Laboratory of Bioinformatics

Applications Publications Abstracts/Posters

Abstracts / Posters

2020

[https://www.hematology.org/meetings/annual-meeting]

1. RNA Seq Profiles and Bioinformatics Validation in a Large Sample of Sickle Cell Disease Patients."
   Presented by Dr. Jen Judy. []
2. Mitochondrial DNA Variation in Individuals with Sickle Cell Disease."
   Presented by Dr. Maliha Ahmad. []
3. Cfcloud: A Cloud-Based Workflow for Cell-Free DNA Data Analysis."
   Presented by Dr. Ilker Tunc. []
4. Notch-Mediated Expansion of Human Hematopoietic Stem and Progenitor Cells By Culture Under Hypoxia."
   Presented by Dr. Daisuke Araki. []

[https://meetings.cshl.edu/abstracts.aspx?meet=data&year=20]

1. Chen, Yun-Ching
   Changes in peripheral methylome and brain development are associated with symptom changes in attention deficit hyperactivity disorder (ADHD)
2. Seifuddin, Fayaz
   Dysregulation of long non-coding RNA expression in bipolar disorder
3. Singh, Komudi
   SARS-CoV-2 infection of host cells perturbs autophagic and mitochondrial processes

[https://events.cancer.gov/ccr/covid19symposium]

1. Cell-free DNA quantification and methylation profiling to monitor tissue damage in COVID-19 patients.
   Presenting Author: Temesgen Andargie
2. Delineating the common biological signatures in COVID -19 and chronic fatigue syndrome (cfs) patients.
   Presenting Author: Komudi Singh

1. Outcomes of ISHLT Lung Transplant AMR
   Cochrane. A.B. et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.1298 [URL]
2. Lung Transplantation: DSA to AMR Trajectory
   I. Ponor, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.1299 [URL]
3. Donor-Derived-Cell-Free DNA to Identify Primary Graft Dysfunction Patients at Risk of Chronic Lung Allograft Dysfunction
   M.B. Keller, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.959 [URL]
4. Early and Late Pulmonary AMR Show Distinct Profiles; Clinical and Epigenetic Analyses
   S. Agbor-Enoh, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.1300 [URL]
5. Increased Cell Free DNA Levels in African American Patients Early after Heart Transplantation
   A. H. Doshi, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.922 [URL]
6. Early Donor-Derived Cell-Free DNA Predicts Peak Allograft Function in Heart Transplant
   S.B. Brusca, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.1261 [URL]
7. Lung Transplant Recipients with Severe Primary Graft Dysfunction Requiring ECMO Had Similar Donor-Derived Cell-Free DNA Levels and Lung Function as Matched Controls
   I. Timofte, et. al. DOI:https://doi.org/10.1016/j.healun.2020.01.348 [URL]

1. Ultrahigh-Resolution, Short-Length CT Detects Small Cysts That Are Associated with a Decrease in DLCO but Not FEV1 in Patients with Lymphangioleiomyomatosis [URL]
2. Non-Uniform of Cyst Distribution Influence Pulmonary Function in Lymphangioleiomyomatosis [URL]

2019

1. lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs.
   F. Seifuddin; A. Suresh; K. Singh; Y.C. Chen; V. Chaitankar; I. Tunc; M. Pirooznia [URL]
2. IKAP: Identifying K mAjor cell Population groups in single-cell RNA-seq analysis.
   Y. Chen; A. Suresh; K. Singh; F. Seifuddin; M. Pirooznia [URL]
3. Annotation and functional characterization of lncRNAs using integrative GWAS, eQTL and network analysis in lncRNAKB.
   M. Pirooznia; F. Seifuddin; A. Suresh; K. Singh; Y. Chen; V. Chaitankar; I. Tunc [URL]
4. Affected sib-pair analyses identify signaling networks associated with social behavioral deficits in autism.
   T. Wang; T. Niranjan; Y. Chen; I. Tunc; F. Goes; D. Avramopoulos; J. Potash; R. Huganir; P. Zandi; M. Pirooznia [URL]

