Publications and talks

Selected Publications (Full text):
(Manuscripts in preparation or in press or listed at the bottom of the list)

 Alan Mackay, Anna Burfor,… Nikbakht H., et al. Integrated molecular meta-analysis of 1000 paediatric high grade and diffuse intrinsic pontine glioma Cancer Cell (2017)
 Morrissy, A.S., Cavalli, F.M., ……..,Nikbakht H., et al.. Spatial heterogeneity in medulloblastoma. Nature Genetics (2017)
  Ralph Salloum, Melissa K. McConechy, Leonie G. Mikael,…, Hamid Nikbakht; , et al., Characterizing temporal genomic heterogeneity in pediatric high-grade gliomas, Acta Neuropathologica Communications [accepted] (2017).
  Fiset, P.O., Fontebasso, A.M., Jay, N., Gayden, T., Nikbakht, H., Majewski, J., Jabado, N. and Albrecht, S. Longitudinal mutational analysis of a cerebellar pilocytic astrocytoma recurring as a ganglioglioma. Pediatric blood & cancer (2017)
  Nikbakht, Hamid.,  et al.  Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma. Nature Communications (2016)
  Nikbakht, Hamid., Xuhua Xia, and Donal A. Hickey. The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium. Genome (2015)
  Fontebasso AM, Papillon-Cavanagh S, .., Nikbakht H., Gerges N, et al. Recurrent somatic mutations in ACVR1 in pediatric midline high-grade astrocytoma. Nature Genetics (2014)
  Fontebasso, AM., …, Nikbakht, H., … Majewski, & Jabado, N.,.. Epigenetic dysregulation: a novel pathway of oncogenesis in pediatric brain tumors. Acta Neuropathologica (2014)
  Kahle, K. T., Merner, N. D., Friedel, P., Silayeva, L., Liang, B., Khanna, A., …Nikbakht, H., …, & Rouleau, G. A. Genetically encoded impairment of neuronal KCC2 cotransporter function in human idiopathic generalized epilepsy. EMBO Reports (2014)
  Shokralla, S., Gibson, J. F., Nikbakht, H., Janzen, D. H., Hallwachs, W., & Hajibabaei, M. Next?generation DNA barcoding: using next?generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Molecular Ecology Resources (2014)
   (co-first author)
Albu, Mihai*., Hamid Nikbakht,*, D. A. Hickey. “DNA Barcode Linker”, Molecular Ecology Resources (2010).
   M. Kazemian, B. Moshiri, H. Nikbakht, V. Palade, C. Lucas. “Using Classifier Fusion Techniques for Protein Secondary Structure Prediction”, International Journal of Computational Intelligence in Bioinformatics and Systems Biology (2010)
   M. Kazemian, B. Moshiri, H. Nikbakht, C. Lucas. A New Expertness Index for Assessment of Secondary Structure Prediction Engines, Journal of Computational Biology and Chemistry (2007)
   M. Kazemian, B. Moshiri, H. Nikbakht, C. Lucas. Architecture for Biological Database Integration, Special Issue on AI & Specific Applications, ICGST International Journal on Artificial Intelligence and Machine Learning (2006)
  M. Kazemian, B. Moshiri, H. Nikbakht, C. Lucas. Dempster Shafer based Fusion of Protein Secondary Structure, International Conference on Machine Intelligence (IEEE conference, Tozeur, Tunisia, 5-7 November 2005)
Upcoming papers:
   Hamid Nikbakht, Jessa S., et al. “Dormancy and Interval Therapy Affect the Evolution in Metastatic Colorectal Cancer” (submitted to Scientific Reports) (2017)
  Meaghan Boileau*, Margret Shirinian*, Tenzin Gayden*,…, Hamid Nikbakht, et al. Mutated H3 Histones Drive Human Preleukemic Hematopoietic Stem Cell Expansion and Leukemic Aggressiveness. (in submission to Nature Medicine) (2017)
 Nikbakht, Hamid*, Leonie Mikael, et al.  “Dysregulation of RTK Signal Transduction Pathways in H3/IDH Wild Type Pediatric Glioblastoma” (in preparation) (2017)
   Nikbakht, Hamid*, Michele Zeineh*, et al. Recurrent Somatic Mutation in the MYC Associated Factor X in Brain Tumors (in preparation) (2017)
 Nikbakht Omid, Arash Ghorbannia Delavar, Hamid Nikbakht* “Swarm Intelligence Based Optimization Algorithms and Their Applications in Computational Biology” (in preparation for Plos Computational Biology) (2017)

