Selected Publications

Wei R, He S, Bai S, Sei E, Hu M, Thompson A, Chen K, Krishnamurthy S, Navin NE. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol. e-Pub 3/2022. PMID: 35314812.

Mathew MT, Antoniou A, Ramesh N, Hu M, Gaither J, Mouhlas D, Hashimoto S, Humphrey M, Matthews T, Hunter JM, Reshmi S, Schultz M, Lee K, Pfau R, Cottrell C, McBride KL, Navin NE, Chaudhari BP, Leung ML. A Decade's Experience in Pediatric Chromosomal Microarray Reveals Distinct Characteristics Across Ordering Specialties. J Mol Diagn. e-Pub 6/2022. PMID: 35718094.

Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, Grand Challenge PRECISION consortium, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet 54(6):850-860, 6/2022. e-Pub 6/2022. PMCID: PMC9197769.
 

Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 53(10):1456-1468, 10/2021. e-Pub 9/2021. PMCID: PMC8570135.

Wang K, Xiao Z, Yan Y, Ye R, Hu M, Bai S, Sei E, Qiao Y, Chen H, Lim B, Lin SH, Navin NE. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility. Mol Cell. 2021 Oct 21;81(20):4319-4332.e10. doi: 10.1016/j.molcel.2021.09.026. PMID: 34686316.

Minussi DC, Nicholson MD, Ye H, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin YW, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F, Navin NE. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature. 2021 Apr;592(7853):302-308. doi: 10.1038/s41586-021-03357-x. Epub 2021 Mar 24. PMID: 33762732; PMCID: PMC8049101.

Gao R, Bai S, Henderson YC, Lin Y, Schalck A, Yan Y, Kumar T, Hu M, Sei E, Davis A, Wang F, Shaitelman SF, Wang JR, Chen K, Moulder S, Lai SY, Navin NE. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat Biotechnol. 2021 Jan 18. doi: 10.1038/s41587-020-00795-2. Epub ahead of print. PMID: 33462507.

Wang F, Wang O, Mohanty V, Liang S, Dou J, Han J, Minussi DC, Gao R, Ding L, Navin N, Chen K. MEDALT: single-cell copy number lineage tracing enabling gene discovery. Genome Biol. 70(22(1)):doi: 10.1186/s13059-021-02291-5, 2/2021. PMCID: PMCPMC7901082.

Morita K, Wang F, Jahn K, Hu T, Tanaka T, Sasaki Y, Kuipers J, Loghavi S, Wang SA, Yan Y, Furudate K, Matthews J, Little L, Gumbs C, Zhang J, Song X, Thompson E, Patel KP, Bueso-Ramos CE, DiNardo CD, Ravandi F, Jabbour E, Andreeff M, Cortes J, Bhalla K, Garcia-Manero G, Kantarjian H, Konopleva M, Nakada D, Navin N, Beerenwinkel N, Futreal PA, Takahashi K. Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nat Commun 11(1):5327, 10/2020. PMCID: PMC33087716. 

Naffar-Abu Amara S, Kuiken HJ, Selfors LM, Butler T, Leung ML, Leung CT, Kuhn EP, Kolarova T, Hage C, Ganesh K, Panayiotou R, Foster R, Rueda BR, Aktipis A, Spellman P, Ince TA, Xiu J, Oberley M, Gatalica Z, Navin N, Mills GB, Bronson RT, Brugge JS. Transient commensal clonal interactions can drive tumor metastasis. Nat Commun 11(1):5799, 11/2020. PMCID: PMCPMC7669858.

Ramesh N, Sei E, Tsai PC, Bai S, Zhao Y, Troncoso P, Corn PG, Logothetis C, Zurita AJ, Navin NE. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol. PMID: 32631448.

Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single-Cell Genomics. Cancer Cell. PMID: 32289270.

Malihi PD, Graf RP, Rodriguez A, Ramesh N, Lee J, Sutton R, Jiles R, Ruiz Velasco C, Sei E, Kolatkar A, Logothetis C, Navin NE, Corn P, Aparicio AM, Dittamore R, Hicks J, Kuhn P, Zurita AJ.  Single-cell circulating tumor cell analysis reveals genomic instability as a distinctive feature of aggressive prostate cancer. Clin Cancer Res. PMID: 32341031.

