C.V.

RESEARCH INTERESTS

  • NGS data management, exploration, reduction, and visualization
  • Making biologist friendly web apps and R packages
  • Developing end-to-end workflow solution
  • Pharmacogenomics

RESEARCH & WORK EXPERIENCE

Apr 2021 : Present ~ Oncology Lab Bioinformatics & Data Analytics Lead at Invitae

  • Serving as the technical and scientific lead for products driven by Bioinformatics & Data Science
  • Overseeing development and deployment of all informatic data analysis pipelines, algorithms, and
    applications serving under IGT platform
  • Integrating variety of external facing analytical systems to help streamline informatics workflows and reporting for PCM/Multi-analyte assays
  • Automating dry-lab operations for lab/data services projects
  • Developing processes & systems to allow effective cross-functional collaboration between teams to drive quality product development

Jul 2019 : Apr 2021 ~ Head of Bioinformatics & Data Science at Genosity (now Invitae)

  • Serving as the technical and scientific lead for Bioinformatics and Data Science.
  • Overseeing development and deployment of all informatic data analysis pipelines, algorithms, and applications.
  • Bioinformatics lead on data analytics service and consultation projects as well as serving as the bioinformatics expert on regulatory submissions.
  • Working closely with the technology development team to ensure data analytics tools are developed to support new technologies, while also working with QA to ensure regulatory requirements for data management are met.
  • Overseeing validation activities for new analytical processes or updates to existing processes in consultation with QA.
  • Developing custom data models and algorithms to improve assay sensitivity and precision.

Jun 2017 : Jul 2019 ~  Bioinformatics Scientist at Thrive Earlier Detection Corp (Formerly PapGene Inc)

  • Played a leading role in maintaining, improving, documenting and ensuring the quality of Bioinformatics Pipeline utilized for DETECT-A and CancerSEEK.
  • Evaluated and developed bioinformatics approaches for massively parallel sequencing assays utilizing SafeSeqS technology.
  • Developed Sample to Reporting workflow with interfaces for paired analysis and automated validations.

Oct 2016 : Jun 2017 ~  Assistant Director of Research & Development at BioReference Laboratories

  • Managed production of analytical bioinformatics software
  • Provided strategic direction for large scale/high volume projects

Aug 2014 : Oct 2016 ~  Research Scientist at BioReference Laboratories

  • Developed a variety of clinical grade NGS pipelines/algorithms for oncology and infectious disease characterization. Collaborative featured products include:
    • ClearView Analytics tool kit for OnkoSight product line (Tumor profiling assays)
    • Specialized Genotyping pipeline for Inherigen (Carrier screening assay)
    • Cluster aware autonomous NGS job management and archiving system
    • Custom Somatic & Germline variant callers utilizing adaptive thresholds

Jun 2007 : Aug 2014  ~  Sr. Programmer Analyst at University of Pennsylvania Perelman School of Medicine.

  • Developed computation tools (web-based/command-line/reproducible report) to aid viral integration site research in vertebrate and invertebrate species.
    • Research area covered monitoring clones in gene therapy trials, genome editing with designer nucleases, and tethering host/viral proteins to alter integration patterns.
  • Streamlined processing & analysis of NGS data
  • Administered and maintained servers: MySQL + HPCs
  • Assisted lab members with technical/IT related issues

EDUCATION

2006 : 2007  ~  University of the Sciences in Philadelphia (USP)

  • Masters in Bioinformatics from Misher College of Arts and Sciences

2002 : 2006  ~  University of the Sciences in Philadelphia (USP)

  • Bachelors in Bioinformatics from Misher College of Arts and Sciences
  • Minor in Biochemistry

