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1.

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

Kim, Jung; Naqvi, Ammar S; Corbett, Ryan J; Kaufman, Rebecca S; Vaksman, Zalman; Brown, Miguel A; Miller, Daniel P; Phul, Saksham; Geng, Zhuangzhuang; Storm, Phillip B; Resnick, Adam C; Stewart, Douglas R; Rokita, Jo Lynne; Diskin, Sharon J.

Bioinformatics ; 40(3)2024 Mar 04.

Article in English | MEDLINE | ID: mdl-38426335

2.

A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.

Rathi, Komal S; Arif, Sherjeel; Koptyra, Mateusz; Naqvi, Ammar S; Taylor, Deanne M; Storm, Phillip B; Resnick, Adam C; Rokita, Jo Lynne; Raman, Pichai.

PLoS Comput Biol ; 16(10): e1008263, 2020 10.

Article in English | MEDLINE | ID: mdl-33119584

3.

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.

Gaonkar, Krutika S; Marini, Federico; Rathi, Komal S; Jain, Payal; Zhu, Yuankun; Chimicles, Nicholas A; Brown, Miguel A; Naqvi, Ammar S; Zhang, Bo; Storm, Phillip B; Maris, John M; Raman, Pichai; Resnick, Adam C; Strauch, Konstantin; Taroni, Jaclyn N; Rokita, Jo Lynne.

BMC Bioinformatics ; 21(1): 577, 2020 Dec 14.

Article in English | MEDLINE | ID: mdl-33317447

4.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black, Kathryn L; Naqvi, Ammar S; Asnani, Mukta; Hayer, Katharina E; Yang, Scarlett Y; Gillespie, Elisabeth; Bagashev, Asen; Pillai, Vinodh; Tasian, Sarah K; Gazzara, Matthew R; Carroll, Martin; Taylor, Deanne; Lynch, Kristen W; Barash, Yoseph; Thomas-Tikhonenko, Andrei.

Nucleic Acids Res ; 46(21): 11357-11369, 2018 11 30.

Article in English | MEDLINE | ID: mdl-30357359

5.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black, Kathryn L; Naqvi, Ammar S; Asnani, Mukta; Hayer, Katharina E; Yang, Scarlett Y; Gillespie, Elisabeth; Bagashev, Asen; Pillai, Vinodh; Tasian, Sarah K; Gazzara, Matthew R; Carroll, Martin; Taylor, Deanne; Lynch, Kristen W; Barash, Yoseph; Thomas-Tikhonenko, Andrei.

Nucleic Acids Res ; 47(2): 1043, 2019 01 25.

Article in English | MEDLINE | ID: mdl-30517739

6.

Heterogeneity of surface CD19 and CD22 expression in B lymphoblastic leukemia.

Rosenthal, Jaclyn; Naqvi, Ammar S; Luo, Minjie; Wertheim, Gerald; Paessler, Michele; Thomas-Tikhonenko, Andrei; Rheingold, Susan R; Pillai, Vinodh.

Am J Hematol ; 93(11): E352-E355, 2018 11.

Article in English | MEDLINE | ID: mdl-30058145

7.

FBXW7ß isoform drives transcriptional activation of the proinflammatory TNF cluster in human pro-B cells.

Yang, Scarlett Y; Hayer, Katharina E; Fazelinia, Hossein; Spruce, Lynn A; Asnani, Mukta; Black, Kathryn L; Naqvi, Ammar S; Pillai, Vinodh; Barash, Yoseph; Elenitoba-Johnson, Kojo S J; Thomas-Tikhonenko, Andrei.

Blood Adv ; 7(7): 1077-1091, 2023 04 11.

Article in English | MEDLINE | ID: mdl-36322817

8.

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

Kim, Jung; Naqvi, Ammar S; Corbett, Ryan J; Kaufman, Rebecca S; Vaksman, Zalman; Brown, Miguel A; Miller, Daniel P; Phul, Saksham; Geng, Zhuangzhuang; Storm, Phillip B; Resnick, Adam C; Stewart, Douglas R; Rokita, Jo Lynne; Diskin, Sharon J.

bioRxiv ; 2023 Dec 01.

Article in English | MEDLINE | ID: mdl-38076939

9.

Modulation of CD22 Protein Expression in Childhood Leukemia by Pervasive Splicing Aberrations: Implications for CD22-Directed Immunotherapies.