Zafar H, Navin N, Chen K, Nakhleh L. SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Genome Res.(11):1847-1859. PMID: 31628257.

Davis A, Gao R, Navin N. SCOPIT: sample size calculations for single-cell sequencing experiments. BMC Bioinformatics 20(1):566. PMID: 31718533.

Wang F, Liang S, Kumar T, Navin N, Chen K. SCMarker: Ab initio marker selection for single cell transcriptome profiling. PLoS Comput Biol. 15(10):e1007445. PMID: 31658262.

Corn PG, Heath EI, Zurita A, Ramesh N, Xiao L, Sei E, Li-Ning-Tapia E, Tu SM, Subudhi SK, Wang J, Wang X, Efstathiou E, Thompson TC, Troncoso P, Navin N, Logothetis CJ, Aparicio AM. Cabazitaxel plus carboplatin for the treatment of men with metastatic castration-resistant prostate cancers: a randomised, open-label, phase 1-2 trial. Lancet Oncol. 20(10):1432-1443. PMID: 31515154.
 

Schalck A, Bernatchez C, Navin N. Resident Breast T Cells: The Troops Are Already There. Trends Mol Med (10):821-822. PMID: 30077643.

Zhang Y, Xiong S, Liu B, Pant V, Celii F, Chau G, Elizondo-Fraire AC, Yang P, You MJ, El-Naggar AK, Navin NE, Lozano G. Somatic Trp53 mutations differentially drive breast cancer and evolution of metastases. Nat Commun 9(1):3953. PMID: 30262850.

Kim C & Gao R, Sei E, Brandt R, Hartman J, Hatshek T, Crosetto N, Foukakis T and Navin N. Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single Cell Sequencing. Cell 173(4):879-893. NIHMSID: NIHMS987904.

Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, Casasent T, Meric-Bernstam F, Edgerton ME, Navin NE. Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing. Cell 172(1-2):205-217. PMID: 29307488.

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Biol. 19;18(1):178.  PMID: 2897434.

Gao R, Davis A, McDonald T, Sei E, Shi X, Wang Y, Tsai P, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F and Navin N.  Punctuated Copy Number Evolution and Clonal Stasis in Triple-Negative Breast Cancer.  Nat Genet. 48(10):1119-30. PMID: 27526321.

Navin N and Chen K.  Genotyping tumor clones from single-cell data. Nat Methods. 29;13(7):555-6. PMID: 27355792.

Davis A and Navin N. Computing tumor trees from single cells. Genome Biol. 26;17(1):113. PMID: 27230879.

Zafar H, Wang Y, Nahkleh L, Navin N & Chen K.  Monovar: Single Nucleotide Variant Detection in Single Cells. Nat Methods.13(6):505-7 PMID: 27088313.

Leung M & Wang Y, Kim C, Gao R, Jiang J, Sei E and Navin NE.  Highly-multiplexed targeted DNA sequencing from single nuclei. Nat Protoc. 11(2):214-35. PMID: 26741407.

Navin N.  The first five years of single-cell cancer genomics and beyond. Genome Res. 25(10):1499-507 PMID: 26430160.

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J. Toward understanding and exploiting tumor heterogeneity. Nat Med. 21(8):846-53. PMID: 26248267.

Navin N.  Delineating Cancer Evolution With Single-Cell Sequencing. Science Trans. Med. 15;7(296) PMID: 26180099.

Wang Y and Navin N.  Advances and Applications of Single Cell Sequencing Technologies. Molecular Cell. 21;58(4):598-609 PMID: 26000845.

Leung M, Wang Y, Waters J and Navin N.  SNES: Single Nuclei Exome Sequencing. Genome Biol 25;16:55 PMID: 25853327.

Malhotra A, Wang Y, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin NE.  Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. Genome Med. 28;7(1)275 PMID: 25729435.

