Harvard Catalyst Profiles

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Amy Ly, M.D.


Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Dias-Santagata D, Heist RS, Bard AZ, da Silva AFL, Dagogo-Jack I, Nardi V, Ritterhouse LL, Spring LM, Jessop N, Farahani AA, Mino-Kenudson M, Allen J, Goyal L, Parikh A, Misdraji J, Shankar G, Jordan JT, Martinez-Lage M, Frosch M, Graubert T, Fathi AT, Hobbs GS, Hasserjian RP, Raje N, Abramson J, Schwartz JH, Sullivan RJ, Miller D, Hoang MP, Isakoff S, Ly A, Bouberhan S, Watkins J, Oliva E, Wirth L, Sadow PM, Faquin W, Cote GM, Hung YP, Gao X, Wu CL, Garg S, Rivera M, Le LP, John Iafrate A, Juric D, Hochberg EP, Clark J, Bardia A, Lennerz JK. Implementation and Clinical Adoption of Precision Oncology Workflows Across a Healthcare Network. Oncologist. 2022 Nov 03; 27(11):930-939. PMID: 35852437; PMCID: PMC9632318.
    Citations:    Fields:    
  2. Villalba JA, Hilburn CF, Garlin MA, Elliott GA, Li Y, Kunitoki K, Poli S, Alba GA, Madrigal E, Taso M, Price MC, Aviles AJ, Araujo-Medina M, Bonanno L, Boyraz B, Champion SN, Harris CK, Helland TL, Hutchison B, Jobbagy S, Marshall MS, Shepherd DJ, Barth JL, Hung YP, Ly A, Hariri LP, Turbett SE, Pierce VM, Branda JA, Rosenberg ES, Mendez-Pena J, Chebib I, Rosales IA, Smith RN, Miller MA, Rosas IO, Hardin CC, Baden LR, Medoff BD, Colvin RB, Little BP, Stone JR, Mino-Kenudson M, Shih AR. Vasculopathy and Increased Vascular Congestion in Fatal COVID-19 and Acute Respiratory Distress Syndrome. Am J Respir Crit Care Med. 2022 Oct 01; 206(7):857-873. PMID: 35671465.
    Citations: 4     Fields:    
  3. Torous VF, Basler D, McEnery C, Astor T, Ly A. Utilization of Oil Red O staining for assessing aspiration risk in lung transplant patients: A multidisciplinary prospective study with clinical practice insights. Cancer Cytopathol. 2022 Aug 10. PMID: 35946954.
    Citations:    Fields:    
  4. Boyraz B, Ly A. Discerning subsets of breast cancer with very low and absent HER2 protein expression. Hum Pathol. 2022 09; 127:50-55. PMID: 35671839.
    Citations:    Fields:    
  5. Yu L, Allen R, Jia L, Sun T, Isakoff SJ, Scherrer-Crosbie M, Kehlmann AM, Zheng H, Ly A, Walmsley CS, Hesler K, Varasteh AN, Pinto CJ, McLoughlin DE, Wu W, Wang X. An Initial Evaluation of Human Plasma cMLC-1: A Potential Protein Biomarker for Trastuzumab-Induced Cardiotoxicity, Breast Cancer Screening and Progression. Front Oncol. 2022; 12:809715. PMID: 35592673; PMCID: PMC9113547.
  6. Torous VF, Ly A. Correlation between cytology Oil Red O staining and lung biopsy specimens: utility of the lipid-laden macrophage index. J Am Soc Cytopathol. 2022 Jul-Aug; 11(4):226-233. PMID: 35597768.
    Citations:    Fields:    Translation:HumansCells
  7. Fernandez AI, Liu M, Bellizzi A, Brock J, Fadare O, Hanley K, Harigopal M, Jorns JM, Kuba MG, Ly A, Podoll M, Rabe K, Sanders MA, Singh K, Snir OL, Soong TR, Wei S, Wen H, Wong S, Yoon E, Pusztai L, Reisenbichler E, Rimm DL. Examination of Low ERBB2 Protein Expression in Breast Cancer Tissue. JAMA Oncol. 2022 04 01; 8(4):1-4. PMID: 35113160; PMCID: PMC8814969.
    Citations: 7     Fields:    Translation:Humans
  8. Zadeh SL, Balassanian R, Cheung MC, Falchi L, Hasserjian R, Lin O, Long SR, Ly A, Menke JR, Mou E, Natkunam Y, Ruiz-Cordero R, Volaric AK, Wang L, Wen KW, Gratzinger D. Global Cytopathology-Hematopathology Practice Trends. Am J Clin Pathol. 2022 Feb 03; 157(2):196-201. PMID: 34508545; PMCID: PMC9630120.