PUBLICATIONS

  • Giovinazzo JA, et.al. Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity. Elife. 2020 May 19. PMID: 32427098.
  • Lennon AM, et.al. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science. 2020 Apr 28. PMID: 32345712.
  • Hallwirth CV, Garg G, Peters TJ, Kramer BA, Malani N, Hyman J, Ruan X, Ginn SL, Hetherington NA, Veeravalli L, Shahab A, Ranganathan S, Wei CL, Liddle C, Thrasher AJ, Bushman FD, Buckley MJ, Alexander IE. Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions. Mol Ther Methods Clin Dev. 2015 Apr 29;2:15015. PMID: 26029726
  • Aiyer S, Rossi P, Malani N, Schneider WM, Chandar A, et al. Structural and sequencing analysis of local target DNA recognition by MLV integrase. Nucleic acids research. 2015; PMID: 25969444
  • Hacein-Bey Abina S, Gaspar HB, Blondeau J, Caccavelli L, Charrier S, Buckland K, Picard C, Six E, Himoudi N, Gilmour K, McNicol AM, Hara H, Xu-Bayford J, Rivat C, Touzot F, Mavilio F, Lim A, Treluyer JM, Héritier S, Lefrère F, Magalon J, Pengue-Koyi I, Honnet G, Blanche S, Sherman EA, Male F, Berry C, Malani N, Bushman FD, Fischer A, Thrasher AJ, Galy A, Cavazzana M. Outcomes Following Gene Therapy in Patients With Severe Wiskott-Aldrich Syndrome. JAMA. 2015 Apr 21. PMID: 25898053.
  • Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry CC, Blanche S, Bleesing J, Blondeau J, de Boer H, Buckland KF, Caccavelli L, Cros G, De Oliveira S, Fernández KS, Guo D, Harris CE, Hopkins G, Lehmann LE, Lim A, London WB, van der Loo JC, Malani N, Male F, Malik P, Marinovic MA, McNicol AM, Moshous D, Neven B, Oleastro M, Picard C, Ritz J, Rivat C, Schambach A, Shaw KL, Sherman EA, Silberstein LE, Six E, Touzot F, Tsytsykova A, Xu-Bayford J, Baum C, Bushman FD, Fischer A, Kohn DB, Filipovich AH, Notarangelo LD, Cavazzana M, Williams DA, Thrasher AJ. A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. N Engl J Med. 2014. PMID: 25295500.
  • Gupta K, Brady T, Dyer BM, Malani N, Hwang Y, Male F, Nolte RT, Wang L, Velthuisen E, Jeffrey J, Van Duyne GD, Bushman FD. Allosteric Inhibition of Human Immunodeficiency Virus Integrase: LATE BLOCK DURING VIRAL REPLICATION AND ABNORMAL MULTIMERIZATION INVOLVING SPECIFIC PROTEIN DOMAINS. J Biol Chem. 2014. PMID: 24904063.
  • Sharma A, Slaughter A, Jena N, Feng L, Kessl JJ, Fadel HJ, Malani N, Male F, Wu L, Poeschla E, Bushman FD, Fuchs JR, Kvaratskhelia M. A new class of multimerization selective inhibitors of HIV-1 integrase. PLoS Pathog. 2014 May. PMID: 24874515.
  • Aiyer S, Swapna GV, Malani N, Aramini JM, Schneider WM, Plumb MR, Ghanem M, Larue RC, Sharma A, Studamire B, Kvaratskhelia M, Bushman FD, Montelione GT, Roth MJ. Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction. Nucleic Acids Res. 2014 Mar 12. PMID: 24623816.
  • Larue RC, Plumb MR, Crowe BL, Shkriabai N, Sharma A, Difiore J, Malani N, Aiyer SS, Roth MJ, Bushman FD, Foster MP, Kvaratskhelia M. Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes. Nucleic Acids Res. 2014 Feb 11. PMID: 24520112.
  • Petersen J, Drake MJ, Bruce EA, Riblett AM, Didigu CA, Wilen CB, Malani N, Male F, Lee FH, Bushman FD, Cherry S, Doms RW, Bates P, Briley K Jr. The major cellular sterol regulatory pathway is required for andes virus infection. PLoS Pathog. 2014 Feb 6;10(2):e1003911. doi: 10.1371/journal.ppat.1003911. Feb. PMID: 24516383
  • Berry CC, Ocwieja KE, Malani N, Bushman FD. Comparing DNA integration site clusters with scan statistics. Bioinformatics. 2014 Feb 11. PMID: 24489369.
