scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data von Alquicira-Hernandez, Jose, Sathe, Anuja, Ji, Hanlee P, Nguyen, Quan, Powell, Joseph E

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Single-Cell Genomic Characterization Reveals the Cellular Reprogramming of the Gastric Tumor Microenvironment von Sathe, Anuja, Grimes, Susan M., Lau, Billy T., Chen, Jiamin, Suarez, Carlos, Huang, Robert J., Poultsides, George, Ji, Hanlee P.

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Single-cell analysis can define distinct evolution of tumor sites in follicular lymphoma von Haebe, Sarah, Shree, Tanaya, Sathe, Anuja, Day, Grady, Czerwinski, Debra K., Grimes, Susan M., Lee, HoJoon, Binkley, Michael S., Long, Steven R., Martin, Brock, Ji, Hanlee P., Levy, Ronald

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Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay von Hernández Bustos, Adrián, Martiny, Elisa, Bom Pedersen, Nadia, Parvathaneni, Rohith Pavan, Hansen, Jonas, Ji, Hanlee P., Astakhova, Kira

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Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing von Lau, Billy, Chandak, Shubham, Roy, Sharmili, Tatwawadi, Kedar, Wootters, Mary, Weissman, Tsachy, Ji, Hanlee P.

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KmerKeys: a web resource for searching indexed genome assemblies and variants von Pavlichin, Dmitri S, Lee, HoJoon, Greer, Stephanie U, Grimes, Susan M, Weissman, Tsachy, Ji, Hanlee P

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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions von Mason, Kaishu, Sathe, Anuja, Hess, Paul R, Rong, Jiazhen, Wu, Chi-Yun, Furth, Emma, Susztak, Katalin, Levinsohn, Jonathan, Ji, Hanlee P, Zhang, Nancy

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Performance comparison of whole-genome sequencing platforms von Lam, Hugo Y K, Clark, Michael J, Chen, Rui, Chen, Rong, Natsoulis, Georges, O'Huallachain, Maeve, Dewey, Frederick E, Habegger, Lukas, Ashley, Euan A, Gerstein, Mark B, Butte, Atul J, Ji, Hanlee P, Snyder, Michael

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Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing von Kim, Heon Seok, Grimes, Susan M., Hooker, Anna C., Lau, Billy T., Ji, Hanlee P.

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GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers von Sathe, Anuja, Ayala, Carlos, Bai, Xiangqi, Grimes, Susan M, Lee, Byrne, Kin, Cindy, Shelton, Andrew, Poultsides, George, Ji, Hanlee P

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Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes von Lau, Billy T, Ji, Hanlee P

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Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications von An, Ho Jung, Partha, Mira A, Lee, HoJoon, Lau, Billy T, Pavlichin, Dmitri S, Almeda, Alison, Hooker, Anna C, Shin, Giwon, Ji, Hanlee P

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A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images von Su, Andrew, Lee, HoJoon, Tan, Xiao, Suarez, Carlos J., Andor, Noemi, Nguyen, Quan, Ji, Hanlee P.

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High Sensitivity Detection and Quantitation of DNA Copy Number and Single Nucleotide Variants with Single Color Droplet Digital PCR von Miotke, Laura, Lau, Billy T., Rumma, Rowza T., Ji, Hanlee P.

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Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer von Grimes, Susan M, Kim, Heon Seok, Roy, Sharmili, Sathe, Anuja, Ayala, Carlos I, Bai, Xiangqi, Almeda-Notestine, Alison F, Haebe, Sarah, Shree, Tanaya, Levy, Ronald, Lau, Billy T, Ji, Hanlee P

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Haplotyping germline and cancer genomes with high-throughput linked-read sequencing von Zheng, Grace X Y, Lau, Billy T, Schnall-Levin, Michael, Jarosz, Mirna, Bell, John M, Hindson, Christopher M, Kyriazopoulou-Panagiotopoulou, Sofia, Masquelier, Donald A, Merrill, Landon, Terry, Jessica M, Mudivarti, Patrice A, Wyatt, Paul W, Bharadwaj, Rajiv, Makarewicz, Anthony J, Li, Yuan, Belgrader, Phillip, Price, Andrew D, Lowe, Adam J, Marks, Patrick, Vurens, Gerard M, Hardenbol, Paul, Montesclaros, Luz, Luo, Melissa, Greenfield, Lawrence, Wong, Alexander, Birch, David E, Short, Steven W, Bjornson, Keith P, Patel, Pranav, Hopmans, Erik S, Wood, Christina, Kaur, Sukhvinder, Lockwood, Glenn K, Stafford, David, Delaney, Joshua P, Wu, Indira, Ordonez, Heather S, Grimes, Susan M, Greer, Stephanie, Lee, Josephine Y, Belhocine, Kamila, Giorda, Kristina M, Heaton, William H, McDermott, Geoffrey P, Bent, Zachary W, Meschi, Francesca, Kondov, Nikola O, Wilson, Ryan, Bernate, Jorge A, Gauby, Shawn, Kindwall, Alex, Bermejo, Clara, Fehr, Adrian N, Chan, Adrian, Saxonov, Serge, Ness, Kevin D, Hindson, Benjamin J, Ji, Hanlee P

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New approaches to moderate CRISPR-Cas9 activity: Addressing issues of cellular uptake and endosomal escape von van Hees, Maja, Slott, Sofie, Hansen, Anders Højgaard, Kim, Heon Seok, Ji, Hanlee P., Astakhova, Kira

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Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding von Lau, Billy T, Wood-Bouwens, Christina, Ji, Hanlee P

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ALTEN: A High‐Fidelity Primary Tissue‐Engineering Platform to Assess Cellular Responses Ex Vivo von Law, Andrew M. K., Chen, Jiamin, Colino‐Sanguino, Yolanda, Fuente, Laura Rodriguez de la, Fang, Guocheng, Grimes, Susan M., Lu, Hongxu, Huang, Robert J., Boyle, Sarah T., Venhuizen, Jeron, Castillo, Lesley, Tavakoli, Javad, Skhinas, Joanna N., Millar, Ewan K. A., Beretov, Julia, Rossello, Fernando J., Tipper, Joanne L., Ormandy, Christopher J., Samuel, Michael S., Cox, Thomas R., Martelotto, Luciano, Jin, Dayong, Valdes‐Mora, Fatima, Ji, Hanlee P., Gallego‐Ortega, David

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Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 von Zhou, Bo, Ho, Steve S, Greer, Stephanie U, Zhu, Xiaowei, Bell, John M, Arthur, Joseph G, Spies, Noah, Zhang, Xianglong, Byeon, Seunggyu, Pattni, Reenal, Ben-Efraim, Noa, Haney, Michael S, Haraksingh, Rajini R, Song, Giltae, Ji, Hanlee P, Perrin, Dimitri, Wong, Wing H, Abyzov, Alexej, Urban, Alexander E

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