | |
| 2024-08-21 | Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences [METHODS] | Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T., Zhang, C. | |
| 2024-08-21 | A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data [METHODS] | Zhao, M., Li, J., Liu, X., Ma, K., Tang, J., Guo, F. | |
| 2024-08-21 | CodonBERT large language model for mRNA vaccines [METHODS] | Li, S., Moayedpour, S., Li, R., Bailey, M., Riahi, S., Kogler-Anele, L., Miladi, M., Miner, J., Pertuy, F., Zheng, D., Wang, J., Balsubramani, A., Tran, K., Zacharia, M., Wu, M., Gu, X., Clinton, R., Asquith, C., Skaleski, J., Boeglin, L., Chivukula, S., | |
| 2024-08-21 | High-fidelity, large-scale targeted profiling of microsatellites [METHODS] | Loh, C. A., Shields, D. A., Schwing, A., Evrony, G. D. | |
| 2024-08-21 | The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution [RESEARCH] | Li, X., Mank, J. E., Ban, L. | |
| 2024-08-21 | The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores [RESEARCH] | Liu, Y., Zhai, G., Su, J., Gong, Y., Yang, B., Lu, Q., Xi, L., Zheng, Y., Cao, J., Liu, H., Jin, J., Zhang, Z., Yang, Y., Zhu, X., Wang, Z., Gong, G., Mei, J., Yin, Z., Gozlan, R. E., Xie, S., Han, D. | |
| 2024-07-24 | Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere [CORRIGENDUM] | Wong, L. H., Brettingham-Moore, K. H., Chan, L., Quach, J. M., Anderson, M. A., Northrop, E. L., Hannan, R., Saffery, R., Shaw, M. L., Williams, E., Choo, K. H. A. | |
| 2024-07-24 | DEAD box RNA helicases are pervasive protein kinase interactors and activators [RESOURCES] | Hirth, A., Fatti, E., Netz, E., Acebron, S. P., Papageorgiou, D., Svorinic, A., Cruciat, C.-M., Karaulanov, E., Gopanenko, A., Zhu, T., Sinning, I., Krijgsveld, J., Kohlbacher, O., Niehrs, C. | |
| 2024-07-24 | Global compositional and functional states of the human gut microbiome in health and disease [RESOURCES] | Lee, S., Portlock, T., Le Chatelier, E., Garcia-Guevara, F., Clasen, F., Onate, F. P., Pons, N., Begum, N., Harzandi, A., Proffitt, C., Rosario, D., Vaga, S., Park, J., von Feilitzen, K., Johansson, F., Zhang, C., Edwards, L. A., Lombard, V., Gauthier, F. | |
| 2024-07-24 | Accurate estimation of pathway activity in single cells for clustering and differential analysis [METHODS] | Davis, D., Wizel, A., Drier, Y. | |
| 2024-07-24 | Accurate allocation of multimapped reads enables regulatory element analysis at repeats [METHODS] | Morrissey, A., Shi, J., James, D. Q., Mahony, S. | |
| 2024-07-24 | Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine [METHODS] | Yan, B., Wang, D., Ettwiller, L. | |
| 2024-07-24 | Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters [METHODS] | Ulrich, J.-U., Renard, B. Y. | |
| 2024-07-24 | Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States [RESEARCH] | Bellinzona, G., Nardi, T., Castelli, M., Batisti Biffignandi, G., Adjou, K., Betson, M., Blanchard, Y., Bujila, I., Chalmers, R., Davidson, R., D'Avino, N., Enbom, T., Gomes, J., Karadjian, G., Klotz, C., Östlund, E., Plutzer, J., Rimhanen-Fin | |
| 2024-07-24 | Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins [RESEARCH] | Vakirlis, N., Kupczok, A. | |
| 2024-07-24 | Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior [RESEARCH] | Errbii, M., Gadau, J., Becker, K., Schrader, L., Oettler, J. | |
| 2024-07-24 | Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles [RESEARCH] | Wang, X., Heckel, G. | |
| 2024-07-24 | Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue [RESEARCH] | Venkat, A., Carlino, M. J., Lawton, B. R., Prasad, M. L., Amodio, M., Gibson, C. E., Zeiss, C. J., Youlten, S. E., Krishnaswamy, S., Krause, D. S. | |
