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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 Jul 27. pii: gkz661. doi: 10.1093/nar/gkz661. [Epub ahead of print]


A functional CRISPR/Cas9 screen identifies kinases that modulate FGFR inhibitor response in gastric cancer.

Chen J, Bell J, Lau BT, Whittaker T, Stapleton D, Ji HP.

Oncogenesis. 2019 May 10;8(5):33. doi: 10.1038/s41389-019-0145-z.


Structural variant analysis for linked-read sequencing data with gemtools.

Greer SU, Ji HP.

Bioinformatics. 2019 Apr 2. pii: btz239. doi: 10.1093/bioinformatics/btz239. [Epub ahead of print]


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.

Sci Rep. 2019 Mar 14;9(1):4536. doi: 10.1038/s41598-019-40809-x.


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 May 7;47(8):3846-3861. doi: 10.1093/nar/gkz169.


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. doi: 10.1101/gr.234948.118. Epub 2019 Feb 8.


Covalent "Click Chemistry"-Based Attachment of DNA onto Solid Phase Enables Iterative Molecular Analysis.

Lau BT, Ji HP.

Anal Chem. 2019 Feb 5;91(3):1706-1710. doi: 10.1021/acs.analchem.8b05139. Epub 2019 Jan 22.


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. doi: 10.1182/blood-2018-08-862292. Epub 2018 Dec 27.


[Exogenous CRX gene induces Müller cell-derived progenitors to differentiate into photoreceptors].

Ji HP, Gao ZL, Xiong Y, Yao F, Song WT, Zhang ED, Zhou RR, Xia XB.

Zhonghua Yan Ke Za Zhi. 2018 Dec 11;54(12):923-928. doi: 10.3760/cma.j.issn.0412-4081.2018.12.010. Chinese.


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). doi: 10.1093/gigascience/giy081.


Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping.

Wood-Bouwens CM, Ji HP.

Methods Mol Biol. 2018;1768:323-333. doi: 10.1007/978-1-4939-7778-9_18.


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. doi: 10.1038/s41525-017-0041-4. eCollection 2018.


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. doi: 10.1093/nar/gkx1193.


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. doi: 10.1021/acs.analchem.7b02688. Epub 2017 Nov 7.


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. doi: 10.1093/nar/gkx712.


MicroRNA-28 potentially regulates the photoreceptor lineage commitment of Müller glia-derived progenitors.

Ji HP, Xiong Y, Song WT, Zhang ED, Gao ZL, Yao F, Su T, Zhou RR, Xia XB.

Sci Rep. 2017 Sep 12;7(1):11374. doi: 10.1038/s41598-017-11112-4.


Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA.

Wood-Bouwens C, Lau BT, Handy CM, Lee H, Ji HP.

J Mol Diagn. 2017 Sep;19(5):697-710. doi: 10.1016/j.jmoldx.2017.05.003. Epub 2017 Aug 14.


Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity.

Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R, Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH, Kuo CJ.

Cell Stem Cell. 2017 Jul 6;21(1):78-90.e6. doi: 10.1016/j.stem.2017.06.014.


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 Med. 2017 Jun 19;9(1):57. doi: 10.1186/s13073-017-0447-8.


Genomic Instability in Cancer: Teetering on the Limit of Tolerance.

Andor N, Maley CC, Ji HP.

Cancer Res. 2017 May 1;77(9):2179-2185. doi: 10.1158/0008-5472.CAN-16-1553. Epub 2017 Apr 21. Review.


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. doi: 10.1021/acs.analchem.7b00646. Epub 2017 Apr 7.


Which has more stem-cell characteristics: Müller cells or Müller cells derived from in vivo culture in neurospheres?

Ji HP, Xiong Y, Zhang ED, Song WT, Gao ZL, Yao F, Sun H, Zhou RR, Xia XB.

Am J Transl Res. 2017 Feb 15;9(2):611-619. eCollection 2017.


CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis.

Shin G, Grimes SM, Lee H, Lau BT, Xia LC, Ji HP.

Nat Commun. 2017 Feb 7;8:14291. doi: 10.1038/ncomms14291.


N-methyl-N-nitrosourea induces retinal degeneration in the rat via the inhibition of NF-κB activation.

Xiong Y, Ji HP, Song WT, Yin YW, Xia CH, Xu B, Xu Y, Xia XB.

Cell Biochem Funct. 2016 Dec;34(8):588-596. doi: 10.1002/cbf.3232. Epub 2016 Nov 13.


A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.

Xia LC, Sakshuwong S, Hopmans ES, Bell JM, Grimes SM, Siegmund DO, Ji HP, Zhang NR.

Nucleic Acids Res. 2016 Sep 6;44(15):e126. doi: 10.1093/nar/gkw481. Epub 2016 Jun 20.


Application of digital tomosynthesis in diagnosing spinal tuberculosis.

Jiao D, Yang HS, Yang DY, Tian W, Wang H, Ji HP.

