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Contemporary Trends in Percutaneous Nephrolithomy Across New York State: A Review of the Statewide Planning and Research Cooperative System (SPARCS).

Patel NH, Parikh S, Bloom J, Schulman A, Wagmaister J, Fullerton S, Phillips JL, Choudhury M, Eshghi M.

J Endourol. 2019 Jun 10. doi: 10.1089/end.2019.0115. [Epub ahead of print]


Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J; International IBD Genetics Consortium; NIDDK IBD Genetics Consortium; T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ.

PLoS Genet. 2019 May 30;15(5):e1008190. doi: 10.1371/journal.pgen.1008190. eCollection 2019 May.


Use of multiparmetric MRI and Fusion-Guided Biopsies to Properly Select and Follow African-American Men on Active Surveillance.

Bloom JB, Lebastchi AH, Gold SA, Hale GR, Sanford T, Mehralivand S, Ahdoot M, Rayn KN, Czarniecki M, Smith C, Valera V, Wood BJ, Merino MJ, Choyke PL, Parnes HL, Turkbey B, Pinto PA.

BJU Int. 2019 May 29. doi: 10.1111/bju.14835. [Epub ahead of print]


Germline genome protection: implications for gamete quality and germ cell tumorigenesis.

Bloom JC, Loehr AR, Schimenti JC, Weiss RS.

Andrology. 2019 May 22. doi: 10.1111/andr.12651. [Epub ahead of print] Review.


Massively Parallel Profiling of HIV-1 Resistance to the Fusion Inhibitor Enfuvirtide.

Dingens AS, Arenz D, Overbaugh J, Bloom JD.

Viruses. 2019 May 15;11(5). pii: E439. doi: 10.3390/v11050439.


Anatomy, Head and Neck, Eye Levator Labii Superioris Muscle.

Bloom J, Rayi A.

StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-.
2019 May 5.


Single-cell virus sequencing of influenza infections that trigger innate immunity.

Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJW, Bloom JD.

J Virol. 2019 May 8. pii: JVI.00500-19. doi: 10.1128/JVI.00500-19. [Epub ahead of print]


Treatment Refusal in Arizona's Jail-Based Competency to Stand Trial Restoration Programs.

Bloom JD, Kirkorsky SE.

J Am Acad Psychiatry Law. 2019 Jun;47(2):233-239. doi: 10.29158/JAAPL.003840-19. Epub 2019 May 2.


Neuroendocrine carcinoma of the colon presenting as acute meningitis.

Bloom JR, Brickman A, Yang FJ, Park JW, Cheponis J.

BMC Neurol. 2019 May 1;19(1):76. doi: 10.1186/s12883-019-1310-x.


Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans.

Soh YS, Moncla LH, Eguia R, Bedford T, Bloom JD.

Elife. 2019 Apr 30;8. pii: e45079. doi: 10.7554/eLife.45079.


The Migration of Arizona's Post-Insanity Defense Procedures to a Modified GBMI Model.

Kirkorsky SE, Shao W, Bloom JD.

J Am Acad Psychiatry Law. 2019 Jun;47(2):217-223. doi: 10.29158/JAAPL.003834-19. Epub 2019 Apr 26.


Super active surveillance for low-risk prostate cancer | Opinion: No.

Ghodoussipour S, Lebastchi AH, Bloom JB, Pinto PA, Berger A.

Int Braz J Urol. 2019 Mar-Apr;45(2):215-219. doi: 10.1590/S1677-5538.IBJU.2019.02.03. No abstract available.


Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance.

Hom N, Gentles L, Bloom JD, Lee KK.

J Virol. 2019 Jun 14;93(13). pii: e00161-19. doi: 10.1128/JVI.00161-19. Print 2019 Jul 1.


mpMRI preoperative staging in men treated with antiandrogen and androgen deprivation therapy before robotic prostatectomy.

Gold SA, VanderWeele DJ, Harmon S, Bloom JB, Karzai F, Hale GR, Marhamati S, Rayn KN, Mehralivand S, Merino MJ, Gulley JL, Bilusic M, Madan RA, Choyke PL, Turkbey B, Dahut W, Pinto PA.

