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
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,
Loh & Khiabanian. Curr Stem Cell Rep 2019Khiabanian 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,
Severson, Riedlinger et al. Blood 2018
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
Khiabanian et al. JCO Precis. Oncol. 2018
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
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,
Emmett et al. PLoS Curr. 2015
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
Zairis et al. LNCS 2014
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 †,
Fabbri, Khiabanian et al. JEM 2013
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,
Trifonov, Khiabanian, Rabadan. NEJM 2009
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
Khiabanian et al. ApJ 2008
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