Book Chapter:

M. Kazemian, B. Moshiri, H. Nikbakht, C. Lucas. Protein Secondary Structure Classifiers Fusion using OWA, Lecture Notes in Computer Science (2015) Springer-Verlag Berlin Heidelberg.


Selected Conference talks:

[1] Recurrent somatic mutation Myc Associated factor X in brain tumors, Human Genome Meeting (Translational Genomics) – 2016 – Houston, TX, USA
[2] Recurrent somatic mutation Myc Associated factor X in brain tumors, American Society of Human Genetics meeting (ASHG) – 2015 – Baltimore, MD, USA (Epstein award of excellence in human genetics research, finalist)
[3] Studying the Evolution of Cancer Tumours in pGBM Samples. 3rd Annual Canadian Human and Statistical Genetics Meeting – 2014 – Victoria, BC, Canada
[4] Sequence Analysis of the Secondary Structure of Proteins, First Iranian international conference on Bioinformatics – 2005 – Institute for Biochemistry and Biophysics, University of Tehran, Iran

Selected Publications (Abstract):
(Chronologically sorted)

[1] Jian Carrot-Jang ,Nikbakht, H., Majewski, (2015).  Speciman: A new low-frequency variant caller with significantly increased specificity. American Society of Human Genetics.
[2] Jian Carrot-Zhang, Hamid Nikbakht & Jacek Majewski. (2014). LVpicker: Picking up True, Low-frequency Variants to Study Tumour Heterogeinty. American Society of Human Genetics.
[3] Kieran, M., Fontebasso, AM., …, Nikbakht, H., … Majewski, J., Gupta, N., ,& Jabado, N.,. (2014). The BATS DIPG Study: A National Clinical Trial Of Upfront Biopsy and Treatment Stratification For Newly Diagnosed Diffuse Intrinsic Pontine Glioma (DFCI #10-321) . Neuro-Oncology, 16(suppl 1), i40-i59.
[4] Nikbakht H., Jabado N., and Majewski J. Studying the Evolution of Cancer Tumours in pGBM Samples 3rd Annual Canadian Human and Statistical Genetics Meeting (2014)
[5] M. Albu, H. Nikbakht, and Donal Hickey. DNA Barcode Linker, An efficient web tool for specimen identification. Third International Barcode of Life Conference. Mexico City, Mexico, (2009).
[6] H. Nikbakht, Lee Zamparo, Gregory Singer and Donal Hickey. Developing a Simple Online Barcode Search Application Canadian Barcode of Life Netwok, Science Symposium. Guelph, Ontario, Canada (2007).
[7] Bahram Goliaei, Zarrin Minuchehr, H. Nikbakht, Mehdi Goudarzi. Sequence Analysis of the Secondary Structure of Proteins. 8th Iranian Congress of Biochemistry and First International Congress of Biochemistry & Molecular Biology September 11-15, 2005.
[8] Bahram Goliaei, H. Nikbakht. Position Specific Analysis of Amino acids in Alpha Helices. 20th Congress of European Life Science Organization (ELSO) 2003.
[9] Bahram Goliaei, H. Nikbakht. Developing software to isolate Secondary Structures of Proteins using DSSP. First Iranian Congress of Bioinformatics. Sept. 2003.

Ongoing works:

[1] Hamid Nikbakht, Donal A. Hickey. Background selection re-shapes the genomic nucleotide content
[2] Hamid Nikbakht, Jacek Majewski, CNAXX: A deep-learning approach to copy number variation detection using whole exome and whole genome sequencing data