| 2024-07-24 | Single-cell discovery of m6A RNA modifications in the hippocampus [RESEARCH] | Feng, S., Tellaetxe-Abete, M., Zhang, Y., Peng, Y., Zhou, H., Dong, M., Larrea, E., Xue, L., Zhang, L., Koziol, M. J. | |
| 2024-07-24 | Large-scale genomic analysis of the domestic dog informs biological discovery [MINI-REVIEW] | Buckley, R. M., Ostrander, E. A. | |
| 2024-06-25 | A harmonized public resource of deeply sequenced diverse human genomes [RESOURCES] | Koenig, Z., Yohannes, M. T., Nkambule, L. L., Zhao, X., Goodrich, J. K., Kim, H. A., Wilson, M. W., Tiao, G., Hao, S. P., Sahakian, N., Chao, K. R., Walker, M. A., Lyu, Y., gnomAD Project Consortium, Rehm, H. L., Neale, B. M., Talkowski, M. E., Daly, M. J | |
| 2024-06-25 | Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic [ERRATUM] | Shaw, J., Yu, Y. W. | |
| 2024-06-25 | Simulation of nanopore sequencing signal data with tunable parameters [METHODS] | Gamaarachchi, H., Ferguson, J. M., Samarakoon, H., Liyanage, K., Deveson, I. W. | |
| 2024-06-25 | Identifying genes within pathways in unannotated genomes with PaGeSearch [METHODS] | Won, S., Yu, J., Kim, H. | |
| 2024-06-25 | GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes [METHODS] | Bruna, T., Lomsadze, A., Borodovsky, M. | |
| 2024-06-25 | BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA [METHODS] | Gabriel, L., Bruna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., Stanke, M. | |
| 2024-06-25 | Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis) [RESEARCH] | Lv, P., Yang, X., Zhao, X., Zhao, Z., Du, J. | |
| 2024-06-25 | Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote [RESEARCH] | Sheng, Y., Wang, Y., Yang, W., Wang, X. Q., Lu, J., Pan, B., Nan, B., Liu, Y., Ye, F., Li, C., Song, J., Dou, Y., Gao, S., Liu, Y. | |
| 2024-06-25 | Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary [RESEARCH] | Srivastav, S. P., Feschotte, C., Clark, A. G. | |
| 2024-06-25 | Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice [RESEARCH] | Boukas, L., Luperchio, T. R., Razi, A., Hansen, K. D., Bjornsson, H. T. | |
| 2024-06-25 | Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer [RESEARCH] | Razavi-Mohseni, M., Huang, W., Guo, Y. A., Shigaki, D., Ho, S. W. T., Tan, P., Skanderup, A. J., Beer, M. A. | |
| 2024-06-25 | Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy [RESEARCH] | Chen, L., Kong, X., Johnston, K. G., Mortazavi, A., Holmes, T. C., Tan, Z., Yokomori, K., Xu, X. | |
| 2024-06-25 | Toward telomere-to-telomere cat genomes for precision medicine and conservation biology [MINI-REVIEW] | Murphy, W. J., Harris, A. J. | |
| 2024-05-16 | A new framework for exploratory network mediator analysis in omics data [METHODS] | Cai, Q., Fu, Y., Lyu, C., Wang, Z., Rao, S., Alvarez, J. A., Bai, Y., Kang, J., Yu, T. | |
| 2024-05-16 | Probabilistic association of differentially expressed genes with cis-regulatory elements [METHODS] | Roberts, B. S., Anderson, A. G., Partridge, E. C., Cooper, G. M., Myers, R. M. | |
| 2024-05-16 | Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples [METHODS] | Ji, S., Zhu, T., Sethia, A., Wang, W. | |
| 2024-05-16 | Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in a Drosophila knock-in tauopathy model [RESEARCH] | Bukhari, H., Nithianandam, V., Battaglia, R. A., Cicalo, A., Sarkar, S., Comjean, A., Hu, Y., Leventhal, M. J., Dong, X., Feany, M. B. | |
| 2024-05-16 | Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence [RESEARCH] | Ferguson, S., Jones, A., Murray, K., Andrew, R., Schwessinger, B., Borevitz, J. | |
| 2024-05-16 | Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy [RESEARCH] | Iyer, D. P., Moyon, L., Wittler, L., Cheng, C.-Y., Ringeling, F. R., Canzar, S., Marsico, A., Bulut-Karslioglu, A. | |
