The cellular genomic diversity, regulatory states and networking of the metastatic colorectal cancer microenvironmentSathe A, Grimes S, Lau B, Bai X, Chen J, Suarez C, Poultsides G, Ji HP:

Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution. Andor N, Lau BT, Catalanotti C, Sathe A, Kubit M, Chen J, Blaj C, Cherry A, Bangs C, Grimes SM, Suarez CJ, Ji HP: NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020.

Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer.  Xia LC, Van Hummelen P, Kubit M, Lee H, Bell JM, Grimes SM, Wood-Bouwens C, Greer SU, Barker T, Haslem DS, Ford J, Fulde G, Ji HP, Nadauld LD:Sci Rep 10, 5009 (2020). 

CRISPRpic: fast and precise analysis for CRISPR-induced mutations via prefixed index counting. Lee H, Chang HY, Cho SW, Ji HP: NAR Genom Bioinform. 2020;2(2):lqaa012. doi:10.1093/nargab/lqaa012 

One Size Does Not Fit All: Marked Heterogeneity in Incidence of and Survival from Gastric Cancer among Asian American Subgroups. Huang RJ, Sharp N, Talamoa RO, Ji HP, Hwang J, Palaniappan LP: Cancer Epidemiol Biomarkers, 2020.  

Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment. Sathe A, Grimes SM, Lau BT, Chen J, Suarez C, Huang RJ, et al. Clin Cancer Res 2020.


scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data; Alquicira-Hernandez J, Sathe A, Ji HP, Nguyen Q, Powell J. Genome Biol 20, 264 (2019).

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression. Andor N, Lau B, Catalanotti C, Kumar J, Sathe A, Belhocine K, Wheeler T, Price A, Song M, Stafford D, Bent Z, DeMare L, Hepler L, Jett S, Lin B, Maheshwari S, Makareswicz A, Rahimi M, Sawhney S, Sauzade M, Shuga J, Sullivan-Bibee K, Weinstein A, Yang W, Yin Y, Kubit M, Chen J, Grime S, Suarez C, Poultsides G, Schnall-Levin M, Bharadwaj R, Ji H. 

A functional CRISPR/Cas9 screen identifies kinases that modulate FGFR inhibitor response in gastric cancer. Chen J, Bell J, Lau B, Whittaker T, Stapleton D, Ji HP: Oncogenesis, 2019.

Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes; Shin G, Greer SU, Xia LC, Lee H, Zhou J, Boles TC, Ji HP: Nucleic Acids Res. 2019 Nov 4;47(19):e115.

Genetic risk of cholangiocarcinoma is linked to the autophagy gene ATG7Greer SU, Ogmundsdottir MH, Chen J, Lau BT, Delcruz RG, Sandoval I, Kristjansdottir S, Jones DA, Haslem DS, Romero R, Fulde G, Bell JM, Jonasson JG, Steingrimsson E, Ji HP, Nadauld LD: bioRxiv (pre-print), Nov 2019.

Structural variant analysis for linked-read sequencing data with gemtools; Greer SU, Ji HP: Bioinformatics, 2019 Apr 2;pii: btz239.

Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model; Chen J, Lau BT, Andor N, Grimes SM, Handy C, Wood-Bouwens C, Ji HP: Scientific Reports, 2019 Mar 14; 9(1):4536.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2; Zhou B, Ho SS, Greer SU, Spies N, Bell JM, Zhang X, Zhu X, Arthur JG, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong WH, Ji HP, Abyzov A, Urban AE: Nucleic Acids Res. 2019 Mar 13;pii: gkz169.

Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints; Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, Levy R, Ji HP: Blood, 2019 Mar 7;133(10):1119-1129.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562; Zhou B, Ho SS, Greer SU, Zhu X, Bell JM, Arthur JG, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney MS, Haraksingh RR, Song G, Ji HP, Perrin D, Wong, WH, Abyzov A, Urban AE: Genome Res. 2019 Mar;29(3):472-484.

Covalent “Click Chemistry”-Based Attachment of DNA onto Solid Phase Enables Iterative Molecular Analysis; Lau BT, Ji HP: Analytical Chemistry, 2019 Feb 5;91(3):1706-1710.

Dynamic Immune Modulation Seen By Single Cell RNA-Sequencing of Serial Lymphoma Biopsies in Patients Undergoing in Situ Vaccination. Shree T, Haebe S, Sathe A, Day G, Lee H, Czerwinski DK, Grimes S, Ji HP, Levy R: Blood, 2019 (Supplement_1): 1479.