  • De Rijck J, de Kogel C, Demeulemeester J, Vets S, El Ashkar S, Malani N, Bushman FD, Landuyt B, Husson SJ, Busschots K, Gijsbers R, Debyser Z. The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites. Cell Rep. 2013 Nov 27;5(4):886-94. doi: 10.1016/j.celrep.2013.09.040. Epub 2013 Oct 31. PMID: 24183673.
  • Sherrill-Mix S, Lewinski MK, Famiglietti M, Bosque A, Malani N, Ocwieja KE, Berry CC, Looney D, Shan L, Agosto LM, Pace MJ, Siliciano RF, O\’Doherty U, Guatelli J, Planelles V, Bushman FD. HIV latency and integration site placement in five cell-based models. Retrovirology. 2013 Aug 16;10:90. doi: 10.1186/1742-4690-10-90. PMID: 23953889.
  • Sharma A, Larue RC, Plumb MR, Malani N, Male F, Slaughter A, Kessl JJ, Shkriabai N, Coward E, Aiyer SS, Green PL, Wu L, Roth MJ, Bushman FD, Kvaratskhelia M. BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):12036-41. doi: 10.1073/pnas.1307157110. Epub 2013 Jul 1. PMID: 23818621.
  • Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB Jr, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineering. Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):E2279-87. doi: 10.1073/pnas.1305987110. Epub 2013 May 30. PMID: 23723351; PMCID: PMC3690869.
  • Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N. Bringing it all together: big data and HIV research. AIDS. 2013 Mar 13;27(5):835-8. doi: 10.1097/QAD.0b013e32835cb785. PMID: 23719353.
  • Schneider WM, Brzezinski JD, Aiyer S, Malani N, Gyuricza M, Bushman FD, Roth MJ. Viral DNA tethering domains complement replication-defective mutations in the p12 protein of MuLV Gag. Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9487-92. doi: 10.1073/pnas.1221736110. Epub 2013 May 9. PMID: 23661057
  • Zhong L, Malani N, Li M, Brady T, Xie J, Bell P, Li S, Jones H, Wilson JM, Flotte TR, Bushman FD, Gao G. rAAV Integration Sites in Murine Liver After OTC Gene Correction. Hum Gene Ther. 2013 Apr 28. PMID: 23621841.
  • Brady T, Kelly BJ, Male F, Roth S, Bailey A, Malani N, Gijsbers R, O’Doherty U, Bushman FD. Quantitation of HIV DNA integration: Effects of differential integration site distributions on Alu-PCR assays. J Virol Methods. 2013 Apr;189(1):53-7. doi: 10.1016/j.jviromet.2013.01.004. Epub 2013 Jan 21. PubMed PMID: 23348058.
  • Woodard LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. Comparative Analysis of the Recently Discovered hAT Transposon TcBuster in Human Cells. PLoS One. 2012;7(11):e42666. doi: 10.1371/journal.pone.0042666. Epub 2012 Nov 15. PubMed PMID: 23166581.
  • Li X, Ewis H, Hice RH, Malani N, Parker N, Zhou L, Feschotte C, Bushman FD, Atkinson PW, Craig NL. A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. Proc Natl Acad Sci U S A. 2012 Oct 22. PubMed PMID: 23091042.
  • Schrijvers R, Vets S, De Rijck J, Malani N, Bushman FD, Debyser Z, Gijsbers R. HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells. Retrovirology. 2012 Oct 9;9:84. doi: 10.1186/1742-4690-9-84. PubMed PMID: 23046603.
  • Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z. Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. J Biol Chem. 2011 Dec 2;286(48):41812-25. Epub 2011 Oct 10. PMID: 21987578.
  • Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics. 2011 Jul 26;12:378. PMID: 21791101.
  • Roth SL, Malani N, Bushman FD. Gammaretroviral integration into nucleosomal target DNA in vivo. J Virol. 2011 Jul;85(14):7393-401. Epub 2011 May 11. PMID: 21561906.
  • Ronen K, Negre O, Roth S, Colomb C, Malani N, Denaro M, Brady T, Fusil F, Gillet- Legrand B, Hehir K, Beuzard Y, Leboulch P, Down JD, Payen E, Bushman FD. Distribution of lentiviral vector integration sites in mice following therapeutic gene transfer to treat β-thalassemia. Mol Ther. 2011 Jul;19(7):1273-86. doi: 10.1038/mt.2011.20. Epub 2011 Mar 8. PMID: 21386821.
