Khiabanian Lab

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Pre-prints ‡ co-lead    † equal contribution    lab members underlined Singh A, Khiabanian H. Feature selection followed by a residuals-based normalization simplifies and improves single-cell gene expression analysis. 2023. PDF da Silva-Diz V, Singh A, Lancho O, Aleksandrova M, Mandleywala K, Nunes P, Khatun J, Kim O, Affronti H, Chiles E, Su X, Khiabanian H, Wellen KE, Herranz D. Therapeutic targeting of ACLY in T-ALL in vivo. 2023. PDF Fu X, Reglero C, Swamy V, Loh J-W, Khiabanian H, Albero R, Forouhar F, AlQuraishi M, Ferrando A, Rabadan R. Computational structure prediction methods enable the systematic identification of oncogenic mutations. 2022. PDF Zeeshan S, Mendelez RA, Zingone A, Khiabanian H, Pine SR, Ryan BM. Global profiling of alternative splicing in non-small cell lung cancer reveals novel histological and population differences. 2022. PDF Zairis S, Khiabanian H, Blumberg A, Rabadan R. Genomic data analysis in tree spaces. 2016. PDF   Publications ‡ co-lead    † equal contribution    lab members underlined Lancho O, Singh A, da Silva-Diz V, Tottone L, Nunes P, Aleksandrova M, Khatun J, Luo S, Zhao C, Zheng H, Chiles E, Zuo Z, Rocha P, Su X, Khiabanian H, Herranz D. A therapeutically targetable NOTCH1-SIRT1-KAT7 axis in T-cell Leukemia. Blood Cancer Discovery 2023. PMID:36322781 Bal E, Kumar R, Hadigol M, Holmes A, Hilton L, Loh J-W, Dreval K, Wong J, Soni R, Vlasevska S, Corinaldesi C, Basso K, Morin R, Khiabanian H ‡, Pasqualucci L ‡, Dalla-Favera R ‡. Super-Enhancer Hypermutation Alters Oncogene Expression in B-cell Lymphoma. Nature 2022 PMID:35794478 Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. Molecular Cell 2022 PMID:35794478 Jalloul N, Ganesan S, Garber JE, Khiabanian H. Reply to Ménard: Inferences of Mutational Status for Variants Detected from Tumor-Only Sequencing –A Quality Assurance Strategy. JCO Precision Oncology 2022 PMID:34820595 Jalloul N †, Gomy I †, Stokes S, Gusev A, Johnson BE, Lindeman N, Macconaill L, Ganesan S, Garber JE ‡, Khiabanian H ‡. Germline testing data validate inferences of mutational status for variants detected from tumor-only sequencing. JCO Precision Oncology 2021. PMID:34820595 Rajagopalan S, Singh A, Khiabanian H. Cilium Expression Score Predicts Glioma Survival. Frontiers Genetics 2021. PMID:34868236 Bonfiglio F, Bruscaggin A, Guidetti F, Terzi di Bergamo L, et al. Genetic and Phenotypic Attributes of Splenic Marginal Zone Lymphoma. Blood 2021. PMID:34653238 Sabaawy HE, Ryan BM, Khiabanian H, Pine SR. JAK/STAT of all trades: Linking inflammation with cancer development, tumor progression, and therapy resistance. Carcinogenesis 2021. PMID:34415330 da Silva-Diz V, Cao B, Lancho O, Chiles E, Alasadi A, Aleksandrova M, Luo S, Singh A, Tao H, Augeri D, Minuzzo S, Indraccolo S, Khiabanian H, Su X, Jin S, Herranz D. A novel and highly effective mitochondrial uncoupling drug in T-cell leukemia. Blood 2021. PMID:33876224 Tottone L, Lancho O †, Loh J-W †, Singh A †, Kimura S, Roels J, Kuchmiy A, Strubbe S, Lawlor MA, da Silva-Diz V, Luo S, Gachet S, García-Prieto CA, Hagelaar R, Esteller M, Meijerink JP, Soulier J, Taghon T, Van Vlierberghe P, Mullighan CG, Khiabanian H, Rocha PP, Herranz D. A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Blood Cancer Discovery 2021. PMID:33458694 Loh J-W, Guiccione C, Di Clemente F, Riedlinger G, Ganesan S, Khiabanian