Zheng, Sisi; Gillespie, Elisabeth; Naqvi, Ammar S; Hayer, Katharina E; Ang, Zhiwei; Torres-Diz, Manuel; Quesnel-Vallières, Mathieu; Hottman, David A; Bagashev, Asen; Chukinas, John; Schmidt, Carolin; Asnani, Mukta; Shraim, Rawan; Taylor, Deanne M; Rheingold, Susan R; O'Brien, Maureen M; Singh, Nathan; Lynch, Kristen W; Ruella, Marco; Barash, Yoseph; Tasian, Sarah K; Thomas-Tikhonenko, Andrei.

Blood Cancer Discov ; 3(2): 103-115, 2022 03 01.

Article in English | MEDLINE | ID: mdl-35015683

10.

Targeting CD123 in blastic plasmacytoid dendritic cell neoplasm using allogeneic anti-CD123 CAR T cells.

Cai, Tianyu; Gouble, Agnès; Black, Kathryn L; Skwarska, Anna; Naqvi, Ammar S; Taylor, Deanne; Zhao, Ming; Yuan, Qi; Sugita, Mayumi; Zhang, Qi; Galetto, Roman; Filipe, Stéphanie; Cavazos, Antonio; Han, Lina; Kuruvilla, Vinitha; Ma, Helen; Weng, Connie; Liu, Chang-Gong; Liu, Xiuping; Konoplev, Sergej; Gu, Jun; Tang, Guilin; Su, Xiaoping; Al-Atrash, Gheath; Ciurea, Stefan; Neelapu, Sattva S; Lane, Andrew A; Kantarjian, Hagop; Guzman, Monica L; Pemmaraju, Naveen; Smith, Julianne; Thomas-Tikhonenko, Andrei; Konopleva, Marina.

Nat Commun ; 13(1): 2228, 2022 04 28.

Article in English | MEDLINE | ID: mdl-35484100

11.

Enhancing childhood cancer targetability.

Naqvi, Ammar S; Rokita, Jo Lynne.

Nat Cancer ; 4(2): 153-155, 2023 02.

Article in English | MEDLINE | ID: mdl-36585448

12.

Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets.

Karaiskos, Spyros; Naqvi, Ammar S; Swanson, Karl E; Grigoriev, Andrey.

Biol Direct ; 10: 51, 2015 Sep 16.

Article in English | MEDLINE | ID: mdl-26374501

13.

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19.

Asnani, Mukta; Hayer, Katharina E; Naqvi, Ammar S; Zheng, Sisi; Yang, Scarlett Y; Oldridge, Derek; Ibrahim, Fadia; Maragkakis, Manolis; Gazzara, Matthew R; Black, Kathryn L; Bagashev, Asen; Taylor, Deanne; Mourelatos, Zissimos; Grupp, Stephan A; Barrett, David; Maris, John M; Sotillo, Elena; Barash, Yoseph; Thomas-Tikhonenko, Andrei.

Leukemia ; 34(4): 1202-1207, 2020 04.

Article in English | MEDLINE | ID: mdl-31591467

14.

The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins.

Li, Ning; Yousefi, Maryam; Nakauka-Ddamba, Angela; Li, Fan; Vandivier, Lee; Parada, Kimberly; Woo, Dong-Hun; Wang, Shan; Naqvi, Ammar S; Rao, Shilpa; Tobias, John; Cedeno, Ryan J; Minuesa, Gerard; Y, Katz; Barlowe, Trevor S; Valvezan, Alexander; Shankar, Sheila; Deering, Raquel P; Klein, Peter S; Jensen, Shane T; Kharas, Michael G; Gregory, Brian D; Yu, Zhengquan; Lengner, Christopher J.

Cell Rep ; 13(11): 2440-2455, 2015 Dec 22.

Article in English | MEDLINE | ID: mdl-26673327

15.

The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.

Liu, Nan; Abe, Masashi; Sabin, Leah R; Hendriks, Gert-Jan; Naqvi, Ammar S; Yu, Zhenming; Cherry, Sara; Bonini, Nancy M.

Curr Biol ; 21(22): 1888-93, 2011 Nov 22.

Article in English | MEDLINE | ID: mdl-22055292

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AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

A transcriptome-based classifier to determine molecular subtypes in medulloblastoma.

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Heterogeneity of surface CD19 and CD22 expression in B lymphoblastic leukemia.

FBXW7ß isoform drives transcriptional activation of the proinflammatory TNF cluster in human pro-B cells.

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

Modulation of CD22 Protein Expression in Childhood Leukemia by Pervasive Splicing Aberrations: Implications for CD22-Directed Immunotherapies.

Targeting CD123 in blastic plasmacytoid dendritic cell neoplasm using allogeneic anti-CD123 CAR T cells.

Enhancing childhood cancer targetability.

Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets.

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19.

The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins.

The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.