1. Spatial Genomic Heterogeneity in Chronic Lymphocytic Leukemia
   Clare Sun, MD , Yun-Ching Chen, PhD , Aina Zurita Martinez , Delong Liu, PhD , Daniel Rosebrock , Gad Getz, PhD , Mehdi Pirooznia, MD PhD , Catherine J. Wu, MD , Adrian Wiestner, MD PhD [URL]
2. Diverging Clonal Evolution during Sequential Therapy with Chemoimmunotherapy Followed By BTK Inhibitors
   Inhye E Ahn, MD , Yun-Ching Chen, PhD , Chingiz Underbayev, MD PhD , Erika M Gaglione , Clare Sun, MD , Susan Soto , Pia Nierman , Mehdi Pirooznia, MD PhD , Adrian Wiestner, MD PhD [URL]
3. Platelet Phenotype Prediction from Whole Genome Sequencing in 621 Sickle Cell Disease Patients
   Celina Montemayor Garcia, MD PhD , Julie K. Weisman, MD , Xunde Wang, PhD , Divya Gandla , James Owen Long, MD , Clifton L. Dalgard, PhD , Mehdi Pirooznia, MD PhD , Harvey Klein, MD , Swee Lay Thein, DSc, MBBS [URL]
4. Whole Exome Sequencing Reveals Multiple Driver Events in Chronic Lymphocytic Leukemia Patients with Acquired Ibrutinib Resistance
   Chingiz Underbayev, MD PhD , Inhye E Ahn, MD , Hailey Harris , Lauren T Vaughn , Mehdi Pirooznia, MD PhD , Liqiang Xi, MD , Mark Raffeld, MD , Sarah E. M. Herman , Adrian Wiestner, MD PhD [URL]

1. Critical Assessment of CNV Calling Using Next Generation Sequencing
   Yun-Ching Chen, Fayaz Seifuddin, Cu Nguyen, Chunhua Yan, Qingrong Chen, Wenming Xiao, Mehdi Pirooznia and Daoud Meerzaman [URL]
2. Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing
   Wenming Xiao and The Somatic Mutation Working Group of the SEQC-IIConsortium [URL]
3. Establishing reference samples for universal benchmarking study of NGS technologies
   Li Tai Fang, Wenming Xiao and Somatic Mutation Working Group of the SEQC-II Consortium [URL]

1. Apolipoprotein E Induces CXCL5 Secretion by Asthmatic Airway Epithelial Cells via TLR4-Dependent Activation of TAK1/NF-kB/MAP3K8/JNK Signaling Pathways
   O. Kalchiem-Dekel, X. Yao, D.M. Figueroa, E.M. Gordon, M. Kaler, A.V. Barochia, L. Poching, Y. Li, F. Seifuddin, M. Pirooznia, S.J. Levine [URL]

1. Pulmonary Antibody-Mediated Rejection (AMR) Accelerates Aging-Evidence from Whole Genome DNA Methylation Sequencing
   S. Agbor-Enoh, F. Seifuddin, M. Pirooznia, M. Jang, H. Valantine [URL]
2. Linking CLAD in Lung Transplant Recipients after 3 Years Follow Up with Transplant Arteriosclerosis in Humanized Mice
   T. Siemeni, A. Kn\F6fel, F. Ius, J. Salman, G. Warnecke [URL]
3. Characteristics of Urine Cell-Free DNA in Heart and Lung Transplant
   K.Bhatti, S.Agbor-Enoh, I.Tunc, et. al. J.Zhu, M.Pirooznia, M.Jang, H.Valantine [URL]

1. Overview of Bioinformatics and Computational Biology Core at the MHLBI.
   M Pirooznia
   
   
2. lncRNAKB: A comprehensive knowledge-base (KB) of long-noncoding RNA.
   F. Seifuddin, K. Singh, A. Suresh, V. Chaitankar, I. Tunc, YC. Chen, H. Cao, M. Pirooznia.
   Bioinformatics and Computational Biology Core.
   
   
3. A pipeline to make sense of the long non-coding RNA (lncRNA) knowledge-base (KB): integrative GWAS, eQTL and network analysis.
   A. Suresh., F. Seifuddin., K. Singh., V. Chaitankar., I. Tunc, Y.-C. Chen., H. Cao., M. Pirooznia.
   Bioinformatics and Computational Biology Core.
   