    Citations:    Fields:    Translation:Humans
  9. Zadeh SL, Balassanian R, Cheung MC, Falchi L, Hasserjian R, Lin O, Long SR, Ly A, Menke JR, Mou E, Natkunam Y, Ruiz-Cordero R, Volaric AK, Wang L, Wen KW, Gratzinger D. Corrigendum to: Global Cytopathology-Hematopathology Practice Trends. Am J Clin Pathol. 2022 Jan 06; 157(1):155. PMID: 34595513.
    Citations:    Fields:    
  10. Tapias LF, Lanuti M, Wright CD, Hron TA, Ly A, Mathisen DJ, Ott HC. COVID-19-related Post-intubation Tracheal Stenosis: Early Experience With Surgical Treatment. Ann Surg. 2022 01 01; 275(1):e271-e273. PMID: 33856373; PMCID: PMC8683075.
    Citations: 2     Fields:    Translation:Humans
  11. Makarenko VV, DeLelys ME, Hasserjian RP, Ly A. Lymph node FNA cytology: Diagnostic performance and clinical implications of proposed diagnostic categories. Cancer Cytopathol. 2022 02; 130(2):144-153. PMID: 34661975.
    Citations:    Fields:    Translation:Humans
  12. Nandy S, Helland TL, Roop BW, Raphaely RA, Ly A, Lew M, Berigei SR, Villiger M, Sorokina A, Szabari MV, Fintelmann FJ, Suter MJ, Hariri LP. Rapid non-destructive volumetric tumor yield assessment in fresh lung core needle biopsies using polarization sensitive optical coherence tomography. Biomed Opt Express. 2021 Sep 01; 12(9):5597-5613. PMID: 34692203; PMCID: PMC8515979.
    Citations: 3     
  13. Mou E, Falchi L, Sundaram V, Abramson JS, Balassanian R, Beygi S, Fitzpatrick MJ, Frank AK, Gupta S, Lin O, Reed JR, Long SR, Ly A, Menke JR, Reed DR, Ruiz-Cordero R, Volaric AK, Xie Y, Wang L, Wen KW, Zadeh SL, Natkunam Y, Cheung MC, Gratzinger D. Impact of initial biopsy type on the time to final diagnostic biopsy in patients with follicular lymphoma and suspected histologic transformation. Leuk Lymphoma. 2021 12; 62(12):2864-2872. PMID: 34176413.
    Citations:    Fields:    Translation:Humans
  14. Pathoulas JT, Flanagan KE, Walker CJ, Ly A, Krajewski KM, Pupo Wiss I, Senna MM. Subcutaneous metastasis from an atypical pulmonary carcinoid tumor. Dermatol Online J. 2021 May 15; 27(5). PMID: 34118814.
    Citations:    Fields:    Translation:Humans
  15. Choy B, Ly A. The patient experience in a cytopathologist-performed ultrasound-guided fine needle aspiration clinic: potential complications and feedback. J Am Soc Cytopathol. 2021 Jul-Aug; 10(4):429-434. PMID: 33839072.
    Citations:    Fields:    Translation:Humans
  16. Villalba JA, Shih AR, Sayo TMS, Kunitoki K, Hung YP, Ly A, Kem M, Hariri LP, Muniappan A, Gaissert HA, Colson YL, Lanuti MD, Mino-Kenudson M. Accuracy and Reproducibility of Intraoperative Assessment on Tumor Spread Through Air Spaces in Stage 1 Lung Adenocarcinomas. J Thorac Oncol. 2021 04; 16(4):619-629. PMID: 33348084; PMCID: PMC8836021.
    Citations: 4     Fields:    Translation:Humans
  17. Hariri LP, North CM, Shih AR, Israel RA, Maley JH, Villalba JA, Vinarsky V, Rubin J, Okin DA, Sclafani A, Alladina JW, Griffith JW, Gillette MA, Raz Y, Richards CJ, Wong AK, Ly A, Hung YP, Chivukula RR, Petri CR, Calhoun TF, Brenner LN, Hibbert KA, Medoff BD, Hardin CC, Stone JR, Mino-Kenudson M. Lung Histopathology in Coronavirus Disease 2019 as Compared With Severe Acute Respiratory Sydrome and H1N1 Influenza: A Systematic Review. Chest. 2021 01; 159(1):73-84. PMID: 33038391; PMCID: PMC7538870.
    Citations: 59     Fields:    Translation:HumansCells
  18. Spring LM, Specht MC, Jimenez RB, Isakoff SJ, Wang GX, Ly A, Shin JA, Bardia A, Moy B. Case 22-2020: A 62-Year-Old Woman with Early Breast Cancer during the Covid-19 Pandemic. N Engl J Med. 2020 Jul 16; 383(3):262-272. PMID: 32610007; PMCID: PMC7346678.