  • Li H, Haurigot V, Doyon Y, Li T, Wong SY, Bhagwat AS, Malani N, Anguela XM, Sharma R, Ivanciu L, Murphy SL, Finn JD, Khazi FR, Zhou S, Paschon DE, Rebar EJ, Bushman FD, Gregory PD, Holmes MC, High KA. In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature. 2011 Jun 26;475(7355):217-21. doi: 10.1038/nature10177. PMID: 21706032.
  • Brady T, Roth SL, Malani N, Wang GP, Berry CC, Leboulch P, Hacein-Bey-Abina S, Cavazzana-Calvo M, Papapetrou EP, Sadelain M, Savilahti H, Bushman FD. A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Res. 2011 Jun;39(11):e72. Epub 2011 Mar 16. PMID: 21415009.
  • Li H, Malani N, Hamilton SR, Schlachterman A, Bussadori G, Edmonson SE, Shah R, Arruda VR, Mingozzi F, Wright JF, Bushman FD, High KA. Assessing the potential for AAV vector genotoxicity in a murine model. Blood. 2011 Mar 24;117(12):3311-9. Epub 2010 Nov 24. Erratum in: Blood. 2011 Jun 16;117(24):6739. PMID: 21106988.
  • Gillet NA, Malani N, Melamed A, Gormley N, Carter R, Bentley D, Berry C, Bushman FD, Taylor GP, Bangham CR. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood. 2011 Mar 17;117(11):3113-22. Epub 2011 Jan 12. PMID: 21228324.
  • Ocwieja KE, Brady TL, Ronen K, Huegel A, Roth SL, Schaller T, James LC, Towers GJ, Young JA, Chanda SK, König R, Malani N, Berry CC, Bushman FD. HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. PLoS Pathog. 2011 Mar;7(3):e1001313. Epub 2011 Mar 10. PMID: 21423673.
  • Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, Leslie C, Bushman FD, Studer L, Sadelain M. Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol. 2011 Jan;29(1):73-8. Epub 2010 Dec 12. PMID: 21151124
  • Cattoglio C, Maruggi G, Bartholomae C, Malani N, Pellin D, Cocchiarella F, Magnani Z, Ciceri F, Ambrosi A, von Kalle C, Bushman FD, Bonini C, Schmidt M, Mavilio F, Recchia A. High-definition mapping of retroviral integration sites defines the fate of allogeneic T cells after donor lymphocyte infusion. PLoS One. 2010 Dec 22;5(12):e15688. PMID: 21203516.
  • Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana- Calvo M, Bushman FD. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood. 2010 Jun 3;115(22):4356-66. Epub 2010 Mar 12. PMID: 20228274.
  • Gijsbers R, Ronen K, Vets S, Malani N, De Rijck J, McNeely M, Bushman FD, Debyser Z. LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Mol Ther. 2010 Mar;18(3):552-60. Epub 2010 Jan 5. PMID: 20195265.
  • Brady T, Agosto LM, Malani N, Berry CC, O\’Doherty U, Bushman F. HIV integration site distributions in resting and activated CD4+ T cells infected in culture. AIDS. 2009 Jul 31;23(12):1461-71. PMID: 19550285.
  • Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells. Mol Ther. 2009 May;17(5):844-50. Epub 2009 Mar 3. PMID: 19259065.
  • Bushman FD, Malani N, Fernandes J, D\’Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome- wide studies. PLoS Pathog. 2009 May;5(5):e1000437. Epub 2009 May 29. Review. PMID: 19478882.
  • Ciuffi A, Ronen K, Brady T, Malani N, Wang G, Berry CC, Bushman FD. Methods for integration site distribution analyses in animal cell genomes. Methods. 2009 Apr;47(4):261-8. Epub 2008 Nov 25. PMID: 19038346.
  • Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 2009 Mar 1;23(5):633-42. PMID: 19270161.
  • Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res. 2008 Dec;36(22):e148. Epub 2008 Oct 25. PMID: 18953026.
  • Bushman FD, Hoffmann C, Ronen K, Malani N, Minkah N, Rose HM, Tebas P, Wang GP. Massively parallel pyrosequencing in HIV research. AIDS. 2008 Jul 31;22(12):1411-5. Review. PMID: 18614863.