Urol Oncol. 2019 Jun;37(6):352.e25-352.e30. doi: 10.1016/j.urolonc.2019.01.012. Epub 2019 Apr 15.


Device Malfunctions and Complications Associated with Benign Prostatic Hyperplasia Surgery: Review of the Manufacturer and User Facility Device Experience Database.

Patel NH, Uppaluri N, Iorga M, Schulman A, Bloom JB, Phillips J, Fullerton S, Konno S, Choudhury M, Eshghi M.

J Endourol. 2019 Jun;33(6):448-454. doi: 10.1089/end.2019.0067. Epub 2019 May 24.


A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing.

Jones EM, Jajoo R, Cancilla D, Lubock NB, Wang J, Satyadi M, Cheung R, de March C, Bloom JS, Matsunami H, Kosuri S.

Cell Syst. 2019 Mar 27;8(3):254-260.e6. doi: 10.1016/j.cels.2019.02.009. Epub 2019 Mar 20.


Determinants of Zika virus host tropism uncovered by deep mutational scanning.

Setoh YX, Amarilla AA, Peng NYG, Griffiths RE, Carrera J, Freney ME, Nakayama E, Ogawa S, Watterson D, Modhiran N, Nanyonga FE, Torres FJ, Slonchak A, Periasamy P, Prow NA, Tang B, Harrison J, Hobson-Peters J, Cuddihy T, Cooper-White J, Hall RA, Young PR, Mackenzie JM, Wolvetang E, Bloom JD, Suhrbier A, Khromykh AA.

Nat Microbiol. 2019 May;4(5):876-887. doi: 10.1038/s41564-019-0399-4. Epub 2019 Mar 18.


Cardiac Surgery Trainees as "Skin-to-Skin" Operating Surgeons: Midterm Outcomes.

Bloom JP, Heng E, Auchincloss HG, Melnitchouk SI, D'Alessandro DA, Villavicencio MA, Sundt TM, Tolis G Jr.

Ann Thorac Surg. 2019 Mar 14. pii: S0003-4975(19)30345-5. doi: 10.1016/j.athoracsur.2019.02.008. [Epub ahead of print]


Reconciling disparate estimates of viral genetic diversity during human influenza infections.

Xue KS, Bloom JD.

Nat Genet. 2019 Feb 25. doi: 10.1038/s41588-019-0349-3. [Epub ahead of print] No abstract available.


Female-biased embryonic death from inflammation induced by genomic instability.

McNairn AJ, Chuang CH, Bloom JC, Wallace MD, Schimenti JC.

Nature. 2019 Mar;567(7746):105-108. doi: 10.1038/s41586-019-0936-6. Epub 2019 Feb 20.


An Antigenic Atlas of HIV-1 Escape from Broadly Neutralizing Antibodies Distinguishes Functional and Structural Epitopes.

Dingens AS, Arenz D, Weight H, Overbaugh J, Bloom JD.

Immunity. 2019 Feb 19;50(2):520-532.e3. doi: 10.1016/j.immuni.2018.12.017. Epub 2019 Jan 29.


When to Biopsy the Seminal Vesicles: A Validated Multiparametric Magnetic Resonance Imaging and Target Driven Model to Detect Seminal Vesicle Invasion in Prostate Cancer.

Gold SA, Shih JH, Rais-Bahrami S, Bloom JB, Vourganti S, Singla N, Baroni RH, Coker MA, Fialkoff J, Noschang J, Roehrborn CG, Turkbey B, Pinto PA; Collaborators.

J Urol. 2019 Jan 23. doi: 10.1097/JU.0000000000000112. [Epub ahead of print]


Comprehensive profiling of translation initiation in influenza virus infected cells.

Machkovech HM, Bloom JD, Subramaniam AR.

PLoS Pathog. 2019 Jan 23;15(1):e1007518. doi: 10.1371/journal.ppat.1007518. eCollection 2019 Jan.


A Grading System for the Assessment of Risk of Extraprostatic Extension of Prostate Cancer at Multiparametric MRI.