Site to Site Comparison of Follicular Lymphoma Biopsies By Single Cell RNA SequencingHaebe S, Shree T, Sathe A, Day G, Lee H, Czerwinski DK, Grimes S, Ji HP, Levy R: Blood, 2019; 134 (Supplement_1): 297. 

Overcoming High Nanopore Basecaller Error Rates for DNA Storage Via Basecaller-Decoder Integration and Convolutional Codes. Chandak S, Neu J, Tatwawadi K, Mardia J, Lau B, Kubit M, Hulett R, Griffin P, Wootters M, Weissman T, Ji HP: bioRxiv, 2019.12.20.871939. 

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes. Chandak S, Tatwawadi K, Lau B, Mardia J, Kubit M, Neu J, Griffin P, Wootters M, Weissman T, Ji HP: bioRxiv 77032.  


SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution; Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP: Gigascience, 2018 Jul 1;7(7).

Identification of large rearrangements in cancer genomes with barcode linked reads; Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP: Nucleic Acids Res. 2018 Feb 28;46(4):e19.

A robust targeted sequencing approach for low input and variable quality DNA from clinical samples; So AP, Vilborg A, Bouhlal Y, Koehler RT, Grimes SM, Pouliot Y, Mendoza D, Ziegle J, Stein J, Goodsaid F, Lucero MY, De La Vega FM, Ji HP. NPJ Genom Med. 2018 Jan 15;3:2.

Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping; Wood-Bouwens CM, Ji HP: Methods Mol Biol. 2018;1768:323-333.


Robust Multiplexed Clustering and Denoising of Digital PCR Assays by Data Gridding; Lau BT, Wood-Bouwens C, Ji HP. Anal Chem. 2017 Nov 21;89(22):11913-11917.

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy; Bell JM, Lau BT, Greer SU, Wood-Bouwens C, Xia LC, Connolly ID, Gephart MH, Ji HP. Nucleic Acids Res. 2017 Nov 2;45(19):e162.

Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes; Lau BT, Ji HP. BMC Genomics. 2017 Sep 21;18(1):745.

Single color digital PCR provides high performance detection of cancer mutations from circulating DNA; Wood-Bouwens C, Lau BT, Handy C, Lee H, Ji HP. The Journal of Molecular Diagnostics. 2017, 19 (5):697-710

Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity; Grimes SM, Ji HP (authors 17 & 42 respectively of 46); Cell Stem Cell. 2017 Jul 6;21(1):78-90.e6.

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases; Greer SU, Nadauld LD, Lau BT, Chen J, Wood-Bouwens C, Ford JM, Kuo CJ, Ji HP: Genome Medicine. 2017, 9:57.

Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence; Taskova M, Uhd J, Miotke L, Kubit M, Bell J, Ji HP, Astakhova K; Anal Chem. 2017 Apr 18;89(8):4363-4366.

CRISPR–Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis; Shin G, Grimes SM, Lee H, Lau BT, Xia LC, Ji HP:  Nature Communications. 2017, 8, 1429


Pan-cancer analysis of the extent and consequences of intra-tumor heterogeneity; Andor, N., Graham, T., Jansen, M., Xia, LC., Aktipis, CA., Petritsch, C., Ji, HP., Maley, CC: Nature Medicine. 2016, 22, 105-113

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size; Xia LC, Sakshuwong S, Hopmans E, Bell J, Grimes S, Siegmund D, Ji H, Zhang N: Nucleic Acids Res. 2016, 44 (15):e126.

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing; Lau BT, Bell JM, Hopmans ES, Wood C, Grimes SM, Greer S, Ji HP (authors 2, 5, 30, 31, 38, 39, & 58 respectively of 58); Nat Biotechnol. 2016 Mar;34(3):303-11.


The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations. Lee H, Palm J, Grimes SM, Ji HP Genome Med. 2015, 7:112

Emergence of Hemagglutinin Mutations During the Course of Influenza Infection. Cushing A, Kamali A, Winters M, Hopmans E, Bell JM, Grimes SM, Xia LC, Zhang NR, Moss RB, Holodniy M, Ji HP: Scientific Reports. 2015, 5:16178.

Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy; Miotke L, Maity A, Ji H, Brewer J, Astakhova K; PLoS One. 2015 Aug 27;10(8):e0136720.

Allele-specific copy number profiling by next-generation DNA sequencing; Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR; Nucleic Acids Res. 2015 Feb 27;43(4):e23.


MendeLIMS: a web-based laboratory information management system for clinical genome sequencing; Grimes SM, Ji HP: BMC Bioinformatics. 2014;15(1):290.

Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer; Lincoln D Nadauld, Sarah Garcia, Georges Natsoulis, John M Bell, Laura Miotke, Erik S Hopmans, Hanlee P Ji et al.; Genome Biology, August 2014; 15:428.

Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture; Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD, Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ; Nat Med. 2014 Jul;20(7):769-77.

A programmable method for massively parallel targeted sequencing; Erik S. Hopmans, Georges Natsoulis, John M. Bell, Susan M. Grimes, Weiva Sieh and Hanlee P. Ji; Nucleic Acids Research, 2014; 10.1093/nar/gku282.

High Sensitivity Detection and Quantitation of DNA Copy Number and Single Nucleotide Variants with Single Color Droplet Digital PCR; Miotke LK, Lau BT, Rumma RT, Ji HP; Analytical Chemistry, 2014.


Identification of Insertion Deletion Mutations from Deep Targeted Resequencing; Natsoulis G, Zhang N, Welch K, Bell J, Ji HP; J Data Mining Genomics Proteomics, 2013; 4(3)

Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis; Lee H, Flaherty P, Ji HP.; BMC Med Genomics, 2013; 5;6:54.

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing; Cushing A, Flaherty P, Hopmans E, Bell JM, Ji HP; BMC Res Notes. 2013 May 23;6:206.

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma; Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA; Blood. 2013 Feb 28;121(9):1604-11.

Detecting mutations in mixed sample sequencing data using empirical Bayes; Muralidharan O, Natsoulis G, Bell J, Ji HP, Zhang N; Annals of Applied Statistics, 2013; 6(3), 1047-1067.


Improving bioinformatic pipelines for exome variant calling; Ji HP; Genome Medicine, 2012; 4:7.

Quantitative and sensitive detection of cancer genome amplifications from formalin fixed paraffin embedded tumors with droplet digital PCR; Nadauld L, Regan JF, Miotke L, Pai RK, Longacre TA, Kwok SS, Saxonov S, Ford JM, Ji HP; Translational Medicine, 2012; 2(2), 1-5.

Identification of a novel deletion mutant in Saccharomyces cerevisiae that results in a microsatellite instability phenotype; Ji HP, Morales S, Welch K, Yuen C, Farnam K, Ford JM; BioDiscovery, 2012; 4(1), 1-9.

A cross-sample statistical model for SNP detection in short-read sequencing data; Muralidharan O, Natsoulis G, Bell J, et al.; Nucleic Acids Research, 2012; 40(1):e2.

Ultrasensitive detection of rare mutations using next-generation targeted resequencing; Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell John. Brown S, Holodniy M, Zhang, N, Ji HP; Nucleic Acids Research, 2012; 40(1):e2.


Targeted sequencing library preparation by genomic DNA circularization; Myllykangas S, Georges N, Bell JM and Ji HP; BMC Biotechnology, 2011; 11(1):122.

Performance comparison of whole-genome sequencing platforms(Comparison of two whole genome sequencing platforms); Hugo Y. K. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey F, Habegger L, Ashley E, Gerstein MB, Butte AJ, Ji HP, and Snyder M.; Nature Biotechnology, 2011; 30(1): 78-82.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome; Newburger D, Natsoulis, G, Grimes S, Bell J, Davis RW; Batzoglou S, Ji HP; Nucleic Acids Research, 2011; 40 (Database issue): D1137-43.

Efficient targeted resequencing of human germline and cancer genomes using Oligonucleotide-Selective Sequencing; Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM and Ji HP; Nature Biotechnology, 2011; 29(11): 1024-7.

Flexible approach for highly multiplexed candidate gene targeted resequencing; Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, and Ji HP; PLoS One, 2011; 6(6): e21088.


Detecting simultaneous change-points in multiple sequences; Zhang NR, Siegmund DO, Ji HP and Li JZ; Biometrika, 2010; 97(3), 631-645.

Oncogenic BRAF mutation and CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas; Schiffman JD, Vandenberg SR, Flaherty P, Polley M, Yu M, James CD, Fisher PG, Gutmann DH, Rowitch DH7 Ford J, Berger MS, Ji H, and Hodgson JG; Cancer Research, 2010; 70(2):512-9.


Molecular Inversion Probe Assay for Allelic Quantitation; Welch K and Ji HP; In Methods in Molecular Biology, 2009; New York, Humana, 556, 67-87.