Navin N. Cancer Genomics: One Cell at a Time. Genome Biol. 30;15(8):452 PMID: 25222669.

Wang Y, Waters J, Leung M, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang S, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F and Navin N. Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing. Nature 512(7513): 155-60 PMID: 25079324.

Navin N.  Tumor evolution in response to chemotherapy: phenotype versus genotype. Cell Rep. 13;6(3):417-9. PMID: 24529750.

Chen K, Navin N, Wang Y, Schmidt K, Wallis J, Niu B, Fan X, Zhao H, Mclellan M, Hoadley K, Mardis M, Ley T, Perou C, Wilson R and Ding L. BreakTrans: Uncovering the Genomic Architecture of Gene Fusions.Genome Biol. 23;14(8):77. PMID: 23972288.

Baslan, T., Kendall J., Troge J, Rodgers L, Cook K, Stepansky A, Esposito D, Muthuswamy L, Wigler M Navin N, Hicks J. Genome-Wide Copy Number Analysis of Single Cells. Nature Protocols 3;7(6):1024-41. PMID: 22555242.

Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC. Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression. Cancer Cell. 20(2):173-86. PMID: 21840483.

Navin N, Kendall J, Troge J, Rodgers L, Cook K, Stepansky A, Levy D, Lee Y, Esposito D, Peters A, Muthuswamy L,  McCombie R, Hicks J, Wigler M. Tumor Progression Revealed by Single Cell Sequencing Nature.7;472(7341):9184 PMID: 21399628.

Russnes HG, Navin N, Hicks J, Borresen-Dale AL. Insight into the heterogeneity of breast cancer through next-generation sequencing. J Clin Invest.121(10):3810-8. PMID: 21965338.

Navin N, Hicks J. Future medical applications of single-cell sequencing in cancer. Genome Med. 31;3(5):31. PMID: 21631906.

Blake PM, Decker DA, Glennon TM, Liang YM, Losko S, Navin N, Suh KS. Toward an integrated knowledge environment to support modern oncology. Cancer J. 17(4):257-63. PMID:21799334.

Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P,  Månér S, Zetterberg A, Hicks J, Wigler M.  Inferring Tumor Progression from Genomic Heterogeneity. Genome Research. 20(1):68-832 PMID: 19903760.

Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, Yamrom B, Alex G, Pai D, Navin N, Hufnagel LA, Lee YH, Cook K, Allen SL, Rai KR, Damle RN, Calissano C, Chiorazzi N, Wigler M, Esposito D. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood. 113(6):129857 PMID: 18922857.

Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D. Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci USA. 103(52):19848-53. PMID: 17167050.

Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Månér S, Sebat J, Zetterberg A, Wigler M. PROBER: oligonucleotide FISH probe design software. Bioinformatics. 1;22(19):2437 PMID: 16740623.

Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A.  Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res. 16(12):1465-79. PMID: 17142309.

Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A. High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol. 70:51738.

Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-scale copy number polymorphism in the human genome. Science. 23;305(5683):525-8. PMID: 15273396.

Thomas EE, Srebro N, Sebat J, Navin N, Healy J, Mishra B, Wigler M. Distribution of short paired duplications in mammalian genomes. Proc Natl Acad Sci USA. 13;101(28):10349876 PMID: 15240876.

Komuro A, Nagai M, Navin NE, Sudol M. WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus. J Biol Chem. 29;278(35):33334-41. PMID: 12807903.

Espanel X, Navin N, Kato Y, Tanokura M, Sudol M. Probing WW Domains to Uncover and Refine Determinants of Specificity in Ligand Recognition. Cytotechnology. 43 (1-3):105-11 PMID: 19003214.

Komuro A, Nagai M, Navin NE, Sudol M. WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus. J Biol Chem 278(35):33334-41, 8/2003. PMID: 12807903.

Espanel X, Navin N, Kato Y, Tanokura M, Sudol M. Probing WW Domains to Uncover and Refine Determinants of Specificity in Ligand Recognition. Cytotechnology 43(1-3):105-11, 11/2003. PMID: 19003214.