H. All-FIT: Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data. Bioinformatics 2020. PMID:31750888 Barz MJ, Hof J, Groeneveld-Krentz S, Loh J-W, Szymansky A, Astrahantseff K, von Stackelberg A, Khiabanian H, Ferrando AA, Eckert C, Kirschner-Schwabe R. Subclonal NT5C2 mutations are associated with poor outcomes after relapse of pediatric acute lymphoblastic leukemia. Blood 2020. PMID:31971569 Llanos AAM, Yao S, Singh A, Aremu JB, Khiabanian H, Lin Y, Omene C, Omilian AR, Khoury T, Hong CC, Ganesan S, Foran DJ, Higgins MJ, Ambrosone CB, Bandera EV, Demissie K. Gene expression of adipokines and adipokine receptors in the tumor microenvironment: associations of lower expression with more aggressive breast tumor features. Breast Cancer Res Treat 2020. PMID:33067778 Panda A, Yadav A, Yeerna H, Singh A, Biehl M, Lux M, Schulz A, Klecha T, Doniach S, Khiabanian H, Ganesan S, Tamayo P, Bhanot G. Tissue- and development-stage–specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic Acid Research 2020. PMID:32525984 Sokol ES, Pavlick D, Khiabanian H, … Ganesan S, Chung JH. Pan-Cancer Analysis of BRCA1 and BRCA2 Genomic Alterations and Their Association With Genomic Instability as Measured by Genome-Wide Loss of Heterozygosity. JCO Precision Oncology 2020. PMID:32903788 Singh A, Bhanot G, Khiabanian H. TuBA: Tunable Biclustering Algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer. GigaScience 2019. PMID:31216036 Riedlinger GM, Jalloul N, Poplin E, Mehnert J, Groisberg R, Khiabanian H, Ganesan S. Detection of Three Distinct Clonal Populations Using Circulating Cell Free DNA: A Cautionary Note on the Use of Liquid Biopsy. JCO Precision Oncology 2019. PMID:31588418 Loh J-W and Khiabanian H. Leukemia’s Clonal Evolution in Development, Progression, and Relapse. Curr Stem Cell Rep 2019. Springer Blasco TM, Navas C, et al. Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF. Cancer Cell 2019. PMID:30975481 Snider E, et al. Alterations to the Esophageal Microbiome Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma. Cancer Epidemiology Biomarkers & Prevention 2019. PMID:31466948 Riedlinger GM, Hadigol M, Khiabanian H ‡, Ganesan S ‡. Association of JAK2-V617F Mutations Detected by Solid Tumor Sequencing with Coexistent Myeloproliferative Neoplasms. JAMA Oncology 2019. PMID:30605212 Severson EA †, Riedlinger GM †, Connelly CF, Vergilio J, Goldfinger M, Ramkissoon S, Frampton GM, Ross JS, Fratella-Calabrese A, Gay L, Ali S, Miller V, Elvin J, Hadigol M, Hirshfield KM, Rodriguez L, Ganesan S ‡, Khiabanian H ‡. Detection of Clonal Hematopoiesis of Indeterminate Potential in Clinical Sequencing of Solid Tumor Specimens. Blood 2018. PMID:29678827 Hadigol M and Khiabanian H. MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications. BMC Bioinformatics 2018. PMID:29884116 Tzoneva G, Dieck CL, et al. Clonal evolution mechanisms in NT5C2-mutant relapsed acute lymphoblastic leukemia. Nature 2018. PMID:29342136 Rabadan R, Bhanot G, Marsilio S, Chiorazzi N, Pasqualucci L, Khiabanian H. On statistical modeling of sequencing noise in high depth data to assess tumor evolution. Journal of Statistical Physics 2018. PMID:30034030 Khiabanian H †‡, Hirshfield KM †, Goldfinger M, Bird S, Stein M, Aisner J, Toppmeyer D, Wong S, Chan N, Dhar K, Gheeya J, Vig H, Hadigol M, Pavlick D, Ansari S, Ali S, Xia B, Rodriguez L, Ganesan S ‡. Inference of germline mutational status and evaluation of loss of heterozygosity in high-depth tumor-only sequencing data. JCO Precision Oncology 2018. PMID:30246169 Nobel YR, et al. Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome. Clinical and Translational Gastroenterology 2018. PMID:30356041 Marsilio S, Khiabanian H, Fabbri G, Vergani S, Scuoppo C, Montserrat E, Shpall EJ, Hadigol M, et al. Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity. Leukemia 2018. PMID:29203856 Snider EJ, et al. Barrett’s Esophagus is Associated with a Distinct Oral Microbiome. Clinical and Translational Gastroenterology 2018. PMID:29491399 Gorshein E, Wei C, … Khiabanian H ‡, Strair R ‡. Lactobacillus rhamnosus GG probiotic enteric regimen does not provide protection against GVHD after allogeneic hematopoietic stem cell transplantation. Clinical Transplantation 2017. PMID:28256022 Morgan KM, … Singh A, Khiabanian H, Pine SR. Gamma secretase inhibition by BMS-906024 enhances efficacy of paclitaxel in lung adenocarcinoma. Molecular Cancer Therapeutics 2017. PMID:28978720 Abate F, Almeida da Silva A, et al. Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas. Proceedings of the National Academy of Sciences 2017. PMID:28062691 Uhlemann AC, et al. Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration. mBio 2017. PMID:28096484 Oshima K †, Khiabanian H †, et al. Mutational landscape, clonal evolution patterns and role of RAS mutations in relapsed acute lymphoblastic leukemia. Proceedings of the National Academy of Sciences 2016. PMID:27655895 Spina V †, Khiabanian H †, et al. The Genetics of Nodal Marginal Zone Lymphoma. Blood 2016. PMID:27335277 Rasi S †, Khiabanian H †, et al. Clinical impact of small subclones harboring NOTCH1, SF3B1, or BIRC3 mutations in chronic lymphocytic leukemia. Haematologica 2016. PMID:26819056 Paganin M, et al. A Case of T‐cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia. Pediatr Blood Cancer 2016. PMID:27149388 Paratala B, Dolfi SC, Khiabanian H, et al. Emerging role of genomic rearrangements in breast cancer: applying knowledge from other cancers. Biomarkers in Cancer 2016. PMID:26917980   Earlier publications ‡ co-lead    † equal contribution Almeida da Silva A †, Abate F †, Khiabanian H, et al. The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nature Genetics 2015. PMID:26551667 Lee A †, Kulcsar K †, Elliott O, Khiabanian H, et al. Transcriptome Reconstruction and Annotation of the Egyptian Rousette Bat. BMC Genomics 2015. PMID:26643810 Emmett K, Lee A, Khiabanian H ‡, Rabadan R ‡. High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants. PLoS Currents 2015. PMID:25737802 Rossi D †, Khiabanian H †, et al. Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia. Blood 2014 (Plenary paper). PMID:24501221 Palomero T †, Couronné L †, Khiabanian H †, et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nature Genetics 2014. PMID:24413734 Wang J †, Khiabanian H †, Rossi D. †, et al. Tumor Evolutionary Directed Graphs and the History of Chronic Lymphocytic Leukemia. eLife 2014. PMID:25496728 Khiabanian H ‡, et al. Viral diversity and clonal evolution from unphased genomic data. BMC Genomics 2014. PMID:25573168 Lee A †, Khiabanian H †, et al. Transcriptome Reconstruction and Annotation of Cynomolgus and African Green Monkey. BMC Genomics 2014. PMID:25277458 Zairis S, Khiabanian H, Blumberg A, Rabadan R. Moduli spaces of phylogenetic trees describing tumor evolutionary patterns. Lecture Notes in Computer Science Volume 8609 2014. Link Pasqualucci L, Khiabanian H, et al. Genetics of follicular lymphoma transformation. Cell Reports 2014. PMID:24388756 Melamed R, Khiabanian H, Rabadan R. Data-driven discovery of seasonally linked diseases from an Electronic Health Records system. BMC Bioinformatics 2014. PMID:25078762 Messina M, Del Giudice I, Khiabanian H, et al. Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness. Blood 2014. PMID:24550227 Kode A, et al. Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts. Nature 2014. PMID:24429522 Fabbri G †, Khiabanian H †, et al. Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome. The Journal of Experimental Medicine 2013. PMID:24127483 Tzoneva G †, Perez Garcia A †, Carpenter Z †, Khiabanian H, et al. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL. Nature Medicine 2013. PMID:23377281 Blair DR, et al. A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk. Cell 2013. PMID:24074861 Rossi D, et al. Integrated Mutational and Cytogenetic Analysis Identifies New Prognostics Subgroups in Chronic Lymphocytic Leukemia. Blood 2013. PMID:23243274 Dapito DH, et al. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 2012. PMID:22516259 Holmes AB, Hawson A, Liu F, Friedman C, Khiabanian H ‡, Rabadan R ‡. Discovering Disease Associations by Integrating Electronic Clinical Data and Medical Literature. PLoS One 2011. PMID:21731656 Rossi D, Bruscaggin A, Spina V, Rasi S, Khiabanian H, et al. Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness. Blood 2011. PMID:22039264 Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, et al. Analysis of the Chronic Lymphocytic Leukemia Coding Genome: Role of NOTCH1 Mutational Activation. The Journal of Experimental Medicine 2011. PMID:21670202 Hernandez C, Chan J, Khiabanian H, Rabadan R. Understanding the Origins of a Pandemic Virus. arXiv 2011. PDF Greenbaum B, Trifonov V, Khiabanian H, Levine A, Rabadan R. The Emergence of 2009 H1N1 Pandemic Influenza. In: G. Del Giudice and R. Rappuoli (eds.). Influenza Vaccines for the Future. 2nd edition 2011. Springer Van Vlierberghe P, Palomero T, Khiabanian H, et al. PHF6 mutations in T-cell acute lymphoblastic leukemia. Nature Genetics 2010. PMID:20228800 Khiabanian H, et al. ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data. BMC Research Notes 2010. PMID:20507604 Khiabanian H, et al. Signs of the 2009 Influenza Pandemic in the New York-Presbyterian Hospital Electronic Health Records. PLoS One 2010. PMID:20844592 Khiabanian H, Trifonov V., Rabadan R. Reassortment Patterns in Swine Influenza Viruses. PLoS One 2009. PMID:19809504 Khiabanian H, et al. Differences in Patient Age Distribution between Influenza A Subtypes. PLoS One 2009. PMID:19718262 Trifonov V, Khiabanian H, Rabadan R. Geographic Dependence, Surveillance and the Origins of the 2009 Influenza A (H1N1) Virus. The New England Journal of Medicine 2009. PMID:19474418 Trifonov V, Khiabanian H, Greenbaum B, Rabadan R. The origin of the recent swine influenza A (H1N1) virus infecting humans. Eurosurveillance 2009. PMID:19422769 Kubo J, Khiabanian H, Dell’Antonio I, et al. Dark Matter Staructures in the Deep Lens Survey. The Astrophysical Journal 2009. NASA ADS Khiabanian H and Dell’Antonio I. A Multi-Resolution Weak Lensing Reconstruction Method. The Astrophysical Journal 2008. NASA ADS Khiabanian H. A Maximum-Likelihood Multi-Resolution Weak Lensing Mass Reconstruction Method. Doctoral Dissertation. Brown University 2008. NASA ADS Kubo J, et al. The Mass of Coma Cluster from Weak Lensing in SDSS. The Astrophysical Journal 2007. NASA ADS