   
4. Mediators of Nuclear and Cytoskeletal Interactions Modulate Nuclear Stiffness and Nuclear Envelope Integrity in Confined Metastatic Melanoma Cells.
   MA. Baird1-2, AX. Cartagena-Rivera3, M. Pirooznia4, G. Merlino5, R.S. Fischer1, and C.M. Waterman1
   1 Cell Biology and Physiology Center, USA. 2 Biophysics Program, College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, MD 20740, USA. 3 Section on Auditory Mechanics, (NIDCD), 4Bioinformatics and Computational Biology, 5Cancer Biology and Genetics, National Cancer Institute (NCI).
   
   
5. Transcriptome analysis of a long period line of Drosophila melanogaster.
   S. Kumar1, I. Tunc2, TR. Tansey1, M. Pirooznia2, ST. Harbison1
   1 Laboratory of Systems Genetics. 2 Bioinformatics and Computational Biology Core.
   
   
6. Characteristics of urine cell-free DNA in heart and lung transplant.
   K. Bhatti1,3, S. Agbor-Enoh1,2,3, I. Tunc1,3, et. al., M. Piroozni1,3a, M. Kyoo Jang1,3, H. Valantine1,3.
   1Genomic Research Alliance for Transplantation (GRAfT), Bethesda Maryland, 20982 2Division of Pulmonary and Critical Care Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 3Laboratory of Transplantation Genomics Cardiovascular Branch 4University of Maryland Medical Center, Baltimore, MD.
   
   
7. Fasting blunts human CD4+T cell activation via novel transcriptional networks.
   M. Rodman1, K. Han1, K. Singh1, S. Hassanzadeh1, et. al. H. Teague1, N.N. Mehta1, M. Pirooznia2, M.N. Sack1
   1Cardiovascular Branch, 2Bioinformatics and Computational Core Facility, 3Flow Cytometry Core Facility. 4Center of Human Immunology NIAID.
   
   
8. Apolipoprotein E Induces CXCL5 Secretion by Asthmatic Airway Epithelial Cells via TLR4-dependent Activation of TAK1/NF-kB/MAP3K8/JNK Signaling Pathways.
   O. Kalchiem-Dekel1, X. Yao1, DM. Figueroa1, EM. Gordon1, M. Kaler1, AV. Barochia 1, P. Liu1, Y. Li1, Fayaz Seifuddin1, M. Pirooznia1, SJ. Levine1
   1 Laboratory of Asthma and Lung Inflammation. Pulmonary Branch.
   
   
9. Transgelin: A new gene involved in LDL endocytosis in liver cells identified by a whole-genome CRISPR-Cas9 screen.
   D. Lucero1, M. Mendelson2, P. Islam1, LA. Freeman1, EB. Neufeld1, J. Tang1, M. Pirooznia4, C. Combs5, Y. Li3, AT. Remaley1.
   1Lipoprotein Metabolism Laboratory, 2Boston Children's Hospital Department of Cardiology, Boston, MA 3DNA Sequencing and Genomics Core, 4Bioinformatics and Computational Biology. 5Light Microscopy Core.

2018

1. Cell-Free Mitochondrial DNA Is Elevated in Sickle Cell Disease Patients, and Serve As a Potential Proinflammatory DAMP
   Laxminath Tumburu, Shohini Ghosh-Choudhary, Emilia Alina Barbu, et .al, Mehdi Pirooznia, Jun Zhu and Swee Lay Thein
   Blood 2018 132:1068; [URL]
   
   
2. Red Blood Cell and Platelet Phenotype Prediction from Whole Genome Sequencing in 621 Sickle Cell Disease Patients: Correlation with Alloimmunization History, Serology and Other Genotyping Methods
   Celina Montemayor Garcia, Julie K. Weisman, Divya Gandla, James Owen Long, Clifton Lee Dalgard, Mehdi Pirooznia, Harvey Klein and Swee Lay Thein
   Blood 2018 132:2388; [URL]

1. Apolipoprotein E Is a Concentration-Dependent Regulator of Pro-Inflammatory Mediator Expression by Asthmatic Airway Epithelial Cells
   O. Kalchiem-Dekel, X. Yao, D.M. Figueroa, E.M. Gordon, M. Kaler, A.V. Barochia, L. Poching, Y. Liu, F. Seifuddin, M. Pirooznia, S.J. Levine [URL]

1. Network Biology-based Approach to Decode Complex Diseases
   Harsh Yadav
   Richard Montgomery High School (Maryland) Preceptors: Dr. Vijender Chaitankar, Dr. Mehdi Pirooznia https://www.training.nih.gov/assets/2018_Summer_Poster_Day_Program.pdf