Mehralivand S, Shih JH, Harmon S, Smith C, Bloom J, Czarniecki M, Gold S, Hale G, Rayn K, Merino MJ, Wood BJ, Pinto PA, Choyke PL, Turkbey B.

Radiology. 2019 Mar;290(3):709-719. doi: 10.1148/radiol.2018181278. Epub 2019 Jan 22.


What Have We Learned From Malpractice Claims Involving the Surgical Management of Benign Biliary Disease?: A 128 Million Dollar Question.

Gartland RM, Bloom JP, Fong ZV, DeRoo C, Dwyer K, Quinn G, Lillemoe K, Mort E.

Ann Surg. 2019 May;269(5):785-791. doi: 10.1097/SLA.0000000000003155.


Early Distal Migration of a Self-Expanding Aortic Valve Prosthesis Causing Myocardial Infarction.

Bloom JP, Kwon MH, Tolis G Jr.

Ann Thorac Surg. 2018 Dec 26. pii: S0003-4975(18)31850-2. doi: 10.1016/j.athoracsur.2018.11.050. [Epub ahead of print]


Predicting Gleason Group Progression for Men on Prostate Cancer Active Surveillance: Role of a Negative Confirmatory Magnetic Resonance Imaging-Ultrasound Fusion Biopsy.

Bloom JB, Hale GR, Gold SA, Rayn KN, Smith C, Mehralivand S, Czarniecki M, Valera V, Wood BJ, Merino MJ, Choyke PL, Parnes HL, Turkbey B, Pinto PA.

J Urol. 2019 Jan;201(1):84-90. doi: 10.1016/j.juro.2018.07.051.


The Genetic Basis of Mutation Rate Variation in Yeast.

Gou L, Bloom JS, Kruglyak L.

Genetics. 2019 Feb;211(2):731-740. doi: 10.1534/genetics.118.301609. Epub 2018 Nov 30.


Detection of lymph node metastases in penile cancer.

Bloom JB, Stern M, Patel NH, Zhang M, Phillips JL.

Transl Androl Urol. 2018 Oct;7(5):879-886. doi: 10.21037/tau.2018.08.01. Review.


Lymph node imaging in testicular cancer.

Hale GR, Teplitsky S, Truong H, Gold SA, Bloom JB, Agarwal PK.

Transl Androl Urol. 2018 Oct;7(5):864-874. doi: 10.21037/tau.2018.07.18. Review.


Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.

Hilton SK, Bloom JD.

Virus Evol. 2018 Nov 6;4(2):vey033. doi: 10.1093/ve/vey033. eCollection 2018 Jul.


Prophylactic effect of ethyl pyruvate on renal ischemia/reperfusion injury mediated through oxidative stress.

Bloom J, Patel N, Wagmaister J, Choudhury M, Eshghi M, Konno S.

Int Urol Nephrol. 2019 Jan;51(1):85-92. doi: 10.1007/s11255-018-2020-9. Epub 2018 Oct 31.


Cardioversion of atrial fibrillation in obese patients: Results from the Cardioversion-BMI randomized controlled trial.

Voskoboinik A, Moskovitch J, Plunkett G, Bloom J, Wong G, Nalliah C, Prabhu S, Sugumar H, Paramasweran R, McLellan A, Ling LH, Goh CY, Noaman S, Fernando H, Wong M, Taylor AJ, Kalman JM, Kistler PM.

J Cardiovasc Electrophysiol. 2019 Feb;30(2):155-161. doi: 10.1111/jce.13786. Epub 2018 Nov 14.


Jail-Based Competency Restoration.

Felthous AR, Bloom JD.

J Am Acad Psychiatry Law. 2018 Sep;46(3):364-372. doi: 10.29158/JAAPL.003772-18.


Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses.

Evans KS, Brady SC, Bloom JS, Tanny RE, Cook DE, Giuliani SE, Hippleheuser SW, Zamanian M, Andersen EC.

Genetics. 2018 Dec;210(4):1509-1525. doi: 10.1534/genetics.118.301311. Epub 2018 Oct 19.


Anatomy, Head and Neck, Eye Iris Sphincter Muscle.