| 2024-05-16 | Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription [RESEARCH] | Keenan, C. R., Coughlan, H. D., Iannarella, N., Tapia del Fierro, A., Keniry, A., Johanson, T. M., Chan, W. F., Garnham, A. L., Whitehead, L. W., Blewitt, M. E., Smyth, G. K., Allan, R. S. | |
| 2024-05-16 | Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions [RESEARCH] | Joosten, S. E. P., Gregoricchio, S., Stelloo, S., Yapıcı, E., Huang, C.-C. F., Yavuz, K., Donaldson Collier, M., Morova, T., Altintas, U. B., Kim, Y., Canisius, S., Moelans, C. B., van Diest, P. J., Korkmaz, G., Lack, N. A., Vermeule | |
| 2024-05-16 | Ribosome decision graphs for the representation of eukaryotic RNA translation complexity [PERSPECTIVE] | Tierney, J. A. S., Swirski, M., Tjeldnes, H., Mudge, J. M., Kufel, J., Whiffin, N., Valen, E., Baranov, P. V. | |
| 2024-05-16 | Navigating the landscape of epitranscriptomics and host immunity [REVIEW] | Huang, E., Frydman, C., Xiao, X. | |
| 2024-04-26 | Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data [CORRIGENDUM] | Qin, F., Cai, G., Amos, C. I., Xiao, F. | |
| 2024-04-26 | Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches [METHODS] | Lee, M., Guo, Q., Kim, M., Choi, J., Segura, A., Genceroglu, A., LeBlanc, L., Ramirez, N., Jang, Y. J., Jang, Y., Lee, B.-K., Marcotte, E. M., Kim, J. | |
| 2024-04-26 | The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals [RESOURCES] | Schnitzler, C. E., Chang, E. S., Waletich, J., Quiroga-Artigas, G., Wong, W. Y., Nguyen, A.-D., Barreira, S. N., Doonan, L. B., Gonzalez, P., Koren, S., Gahan, J. M., Sanders, S. M., Bradshaw, B., DuBuc, T. Q., Febrimarsa, , de Jong, D., Nawrocki, E. P., | |
| 2024-04-26 | Phased nanopore assembly with Shasta and modular graph phasing with GFAse [METHODS] | Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H. E., McNulty, B., Porubsky, D., Montague, T. G., Lucas, J. K., Condon, C., Eizenga, J. M., Juul, S., McKenzie, S. K., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E. E., Axel, R., | |
| 2024-04-26 | Robust chromatin state annotation [METHODS] | Foroozandeh Shahraki, M., Farahbod, M., Libbrecht, M. W. | |
| 2024-04-26 | Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species [RESEARCH] | Plessy, C., Mansfield, M. J., Bliznina, A., Masunaga, A., West, C., Tan, Y., Liu, A. W., Grasic, J., del Rio Pisula, M. S., Sanchez-Serna, G., Fabrega-Torrus, M., Ferrandez-Roldan, A., Roncalli, V., Navratilova, P., Thompson, E. M., Onuma, T., Nishida, H. | |
| 2024-04-26 | Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites [RESEARCH] | Reis-Cunha, J. L., Pimenta-Carvalho, S. A., Almeida, L. V., Coqueiro-dos-Santos, A., Marques, C. A., Black, J. A., Damasceno, J., McCulloch, R., Bartholomeu, D. C., Jeffares, D. C. | |
| 2024-04-26 | Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements [RESEARCH] | Selvaraju, D., Wierzbicki, F., Kofler, R. | |
| 2024-04-26 | Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation [RESEARCH] | Mercier, B. C., Labaronne, E., Cluet, D., Guiguettaz, L., Fontrodona, N., Bicknell, A., Corbin, A., Wencker, M., Aube, F., Modolo, L., Jouravleva, K., Auboeuf, D., Moore, M. J., Ricci, E. P. | |
| 2024-04-26 | Systematic identification and characterization of exon-intron circRNAs [RESEARCH] | Zhong, Y., Yang, Y., Wang, X., Ren, B., Wang, X., Shan, G., Chen, L. | |
| 2024-04-26 | Inference of selective forces on house mouse genomes during secondary contact in East Asia [RESEARCH] | Fujiwara, K., Kubo, S., Endo, T., Takada, T., Shiroishi, T., Suzuki, H., Osada, N. | |
| 2024-04-26 | A systematic review on the biochemical threshold of mitochondrial genetic variants [REVIEW] | Smith, K. K., Moreira, J. D., Wilson, C. R., Padera, J. O., Lamason, A. N., Xue, L., Gopal, D. M., Flynn, D. B., Fetterman, J. L. | |