    Citations: 7     Fields:    Translation:HumansCellsPHPublic Health
  19. Liu Z, Ahn MH, Kurokawa T, Ly A, Zhang G, Wang F, Yamada T, Sadagopan A, Cheng J, Ferrone CR, Liss AS, Honselmann KC, Wojtkiewicz GR, Ferrone S, Wang X. A fast, simple, and cost-effective method of expanding patient-derived xenograft mouse models of pancreatic ductal adenocarcinoma. J Transl Med. 2020 06 24; 18(1):255. PMID: 32580742.
    Citations: 2     Fields:    Translation:HumansAnimals
  20. Torous VF, Brackett D, Brown P, Edwin N, Heidarian A, Lobuono C, Sun T, Pitman MB, Ly A. Oil red O staining for lipid-laden macrophage index of bronchoalveolar lavage: interobserver agreement and challenges to interpretation. J Am Soc Cytopathol. 2020 Nov - Dec; 9(6):563-569. PMID: 32674937.
    Citations: 2     Fields:    Translation:HumansCells
  21. Torous VF, Pitman MB, Ly A. Evaluation of the clinical utility of reflex GMS and AFB stains on BAL specimens from lung transplant patients. J Am Soc Cytopathol. 2020 May - Jun; 9(3):166-172. PMID: 32179025.
    Citations:    Fields:    Translation:HumansAnimalsCells
  22. Costa C, Wang Y, Ly A, Hosono Y, Murchie E, Walmsley CS, Huynh T, Healy C, Peterson R, Yanase S, Jakubik CT, Henderson LE, Damon LJ, Timonina D, Sanidas I, Pinto CJ, Mino-Kenudson M, Stone JR, Dyson NJ, Ellisen LW, Bardia A, Ebi H, Benes CH, Engelman JA, Juric D. PTEN Loss Mediates Clinical Cross-Resistance to CDK4/6 and PI3Ka Inhibitors in Breast Cancer. Cancer Discov. 2020 01; 10(1):72-85. PMID: 31594766.
    Citations: 65     Fields:    Translation:HumansAnimalsCells
  23. Hoda RS, Arpin Iii RN, Gottumukkala RV, Hughes KS, Ly A, Brachtel EF. Diagnostic Value of Fine-Needle Aspiration in Male Breast Lesions. Acta Cytol. 2019; 63(4):319-327. PMID: 30904908.
    Citations: 2     Fields:    Translation:Humans
  24. Haitz K, Ly A, Smith G. Idiopathic granulomatous mastitis. Cutis. 2019 Jan; 103(1):38-42. PMID: 30758334.
    Citations: 2     Fields:    Translation:Humans
  25. Frenk NE, Spring L, Muzikansky A, Vadvala HV, Gurski JM, Henderson LE, Mino-Kenudson M, Ly A, Bardia A, Finkelstein D, Engelman J, Mueller PR, Juric D, Weissleder R. High-Content Biopsies Facilitate Molecular Analyses and Do Not Increase Complication Rates in Patients With Advanced Solid Tumors. JCO Precis Oncol. 2017 Nov; 1:1-9. PMID: 35172508.
    Citations: 2     Fields:    
  26. Zhang Y, Schroeder BE, Jerevall PL, Ly A, Nolan H, Schnabel CA, Sgroi DC. A Novel Breast Cancer Index for Prediction of Distant Recurrence in HR+ Early-Stage Breast Cancer with One to Three Positive Nodes. Clin Cancer Res. 2017 Dec 01; 23(23):7217-7224. PMID: 28939745.
    Citations: 7     Fields:    Translation:Humans
  27. Di Xia F, Ly A, Smith GP. Mycophenolate mofetil as a successful therapy for idiopathic granulomatous mastitis. Dermatol Online J. 2017 Jul 15; 23(7). PMID: 29469699.
    Citations: 1     Fields:    Translation:Humans
  28. Aisagbonhi O, DeLelys M, Hartford N, Preffer F, Ly A. Utility of Flow Cytometry in Diagnosing Hematologic Malignancy in Tonsillar Tissue. Int J Surg Pathol. 2017 Aug; 25(5):406-413. PMID: 28351195.
    Citations:    Fields:    Translation:Humans
  29. Merrill AL, Buckley J, Tang R, Brachtel E, Rai U, Michaelson J, Ly A, Specht MC, Yagi Y, Smith BL. A Study of the Growth Patterns of Breast Carcinoma Using 3D Reconstruction: A Pilot Study. Breast J. 2017 Jan; 23(1):83-89. PMID: 27860134.