Bloom J, Motlagh M, Czyz CN.

StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-.
2019 Jun 6.


A Randomized Controlled Trial of Exercise to Prevent Bone Loss in Premenopausal Women with Breast Cancer.

Tabatabai LS, Bloom J, Stewart S, Sellmeyer DE.

J Womens Health (Larchmt). 2019 Jan;28(1):87-92. doi: 10.1089/jwh.2017.6863. Epub 2018 Oct 12.


Computerised Dynamic Posturography in Premanifest and Manifest individuals with Huntington's Disease.

Reyes A, Salomonczyk D, Teo WP, Medina LD, Bartlett D, Pirogovsky-Turk E, Zaenker P, Bloom JC, Simmons RW, Ziman M, Gilbert PE, Cruickshank T.

Sci Rep. 2018 Oct 2;8(1):14615. doi: 10.1038/s41598-018-32924-y.


Different culture media modulate growth, heterogeneity, and senescence in human mammary epithelial cell cultures.

Lee JK, Bloom J, Zubeldia-Plazaola A, Garbe JC, Stampfer MR, LaBarge MA.

PLoS One. 2018 Oct 1;13(10):e0204645. doi: 10.1371/journal.pone.0204645. eCollection 2018.


Percutaneous Radiofrequency Lower Face and Neck Tightening Technique.

Locketz GD, Bloom JD.

JAMA Facial Plast Surg. 2018 Sep 13. doi: 10.1001/jamafacial.2018.0917. [Epub ahead of print] No abstract available.


Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones.

Phillips AM, Ponomarenko AI, Chen K, Ashenberg O, Miao J, McHugh SM, Butty VL, Whittaker CA, Moore CL, Bloom JD, Lin YS, Shoulders MD.

PLoS Biol. 2018 Sep 17;16(9):e3000008. doi: 10.1371/journal.pbio.3000008. eCollection 2018 Sep.


Incidental bladder cancers found on multiparametric MRI of the prostate gland: a single center experience.

Rayn KN, Hale GR, Bloom JB, Gold SA, Carvalho FLF, Mehralivand S, Czarniecki M, Wood BJ, Merino MJ, Choyke P, Türkbey B, Pinto PA, Agarwal PK.

Diagn Interv Radiol. 2018 Sep;24(5):316-320. doi: 10.5152/dir.2018.18102. Review.


Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments.

Bloom JD.

PeerJ. 2018 Sep 3;6:e5578. doi: 10.7717/peerj.5578. eCollection 2018.


Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility.

Farrukee R, Zarebski AE, McCaw JM, Bloom JD, Reading PC, Hurt AC.

Antimicrob Agents Chemother. 2018 Oct 24;62(11). pii: e01081-18. doi: 10.1128/AAC.01081-18. Print 2018 Nov.


Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin.

Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin YS, Bloom JD, Shoulders MD.

Elife. 2018 Sep 6;7. pii: e38795. doi: 10.7554/eLife.38795.


A case of Henoch-Schonlein Purpura with dilated coronary arteries.

Bloom JL, Darst JR, Prok L, Soep JB.

Pediatr Rheumatol Online J. 2018 Sep 4;16(1):54. doi: 10.1186/s12969-018-0270-9.


Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3.

Fu Y, Long MJC, Wisitpitthaya S, Inayat H, Pierpont TM, Elsaid IM, Bloom JC, Ortega J, Weiss RS, Aye Y.

Nat Chem Biol. 2018 Oct;14(10):943-954. doi: 10.1038/s41589-018-0113-5. Epub 2018 Aug 27.


Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P; NHLBI TOPMed Lipids Working Group.

Nat Commun. 2018 Aug 23;9(1):3493. doi: 10.1038/s41467-018-05975-y.


Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S; NHLBI TOPMed Lipids Working Group.

Nat Commun. 2018 Aug 23;9(1):3391. doi: 10.1038/s41467-018-05747-8.


Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.

Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel-Caron M, Dahyot S, Lebeurre J, Prévost G.

BMC Genomics. 2018 Aug 20;19(1):621. doi: 10.1186/s12864-018-4978-1.

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