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

Volltext

Genomic Instability in Cancer: Teetering on the Limit of Tolerance von Andor, Noemi, Maley, Carlo C, Ji, Hanlee P

Volltext

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.

Volltext

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity von Andor, Noemi, Graham, Trevor A, Jansen, Marnix, Xia, Li C, Aktipis, C Athena, Petritsch, Claudia, Ji, Hanlee P, Maley, Carlo C

Volltext

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

Volltext

Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture von Li, Xingnan, Nadauld, Lincoln, Ootani, Akifumi, Corney, David C, Pai, Reetesh K, Gevaert, Olivier, Cantrell, Michael A, Rack, Paul G, Neal, James T, Chan, Carol W-M, Yeung, Trevor, Gong, Xue, Yuan, Jenny, Wilhelmy, Julie, Robine, Sylvie, Attardi, Laura D, Plevritis, Sylvia K, Hung, Kenneth E, Chen, Chang-Zheng, Ji, Hanlee P, Kuo, Calvin J

Volltext

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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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

Volltext

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.

Volltext

Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing von Lau, Billy T, Almeda, Alison, Schauer, Marie, McNamara, Madeline, Bai, Xiangqi, Meng, Qingxi, Partha, Mira, Grimes, Susan M, Lee, HoJoon, Heestand, Gregory M, Ji, Hanlee P

Volltext

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale von Zlitni, Soumaya, Bishara, Alex, Moss, Eli L., Tkachenko, Ekaterina, Kang, Joyce B., Culver, Rebecca N., Andermann, Tessa M., Weng, Ziming, Wood, Christina, Handy, Christine, Ji, Hanlee P., Batzoglou, Serafim, Bhatt, Ami S.

Volltext

Ultrasensitive detection of rare mutations using next-generation targeted resequencing von Flaherty, Patrick, Natsoulis, Georges, Muralidharan, Omkar, Winters, Mark, Buenrostro, Jason, Bell, John, Brown, Sheldon, Holodniy, Mark, Zhang, Nancy, Ji, Hanlee P.

Volltext

CRISPR–Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis von Shin, GiWon, Grimes, Susan M., Lee, HoJoon, Lau, Billy T., Xia, Li C., Ji, Hanlee P.

Volltext

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

Volltext

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

Volltext

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases von Greer, Stephanie U, Nadauld, Lincoln D, Lau, Billy T, Chen, Jiamin, Wood-Bouwens, Christina, Ford, James M, Kuo, Calvin J, Ji, Hanlee P

Volltext

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

Volltext