    Citations: 5     Fields:    Translation:Humans
  30. Dong J, Ly A, Arpin R, Ahmed Q, Brachtel E. Breast fine needle aspiration continues to be relevant in a large academic medical center: experience from Massachusetts General Hospital. Breast Cancer Res Treat. 2016 07; 158(2):297-305. PMID: 27383478.
    Citations: 2     Fields:    Translation:Humans
  31. Ly A, Ono JC, Hughes KS, Pitman MB, Balassanian R. Fine-Needle Aspiration Biopsy of Palpable Breast Masses: Patterns of Clinical Use and Patient Experience. J Natl Compr Canc Netw. 2016 05; 14(5):527-36. PMID: 27160231.
    Citations: 5     Fields:    Translation:Humans
  32. Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol. 2017 10 03; 14(10):1335-1352. PMID: 27002534; PMCID: PMC5711464.
    Citations: 7     Fields:    Translation:AnimalsCells
  33. Sarraj WM, Tang R, Najjar AL, Griffin M, Bui AH, Zambeli-Ljepovic A, Senter-Zapata M, Lewin-Berlin M, Fernandez L, Buckley J, Ly A, Brachtel E, Aftreth O, Gilbertson J, Yagi Y, Gadd M, Hughes KS, Smith BL, Michaelson JS. Prediction of primary breast cancer size and T-stage using micro-computed tomography in lumpectomy specimens. J Pathol Inform. 2015; 6:60. PMID: 26730350; PMCID: PMC4687161.
    Citations: 6     
  34. Solga AC, Pong WW, Kim KY, Cimino PJ, Toonen JA, Walker J, Wylie T, Magrini V, Griffith M, Griffith OL, Ly A, Ellisman MH, Mardis ER, Gutmann DH. RNA Sequencing of Tumor-Associated Microglia Reveals Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth. Neoplasia. 2015 Oct; 17(10):776-88. PMID: 26585233.
    Citations: 56     Fields:    Translation:HumansAnimalsCells
  35. Wang Y, Li W, Patel SS, Cong J, Zhang N, Sabbatino F, Liu X, Qi Y, Huang P, Lee H, Taghian A, Li JJ, DeLeo AB, Ferrone S, Epperly MW, Ferrone CR, Ly A, Brachtel EF, Wang X. Blocking the formation of radiation-induced breast cancer stem cells. Oncotarget. 2014 Jun 15; 5(11):3743-55. PMID: 25003837.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
  36. Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May; 32(5):479-84. PMID: 24752078.
    Citations: 261     Fields:    Translation:HumansCells
  37. Hunt DP, Muse VV, Ly A. Case records of the Massachusetts General Hospital. Case 4-2014. A 39-year-old man with night sweats and abdominal pain. N Engl J Med. 2014 Jan 30; 370(5):467-73. PMID: 24476436.
    Citations:    Fields:    Translation:Humans
  38. Ly A, Beck AH, Pai RK, Kong CS. Increased rate of atypical squamous cells of undetermined significance and declining high-risk human papillomavirus rates following implementation of ThinPrep Imaging System are associated with increased nuclear chromasia. J Am Soc Cytopathol. 2014 Mar - Apr; 3(2):73-78. PMID: 31051704.
    Citations:    Fields:    
  39. Reisenbichler ES, Lester SC, Richardson AL, Dillon DA, Ly A, Brock JE. Interobserver concordance in implementing the 2010 ASCO/CAP recommendations for reporting ER in breast carcinomas: a demonstration of the difficulties of consistently reporting low levels of ER expression by manual quantification. Am J Clin Pathol. 2013 Oct; 140(4):487-94. PMID: 24045544.
    Citations: 20     Fields:    Translation:Humans
  40. Ly A. Talking to patients about a diagnosis of malignancy in a fine-needle aspiration clinic setting. Cancer Cytopathol. 2013 Jul; 121(7):339-40. PMID: 23853169.
    Citations:    Fields:    Translation:Humans
  41. Mills AM, Ly A, Balzer BL, Hendrickson MR, Kempson RL, McKenney JK, Longacre TA. Cell cycle regulatory markers in uterine atypical leiomyoma and leiomyosarcoma: immunohistochemical study of 68 cases with clinical follow-up. Am J Surg Pathol. 2013 May; 37(5):634-42. PMID: 23552380.
    Citations: 19     Fields:    Translation:Humans
  42. Ly A, Lester SC, Dillon D. Prognostic Factors for Patients with Breast Cancer: Traditional and New. Surg Pathol Clin. 2012 Sep; 5(3):775-85. PMID: 26838288.
    Citations: 2     Fields:    
  43. Sahni VA, Ly A, Silverman SG. Usefulness of percutaneous biopsy in diagnosing benign renal masses that mimic malignancy. Abdom Imaging. 2011 Feb; 36(1):91-101. PMID: 20049430.
    Citations: 6     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.