1. Variable Cell-free DNA Characteristics With Different Acute Rejection Phenotypes,
   S. Agbor-Enoh, I. Tunc, M. Jang, S. Gorhan. et. al.
   The Journal of Heart and Lung Transplantation, Volume 37, Issue 4, Supplement, 2018, Page S95, ISSN 1053-2498. [URL]
   
   
2. Clinically-unrecognized Allograft Injury is Common After Lung Transplantion,
   S. Agbor-Enoh, I. Tunc, S. Gorham, et. al.
   The Journal of Heart and Lung Transplantation,, Volume 37, Issue 4, Supplement, 2018, Pages S32-S33, ISSN 1053-2498 [URL]
   
   
3. Antibody-mediated Rejection: Should We Wait for Clinical Diagnosis?.
   S. Agbor-Enoh, A. Jackson, G. Berry, et. al.
   The Journal of Heart and Lung Transplantation, Volume 37, Issue 4, Supplement, 2018, Page S16, ISSN 1053-2498 [URL]

1. A general framework for analysis of clonal heterogeneity and tumor evolution
   Fudan University, Shanghai, China February 24-27, 2018
   Mehdi Pirooznia [URL]

2017

1. Transcriptome Analysis of the Lymph Node Microenvironment in Chronic Lymphocytic Leukemia
   Clare Sun, Delong Liu, Nakhle S. Saba, Sarah E. M. Herman, Mehdi Pirooznia and Adrian Wiestner
   Blood 2017 130:1718; [http://www.bloodjournal.org/content/130/Suppl_1/1718]
   
   

1. Circulating Xenograft-Derived Cell-Free DNA as a Reliable Marker for Injury After Xenotransplantation,
   S. Agbor-Enoh, J.L. Chan, I. Tunc, A. Singh, et. al.
   The Journal of Heart and Lung Transplantation, Volume 36, Issue 4, Supplement, 2017, Page S47, ISSN 1053-2498. [URL]
   
   

1. Exome sequencing of 103 Williams syndrome cases rules out variation in the remaining elastin allele and the larger Williams critical region as a major contributor to variance in blood pressure and arterial stenosis
   PCR Parrish, M Lugo, N Kopp, K Shields, YP Fu, RH Knutsen, M Pirooznia, BA Kozel [URL]

1. Evaluation of Early Biomarkers Associated with Graft Rejection in Patients with Sickle Cell Disease.
   P. Olkhanud1, F. Seifuddin2, M. Pirooznia2, C. Pittman1, A. Biancotto3, R. Pfeiffer4, C. Fitzhugh1; [URL]


2. CRISPR/Cas9-Mediated Dissection of Functional Domains of the Transcription Factor c-MYB.
   N. Angelis, X. Wang, I. Tunc, Y. Li, G. Bogoda, A. Esquinca, M. Pirooznia, S.L. Thein; Sickle Cell Branch. [URL]


3. Cell-Free DNA as a Biomarker in Sickle Cell Disease: Method Optimization and Analysis.
   L. Tumburu, S. Yang, Y. Wakabayashi, N. Igbineweka, M. Pirooznia, I. Tunc, Y. Li, J. Zhu, S.L. Thein; Sickle Cell Branch [URL]

1. Whole Genome Sequencing To Identify De Novo Mutations In Bipolar Disorder,
   Fernando Goes, Mehdi Pirooznia, Martin Tehan, Paula Wolyniec, John McGrath, Gerald Nested, Ann Apulver,
   European Neuropsychopharmacology, Volume 27, Supplement 3, 2017 [URL]


2. Exome Sequencing In Bipolar Disorder With Comorbid Panic: Gene Set And Pathway Based-analyses Suggest A Role For Glutamate And Calcium Signaling
   Sheikh, H., Pirooznia, M., Parla, J., Kramer, M., et. al [URL]


3. Exome Sequencing Of Bipolar Disorder: Family And Case-control Results Show Overlap With Genes Implicated In Autism And Schizophrenia
   Goes, F., Pirooznia, M., Parla, J., Melissa, K., Monson, E., et. al [URL]


4. Rare Bipolar Loci Identification Through Whole Exome Sequencing
   Pirooznia, M., Goes, F., Parla, J., Kramer, E., et. al [URL]