Clin Imaging. 2016 May-Jun;40(3):461-4. doi: 10.1016/j.clinimag.2015.11.003. Epub 2015 Nov 7.


Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Zheng GX, Lau BT, Schnall-Levin M, Jarosz M, Bell JM, Hindson CM, Kyriazopoulou-Panagiotopoulou S, Masquelier DA, Merrill L, Terry JM, Mudivarti PA, Wyatt PW, Bharadwaj R, Makarewicz AJ, Li Y, Belgrader P, Price AD, Lowe AJ, Marks P, Vurens GM, Hardenbol P, Montesclaros L, Luo M, Greenfield L, Wong A, Birch DE, Short SW, Bjornson KP, Patel P, Hopmans ES, Wood C, Kaur S, Lockwood GK, Stafford D, Delaney JP, Wu I, Ordonez HS, Grimes SM, Greer S, Lee JY, Belhocine K, Giorda KM, Heaton WH, McDermott GP, Bent ZW, Meschi F, Kondov NO, Wilson R, Bernate JA, Gauby S, Kindwall A, Bermejo C, Fehr AN, Chan A, Saxonov S, Ness KD, Hindson BJ, Ji HP.

Nat Biotechnol. 2016 Mar;34(3):303-11. doi: 10.1038/nbt.3432. Epub 2016 Feb 1.


Pan-cancer analysis of the extent and consequences of intratumor heterogeneity.

Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, Ji HP, Maley CC.

Nat Med. 2016 Jan;22(1):105-13. doi: 10.1038/nm.3984. Epub 2015 Nov 30.


Emergence of Hemagglutinin Mutations During the Course of Influenza Infection.

Cushing A, Kamali A, Winters M, Hopmans ES, Bell JM, Grimes SM, Xia LC, Zhang NR, Moss RB, Holodniy M, Ji HP.

Sci Rep. 2015 Nov 5;5:16178. doi: 10.1038/srep16178.


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 Oct 27;7:112. doi: 10.1186/s13073-015-0226-3.


Correction to High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR.

Miotke L, Lau BT, Rumma RT, Ji HP.

Anal Chem. 2015 Mar 3;87(5):3114. doi: 10.1021/acs.analchem.5b00061. Epub 2015 Feb 12. No abstract available.


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. doi: 10.1093/nar/gku1252. Epub 2014 Dec 3.


Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.

Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, Xu H, Pai RK, Palm C, Regan JF, Chen H, Flaherty P, Ootani A, Zhang NR, Ford JM, Kuo CJ, Ji HP.

Genome Biol. 2014 Aug 27;15(8):428. doi: 10.1186/s13059-014-0428-9.


MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

Grimes SM, Ji HP.

BMC Bioinformatics. 2014 Aug 27;15:290. doi: 10.1186/1471-2105-15-290.


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. doi: 10.1038/nm.3585. Epub 2014 May 25.


A programmable method for massively parallel targeted sequencing.

Hopmans ES, Natsoulis G, Bell JM, Grimes SM, Sieh W, Ji HP.

Nucleic Acids Res. 2014 Jun;42(10):e88. doi: 10.1093/nar/gku282. Epub 2014 Apr 29.


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 Jul 2;4(3). pii: 1000132.


High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR.

Miotke L, Lau BT, Rumma RT, Ji HP.

Anal Chem. 2014 Mar 4;86(5):2618-24. doi: 10.1021/ac403843j. Epub 2014 Feb 12. Erratum in: Anal Chem. 2014 May 6;86(9):4635. Anal Chem. 2015 Mar 3;87(5):3114.


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 Dec 5;6:54. doi: 10.1186/1755-8794-6-54.


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. doi: 10.1186/1756-0500-6-206.


Improving bioinformatic pipelines for exome variant calling.

Ji HP.

Genome Med. 2012 Jan 30;4(1):7. doi: 10.1186/gm306.


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.

Transl Med (Sunnyvale). 2012;2(2). pii: 1000107.


Performance comparison of whole-genome sequencing platforms.

Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M.

Nat Biotechnol. 2011 Dec 18;30(1):78-82. doi: 10.1038/nbt.2065. Erratum in: Nat Biotechnol. 2012 Jun;30(6):562.


Targeted sequencing library preparation by genomic DNA circularization.

Myllykangas S, Natsoulis G, Bell JM, Ji HP.

BMC Biotechnol. 2011 Dec 14;11:122. doi: 10.1186/1472-6750-11-122.


The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1137-43. doi: 10.1093/nar/gkr973. Epub 2011 Nov 18.


Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.

Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP.

Nat Biotechnol. 2011 Oct 23;29(11):1024-7. doi: 10.1038/nbt.1996.


Ultrasensitive detection of rare mutations using next-generation targeted resequencing.

Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP.

Nucleic Acids Res. 2012 Jan;40(1):e2. doi: 10.1093/nar/gkr861. Epub 2011 Oct 19.


A 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, Ji HP.

PLoS One. 2011;6(6):e21088. doi: 10.1371/journal.pone.0021088. Epub 2011 Jun 30.

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