| 2023-08-25 | Efficient minimizer orders for large values of k using minimum decycling sets [METHODS] | Pellow, D., Pu, L., Ekim, B., Kotlar, L., Berger, B., Shamir, R., Orenstein, Y. | |
| 2023-08-25 | Unsupervised contrastive peak caller for ATAC-seq [METHODS] | Vu, H. T. H., Zhang, Y., Tuteja, G., Dorman, K. S. | |
| 2023-08-25 | Leveraging protein language models for accurate multiple sequence alignments [METHODS] | McWhite, C. D., Armour-Garb, I., Singh, M. | |
| 2023-08-25 | Fast inference of genetic recombination rates in biobank scale data [METHODS] | Naseri, A., Yue, W., Zhang, S., Zhi, D. | |
| 2023-08-25 | Partial alignment of multislice spatially resolved transcriptomics data [METHODS] | Liu, X., Zeira, R., Raphael, B. J. | |
| 2023-08-25 | Efficient mapping of accurate long reads in minimizer space with mapquik [METHODS] | Ekim, B., Sahlin, K., Medvedev, P., Berger, B., Chikhi, R. | |
| 2023-08-25 | Aligning distant sequences to graphs using long seed sketches [METHODS] | Joudaki, A., Meterez, A., Mustafa, H., Groot Koerkamp, R., Kahles, A., Rätsch, G. | |
| 2023-08-25 | Efficient taxa identification using a pangenome index [METHODS] | Ahmed, O., Rossi, M., Boucher, C., Langmead, B. | |
| 2023-08-25 | Modeling and predicting cancer clonal evolution with reinforcement learning [METHODS] | Ivanovic, S., El-Kebir, M. | |
| 2023-08-25 | A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings [METHODS] | Zhang, L., Abhari, N., Colijn, C., Wu, Y. | |
| 2023-08-25 | Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash [METHODS] | Rahman Hera, M., Pierce-Ward, N. T., Koslicki, D. | |
| 2023-08-25 | Improving quartet graph construction for scalable and accurate species tree estimation from gene trees [METHODS] | Han, Y., Molloy, E. K. | |
| 2023-08-25 | Leveraging family data to design Mendelian randomization that is provably robust to population stratification [METHODS] | LaPierre, N., Fu, B., Turnbull, S., Eskin, E., Sankararaman, S. | |
| 2023-08-25 | Ultrafast genome-wide inference of pairwise coalescence times [METHODS] | Schweiger, R., Durbin, R. | |
| 2023-08-25 | Entropy predicts sensitivity of pseudorandom seeds [METHODS] | Maier, B. D., Sahlin, K. | |
| 2023-08-25 | Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models [METHODS] | Liu, Y., Li, X. C., Rashidi Mehrabadi, F., Schäffer, A. A., Pratt, D., Crawford, D. R., Malikic, S., Molloy, E. K., Gopalan, V., Mount, S. M., Ruppin, E., Aldape, K. D., Sahinalp, S. C. | |
| 2023-08-25 | Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic [METHODS] | Shaw, J., Yu, Y. W. | |
| 2023-08-25 | Assessing transcriptomic reidentification risks using discriminative sequence models [METHODS] | Sadhuka, S., Fridman, D., Berger, B., Cho, H. | |
| 2023-08-25 | Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT [METHODS] | Cracco, A., Tomescu, A. I. | |
| 2023-08-25 | Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics [METHODS] | Venkatesaramani, R., Wan, Z., Malin, B. A., Vorobeychik, Y. | |
| 2023-08-25 | Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2 [METHODS] | Baker, D. N., Langmead, B. | |
| 2023-08-25 | Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model [METHODS] | Sanaullah, A., Zhi, D., Zhang, S. | |
| 2023-07-21 | Discordant calls across genotype discovery approaches elucidate variants with systematic errors [RESOURCES] | Atkinson, E. G., Artomov, M., Loboda, A. A., Rehm, H. L., MacArthur, D. G., Karczewski, K. J., Neale, B. M., Daly, M. J. | |
| 2023-07-21 | Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe [METHODS] | Belcour, A., Got, J., Aite, M., Delage, L., Collen, J., Frioux, C., Leblanc, C., Dittami, S. M., Blanquart, S., Markov, G. V., Siegel, A. | |
