Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning von Wang, Bo, Zhu, Junjie, Pierson, Emma, Ramazzotti, Daniele, Batzoglou, Serafim

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Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival von Ramazzotti, Daniele, Lal, Avantika, Wang, Bo, Batzoglou, Serafim, Sidow, Arend

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What is the expectation maximization algorithm? von Do, Chuong B, Batzoglou, Serafim

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A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy von Popic, Victoria, Batzoglou, Serafim

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Network enhancement as a general method to denoise weighted biological networks von Wang, Bo, Pourshafeie, Armin, Zitnik, Marinka, Zhu, Junjie, Bustamante, Carlos D., Batzoglou, Serafim, Leskovec, Jure

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Fast and scalable inference of multi-sample cancer lineages von Popic, Victoria, Salari, Raheleh, Hajirasouliha, Iman, Kashef-Haghighi, Dorna, West, Robert B, Batzoglou, Serafim

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Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome von Kuleshov, Volodymyr, Jiang, Chao, Zhou, Wenyu, Jahanbani, Fereshteh, Batzoglou, Serafim, Snyder, Michael

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Identifying a high fraction of the human genome to be under selective constraint using GERP von Davydov, Eugene V, Goode, David L, Sirota, Marina, Cooper, Gregory M, Sidow, Arend, Batzoglou, Serafim

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Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation von Green, Michael R., Kihira, Shingo, Liu, Chih Long, Nair, Ramesh V., Salari, Raheleh, Gentles, Andrew J., Irish, Jonathan, Stehr, Henning, Vicente-Dueñas, Carolina, Romero-Camarero, Isabel, Sanchez-Garcia, Isidro, Plevritis, Sylvia K., Arber, Daniel A., Batzoglou, Serafim, Levy, Ronald, Alizadeh, Ash A.

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Genome-wide reconstruction of complex structural variants using read clouds von Spies, Noah, Weng, Ziming, Bishara, Alex, McDaniel, Jennifer, Catoe, David, Zook, Justin M, Salit, Marc, West, Robert B, Batzoglou, Serafim, Sidow, Arend

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Extensive Variation in Chromatin States Across Humans von Kasowski, Maya, Kyriazopoulou-Panagiotopoulou, Sofia, Grubert, Fabian, Zaugg, Judith B., Kundaje, Anshul, Liu, Yuling, Boyle, Alan P., Zhang, Qiangfeng Cliff, Zakharia, Fouad, Spacek, Damek V., Li, Jingjing, Xie, Dan, Olarenn-George, Anthony, Steinmetz, Lars M., Hogenesch, John B., Kellis, Manolis, Batzoglou, Serafim, Snyder, Michael

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CONTRAfold: RNA secondary structure prediction without physics-based models von Do, Chuong B., Woods, Daniel A., Batzoglou, Serafim

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HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data von Zhou, Xin, Batzoglou, Serafim, Sidow, Arend, Zhang, Lu

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Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data von Sidow, Arend, Valouev, Anton, Johnson, David S, Sundquist, Andreas, Medina, Catherine, Anton, Elizabeth, Batzoglou, Serafim, Myers, Richard M

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Distribution and intensity of constraint in mammalian genomic sequence von Cooper, Gregory M, Stone, Eric A, Asimenos, George, Green, Eric D, Batzoglou, Serafim, Sidow, Arend

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A machine-compiled database of genome-wide association studies von Kuleshov, Volodymyr, Ding, Jialin, Vo, Christopher, Hancock, Braden, Ratner, Alexander, Li, Yang, Ré, Christopher, Batzoglou, Serafim, Snyder, Michael

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ProbCons: Probabilistic consistency-based multiple sequence alignment von Do, Chuong B, Mahabhashyam, Mahathi S P, Brudno, Michael, Batzoglou, Serafim

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Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements von Kundaje, Anshul, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max, Smith, Cheryl L, Raha, Debasish, Winters, Elliott E, Johnson, Steven M, Snyder, Michael, Batzoglou, Serafim, Sidow, Arend

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Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping von Suhre, Karsten, Venkataraman, Guhan Ram, Guturu, Harendra, Halama, Anna, Stephan, Nisha, Thareja, Gaurav, Sarwath, Hina, Motamedchaboki, Khatereh, Donovan, Margaret K. R., Siddiqui, Asim, Batzoglou, Serafim, Schmidt, Frank

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Read clouds uncover variation in complex regions of the human genome von Bishara, Alex, Liu, Yuling, Weng, Ziming, Kashef-Haghighi, Dorna, Newburger, Daniel E, West, Robert, Sidow, Arend, Batzoglou, Serafim

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