Identification of a biomarker panel using a multiplex proximity ligation assay improves accuracy of pancreatic cancer diagnosis; Chang ST, Zahn JM, Horecka J, Kunz PL, Ford JM, Fisher GA, Le QT, Chang DT, Ji HP and Koong AC; Journal of Translational Medicine, 2009; 105(7).

Molecular Inversion Probes (MIPs) reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia; Schiffman JD, Wang Y, McPherson L, Welch K, Zhang N, Davis RW, Lacayo NJ, Dahl GV, Faham M, Ford JM and Ji HP; Cancer Genetics and Cytogenetics, 2009; 193(1):9-18.

Disperse – A software system for design of selector probes for exon resequencing applications; Stenberg J, Zhang M and Ji HP; Bioinformatics, 2009; 25(5):666-7.


Under-expression of Kalirin-7 increases iNOS activity in cultured cells and correlates to elevated iNOS activity in Alzheimer’s disease hippocampus; Youn H, Ji I, Ji HP, Markesbery WR, Ji TH; J Alzheimers Dis. 2007; Nov;12(3):271-81.

Kalirin is under-expressed in Alzheimer’s disease hippocampus; Youn H, Jeoung M, Koo Y, Ji H, Markesbery WR, Ji I, Ji TH; J Alzheimers Dis. 2007; Jun;11(3):385-97.

Multigene amplification and massively parallel sequencing for cancer mutation discovery; Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, Bicknel D, Bodmer WF, Davis RW, and Ji H; Proceedings of the National Academy of Sciences, 2007; 104(22): 9387-92.

Multiplex amplification of all coding sequence within 10 cancer genes by Gene-Collector; Fredriksson S, Baner J, Dahl F, Chu A, Ji HP, Welsh K and Davis RW; Nucleic Acids Research, 2007; 35(7): e47.

Multiplexed protein detection by proximity ligation applied to biomarker validation in pancreatic cancer; Fredriksson, S, Dixon W, Ji H, Koong A, Mindrinos M and Davis RW; Nature Methods, 2007; 4(4): 327-9.


Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma; Ji HP, Kumm J, Zhang M, Farnam K, Salari K, Faham M, Ford JM, Davis RW; Cancer Research, 2006; 66(16): 7910-9.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements; Shi L, Ji HP (author 77 of 137). et al.; Nature Biotechnology, 2006; 24(9): 1151-1161.

Genomic instability in cancer: Teetering on the limit of tolerance; Andor N., Maley, CC., Ji, HP: Cancer Research. May 1 2017 (77) (9) 2179-2185.

Genetic-based biomarkers and next-generation sequencing: the future of personalized care in colorectal cancer; Kim RY, Xu H, Myllykangas S and Ji H; Personalized Medicine, 2011; 8(3), 331-345.

Targeted deep resequencing of the human cancer genome using next-generation technologies; Myllykangas S and Ji HP; Biotechnology and Genetic Engineering Reviews, 2010; 27, 135-158.

Next generation DNA sequencing; Shendure J, and Ji HP; Nature Biotechnology, 2008; 108(26): 1135-1145.

Kimmel G., Barnholtz-Sloan J., Ji H., Altrock P., Andor N. (2019) “Modeling the Evolution of Ploidy in a Resource Restricted Environment.” In: Bebis G., Benos T., Chen K., Jahn K., Lima E. (eds) Mathematical and Computational Oncology. ISMCO 2019. Lecture Notes in Computer Science, vol 11826. Springer, Cham. 

Christina Wood and Hanlee P Ji. “MIMB Digital PCR Methods”: Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping, Springer, In Press.

HoJoon Lee, Billy T. Lau, and Hanlee P. Ji. “Targeted Sequencing Strategies in Cancer Analysis.” Next Generation Sequencing in Cancer Research, 1: Decoding the Cancer Genome, Springer, 2013, pp. 137-163.

Samuel Myllykangas, Jason Buenrostro, and Hanlee P. Ji. “Overview of Sequencing Technology Platforms.” Bioinformatics for High Throughput Sequencing, Springer, 2012, pp. 11-25.

Data quality in genomics and microarrays; Ji, H and Davis, RW; Nature Biotechnology, 2006; 24(9):1112-3.

Molecular classification of the inherited hamartoma polyposis syndromes: clearing the muddied waters; Eng C and Ji HP; 1999, American Journal of Human Genetics; 62(5): 1020-2.

Reproducibility probability score: a metric incorporating measurement variability across labs for gene selection; Lin G, He X, Shi L, Ji H, Davis RW, Zhong S; Nature Biotechnology, 2006; 24(12): 6-7.