| 2023-07-21 | Genealogical inference and more flexible sequence clustering using iterative-PopPUNK [METHODS] | Zhao, B., Lees, J. A., Wu, H., Yang, C., Falush, D. | |
| 2023-07-21 | Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates [METHODS] | Faulk, C. | |
| 2023-07-21 | Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets [METHODS] | Jourdain, J., Barasc, H., Faraut, T., Calgaro, A., Bonnet, N., Marcuzzo, C., Suin, A., Barbat, A., Hoze, C., Besnard, F., Taussat, S., Grohs, C., Kuchly, C., Iampietro, C., Donnadieu, C., Pinton, A., Boichard, D., Capitan, A. | |
| 2023-07-21 | Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data [METHODS] | Song, L., Bai, G., Liu, X. S., Li, B., Li, H. | |
| 2023-07-21 | Debiased personalized gene coexpression networks for population-scale scRNA-seq data [METHODS] | Lu, S., Keles, S. | |
| 2023-07-21 | Accurate sequencing of DNA motifs able to form alternative (non-B) structures [METHODS] | Weissensteiner, M. H., Cremona, M. A., Guiblet, W. M., Stoler, N., Harris, R. S., Cechova, M., Eckert, K. A., Chiaromonte, F., Huang, Y.-F., Makova, K. D. | |
| 2023-07-21 | Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation [RESEARCH] | Collora, J. A., Ho, Y.-C. | |
| 2023-07-21 | Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster [RESEARCH] | Grandchamp, A., Kühl, L., Lebherz, M., Brüggemann, K., Parsch, J., Bornberg-Bauer, E. | |
| 2023-07-21 | Variation in histone configurations correlates with gene expression across nine inbred strains of mice [RESEARCH] | Tyler, A. L., Spruce, C., Kursawe, R., Haber, A., Ball, R. L., Pitman, W. A., Fine, A. D., Raghupathy, N., Walker, M., Philip, V. M., Baker, C. L., Mahoney, J. M., Churchill, G. A., Trowbridge, J. J., Stitzel, M. L., Paigen, K., Petkov, P. M., Carter, G. | |
| 2023-07-21 | Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution [RESEARCH] | Resztak, J. A., Wei, J., Zilioli, S., Sendler, E., Alazizi, A., Mair-Meijers, H. E., Wu, P., Wen, X., Slatcher, R. B., Zhou, X., Luca, F., Pique-Regi, R. | |
| 2023-06-17 | Corrigendum: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa [CORRIGENDUM] | Villalba de la Pena, M., Summanen, P. A. M., Liukkonen, M., Kronholm, I. | |
| 2023-06-17 | The fine-scale recombination rate variation and associations with genomic features in a butterfly [RESOURCES] | Palahi i Torres, A., Höök, L., Näsvall, K., Shipilina, D., Wiklund, C., Vila, R., Pruisscher, P., Backström, N. | |
| 2023-06-17 | Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser [RESOURCES] | Zhuo, X., Hsu, S., Purushotham, D., Kuntala, P. K., Harrison, J. K., Du, A. Y., Chen, S., Li, D., Wang, T. | |
| 2023-06-17 | CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes [METHODS] | Rossato, M., Marcolungo, L., De Antoni, L., Lopatriello, G., Bellucci, E., Cortinovis, G., Frascarelli, G., Nanni, L., Bitocchi, E., Di Vittori, V., Vincenzi, L., Lucchini, F., Bett, K. E., Ramsay, L., Konkin, D. J., Delledonne, M., Papa, R. | |
| 2023-06-17 | Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library [RESOURCES] | He, J., Zhang, K., Yan, S., Tang, M., Zhou, W., Yin, Y., Chen, K., Zhang, C., Li, M. | |
| 2023-06-17 | Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets [METHODS] | Morin, A., Chu, E. C.-P., Sharma, A., Adrian-Hamazaki, A., Pavlidis, P. | |
| 2023-06-17 | Targeted, programmable, and precise tandem duplication in the mammalian genome [METHODS] | Jiao, Y., Li, M., He, X., Wang, Y., Song, J., Hu, Y., Li, L., Zhou, L., Jiang, L., Qu, J., Xie, L., Chen, Q., Yao, S. | |
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