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Items: 29

1.

Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA.

Wan N, Weinberg D, Liu TY, Niehaus K, Ariazi EA, Delubac D, Kannan A, White B, Bailey M, Bertin M, Boley N, Bowen D, Cregg J, Drake AM, Ennis R, Fransen S, Gafni E, Hansen L, Liu Y, Otte GL, Pecson J, Rice B, Sanderson GE, Sharma A, St John J, Tang C, Tzou A, Young L, Putcha G, Haque IS.

BMC Cancer. 2019 Aug 23;19(1):832. doi: 10.1186/s12885-019-6003-8.

2.

Screening for Tay-Sachs disease carriers by full-exon sequencing with novel variant interpretation outperforms enzyme testing in a pan-ethnic cohort.

Cecchi AC, Vengoechea ES, Kaseniit KE, Hardy MW, Kiger LA, Mehta N, Haque IS, Moyer K, Page PZ, Muzzey D, Grinzaid KA.

Mol Genet Genomic Med. 2019 Aug;7(8):1-12. doi: 10.1002/mgg3.836. Epub 2019 Jul 10.

3.

Current and future perspectives of liquid biopsies in genomics-driven oncology.

Heitzer E, Haque IS, Roberts CES, Speicher MR.

Nat Rev Genet. 2019 Feb;20(2):71-88. doi: 10.1038/s41576-018-0071-5. Review.

PMID:
30410101
4.

Correction: The population genetics of human disease: The case of recessive, lethal mutations.

Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M.

PLoS Genet. 2018 Jul 2;14(7):e1007499. doi: 10.1371/journal.pgen.1007499. eCollection 2018 Jul.

5.

Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification.

Hogan GJ, Vysotskaia VS, Beauchamp KA, Seisenberger S, Grauman PV, Haas KR, Hong SH, Jeon D, Kash S, Lai HH, Melroy LM, Theilmann MR, Chu CS, Iori K, Maguire JR, Evans EA, Haque IS, Mar-Heyming R, Kang HP, Muzzey D.

Clin Chem. 2018 Jul;64(7):1063-1073. doi: 10.1373/clinchem.2018.286823. Epub 2018 May 14.

6.

The population genetics of human disease: The case of recessive, lethal mutations.

Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M.

PLoS Genet. 2017 Sep 28;13(9):e1006915. doi: 10.1371/journal.pgen.1006915. eCollection 2017 Sep. Erratum in: PLoS Genet. 2018 Jul 2;14(7):e1007499.

7.

Clinical Utility of Expanded Carrier Screening: Reproductive Behaviors of At-Risk Couples.

Ghiossi CE, Goldberg JD, Haque IS, Lazarin GA, Wong KK.

J Genet Couns. 2018 Jun;27(3):616-625. doi: 10.1007/s10897-017-0160-1. Epub 2017 Sep 27.

8.

Systematic design and comparison of expanded carrier screening panels.

Beauchamp KA, Muzzey D, Wong KK, Hogan GJ, Karimi K, Candille SI, Mehta N, Mar-Heyming R, Kaseniit KE, Kang HP, Evans EA, Goldberg JD, Lazarin GA, Haque IS.

Genet Med. 2018 Jan;20(1):55-63. doi: 10.1038/gim.2017.69. Epub 2017 Jun 22.

9.

Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods.

Artieri CG, Haverty C, Evans EA, Goldberg JD, Haque IS, Yaron Y, Muzzey D.

Prenat Diagn. 2017 May;37(5):482-490. doi: 10.1002/pd.5036. Epub 2017 Apr 26.

PMID:
28317136
10.

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment.

Vysotskaia VS, Hogan GJ, Gould GM, Wang X, Robertson AD, Haas KR, Theilmann MR, Spurka L, Grauman PV, Lai HH, Jeon D, Haliburton G, Leggett M, Chu CS, Iori K, Maguire JR, Ready K, Evans EA, Kang HP, Haque IS.

PeerJ. 2017 Feb 23;5:e3046. doi: 10.7717/peerj.3046. eCollection 2017.

11.

Smith-Lemli-Opitz syndrome carrier frequency and estimates of in utero mortality rates.

Lazarin GA, Haque IS, Evans EA, Goldberg JD.

Prenat Diagn. 2017 Apr;37(4):350-355. doi: 10.1002/pd.5018. Epub 2017 Mar 9.

12.

Prenatal Carrier Screening.

Haque IS, Lazarin GA, Wapner RJ.

JAMA. 2016 Dec 27;316(24):2675-2676. doi: 10.1001/jama.2016.17401. No abstract available.

PMID:
28027359
13.

Group Testing Approach for Trinucleotide Repeat Expansion Disorder Screening.

Kaseniit KE, Theilmann MR, Robertson A, Evans EA, Haque IS.

Clin Chem. 2016 Oct;62(10):1401-8. doi: 10.1373/clinchem.2016.259796. Epub 2016 Aug 18.

14.

Modeled Fetal Risk of Genetic Diseases Identified by Expanded Carrier Screening.

Haque IS, Lazarin GA, Kang HP, Evans EA, Goldberg JD, Wapner RJ.

JAMA. 2016 Aug 16;316(7):734-42. doi: 10.1001/jama.2016.11139.

PMID:
27533158
15.

Re: Carrier Screening is a Deficient Strategy for Determining Sperm Donor Eligibility and Reducing Risk of Disease in Recipient Children (From: Silver AJ, Larson JL, Silver MJ, et al. Genet Test Mol Biomarkers 2016;20:276-284).

Wong KK, Goldberg JD, Evans EA, Kang HP, Haque IS.

Genet Test Mol Biomarkers. 2016 Aug;20(8):413-4. doi: 10.1089/gtmb.2016.29019.kkw. No abstract available.

PMID:
27505438
16.

Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing.

Kang HP, Maguire JR, Chu CS, Haque IS, Lai H, Mar-Heyming R, Ready K, Vysotskaia VS, Evans EA.

PeerJ. 2016 Jun 28;4:e2162. doi: 10.7717/peerj.2162. eCollection 2016.

17.

Tay-Sachs Carrier Screening by Enzyme and Molecular Analyses in the New York City Minority Population.

Mehta N, Lazarin GA, Spiegel E, Berentsen K, Brennan K, Giordano J, Haque IS, Wapner R.

Genet Test Mol Biomarkers. 2016 Sep;20(9):504-9. doi: 10.1089/gtmb.2015.0302. Epub 2016 Jun 30.

18.

Expanded carrier screening: A review of early implementation and literature.

Lazarin GA, Haque IS.

Semin Perinatol. 2016 Feb;40(1):29-34. doi: 10.1053/j.semperi.2015.11.005. Epub 2015 Dec 21. Review.

19.

Systematic Classification of Disease Severity for Evaluation of Expanded Carrier Screening Panels.

Lazarin GA, Hawthorne F, Collins NS, Platt EA, Evans EA, Haque IS.

PLoS One. 2014 Dec 10;9(12):e114391. doi: 10.1371/journal.pone.0114391. eCollection 2014.

20.

SCISSORS: practical considerations.

Kearnes SM, Haque IS, Pande VS.

J Chem Inf Model. 2014 Jan 27;54(1):5-15. doi: 10.1021/ci400264f. Epub 2013 Dec 16.

21.

Response to Stoll and Resta.

Lazarin GA, Haque IS, Nazareth S, Evans EA.

Genet Med. 2013 Apr;15(4):319-20. doi: 10.1038/gim.2013.19. No abstract available.

22.

An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals.

Lazarin GA, Haque IS, Nazareth S, Iori K, Patterson AS, Jacobson JL, Marshall JR, Seltzer WK, Patrizio P, Evans EA, Srinivasan BS.

Genet Med. 2013 Mar;15(3):178-86. doi: 10.1038/gim.2012.114. Epub 2012 Sep 13.

23.

Knowledge and attitudes regarding expanded genetic carrier screening among women's healthcare providers.

Ready K, Haque IS, Srinivasan BS, Marshall JR.

Fertil Steril. 2012 Feb;97(2):407-13. doi: 10.1016/j.fertnstert.2011.11.007. Epub 2011 Dec 2.

PMID:
22137493
24.

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.

Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS.

J Chem Theory Comput. 2011 Oct 11;7(10):3412-3419.

25.

Anatomy of high-performance 2D similarity calculations.

Haque IS, Pande VS, Walters WP.

J Chem Inf Model. 2011 Sep 26;51(9):2345-51. doi: 10.1021/ci200235e. Epub 2011 Sep 7.

26.

Error bounds on the SCISSORS approximation method.

Haque IS, Pande VS.

J Chem Inf Model. 2011 Sep 26;51(9):2248-53. doi: 10.1021/ci200251a. Epub 2011 Sep 8.

27.

SCISSORS: a linear-algebraical technique to rapidly approximate chemical similarities.

Haque IS, Pande VS.

J Chem Inf Model. 2010 Jun 28;50(6):1075-88. doi: 10.1021/ci1000136.

PMID:
20509629
28.

SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs.

Haque IS, Pande VS, Walters WP.

J Chem Inf Model. 2010 Apr 26;50(4):560-4. doi: 10.1021/ci100011z.

29.

PAPER--accelerating parallel evaluations of ROCS.

Haque IS, Pande VS.

J Comput Chem. 2010 Jan 15;31(1):117-32. doi: 10.1002/jcc.21307.

PMID:
19421991

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