Journal (published or in press - last updated: March 2012)
No of journal papers=26, total number of citations: 687, H-index=12, i10-index=13
J1. Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Gholamreza Haffari, Martin Hirst, Marco Marra, Anne Condon, Samuel Aparicio, and Sohrab Shah, "Feature based classifiers for somatic mutation detection in tumour-normal paired sequencing data," Bioinformatics, 28(2): 167-75, 2012.
Impact Factor: 4.93
J2. Sohrab P. Shah, Andrew Roth*, Rodrigo Goya*, Arusha Oloumi*,
Gavin Ha*, Yongjun Zhao*, Gulisa Turashvili*, Jiarui Ding*, Kane Tse*,
Gholamreza Haffari*, Ali Bashashati*,
Leah Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Andrew
McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza
Heravi-Moussavi, Jamie Rosner, Daniel Lai, Inanc Birol, Richard Varhol,
Angela Tam, Noreen Dhalla, Thomas Zeng, Kevin Ma, Simon Chan, Malachi
Griffith, Annie Moradian, S.-W. Grace Cheng, Gregg Morin, Peter Watson, Karen
Gelmon, Stephen Chia, Suet-Feung Chin, Christina N Curtis, Oscar Rueda, Paul
Pharoah, Sambasivarao Damaraju, John Mackey, Kelly Hoon, Timothy Harkins,
Vasisht Tadigotla, Mahvash Sigaroudinia, Philippe Gascard, Thea Tlsty, Joseph
Costello, Irmtraud M Meyer, Connie J Eaves, Steven Jones, David Huntsman, Martin
Hirst, Carlos Caldas, Marco A Marra, Samuel Aparicio, “Mutational landscapes
of primary triple negative breast cancers reveal individual heterogeneity but
distinct patterns of somatic mutation,” Nature (in press)
* These authors
contributed equally to this work.
Impact Factor: 34.48
J3. Andrew
Roth, Jiarui Ding, Anamaria Crisan, Gavin Ha, Ryan Giuliany, Ali Bashashati,
Gulisa Turashvili, Arusha Oloumi, Martin Hirst, Marco Marra, Sam Aparicio,
Sohrab P. Shah, “JointSNVMix : A Probabilistic Model For Accurate Detection
Of Somatic Mutations In Normal/Tumour Paired Next Generation Sequencing Data,”
Bioinformatics (in press)
Impact
Factor: 4.93
J4. Christina Curtis, Sohrab P. Shah, Suet-Feung Chin, Gulisa
Turashvili, Oscar M. Rueda, Mark J. Dunning, Doug Speed, Andy G. Lynch,
Shamith Samarajiwa, Yinyin Yuan, Stefan Gr, Gavin Ha, Gholamreza Haffari, Ali Bashashati, Roslin Russell,
Steven McKinney, Anita Langer, Andrew Green, Elena Provenzano, Gordon
Wishart, Sarah Pinder, Peter Watson, METABRIC Group, Florian Markowitz, Leigh
Murphy, Ian Ellis, Arnie Purushotham, Anne-Lise Borresen-Dale, James D.
Brenton, Simon Tavar, Carlos Caldas and Samuel Aparicio, “The integrative
genomic and transcriptomic architecture of 1000 breast tumours reveals novel
subgroups,” Nature (in press).
Impact Factor: 34.48
J5. Ali Bashashati*, Nathalie A. Johnson*, Alireza Hadjkhodabakhshi, Matthew
Whiteside, David W. Scott, Kenneth Lo, Silvia Bakovic, Raphael Gottardo,
Fiona Brinkman, Joseph Connors, Graham Slack, Randy D. Gascoyne, Andrew Weng,
Ryan R. Brinkman, “B-cells with high side scatter parameter by flow cytometry
correlate with inferior survival
in diffuse large B cell lymphoma,” American Journal of Clinical Pathology (in press).
* Both authors contributed
equally to this work.
Impact Factor: 2.47
J6. Ali Bashashati*, Habil Zare*,
Robert Kridel, Nima Aghaeepour, Gholamreza Haffari, Joseph Connors, Randy D.
Gascoyne, Arvind Gupta, Ryan R. Brinkman, Andrew Weng, “Automated analysis of
multidimensional flow cytometry data improves diagnostic accuracy between
mantle cell lymphoma and small lymphocytic lymphoma,”American Journal of Clinical Pathology, 137:75-85, 2012.
* Both authors contributed
equally to this work.
Impact Factor: 2.47
J7.
F.S. Garmaroudi, K.J. Holmberg, J.M. Carthy, A. Bashashati, D.
Marchant, M. Zhang, K.P. Murphy, R.T. Ng, H. Luo, D. Yang, K.A. Janes and
B.M. McManus, “An ERK-p38 subnetwork coordinates host-cell apoptosis and
necrosis during coxsackievirus B3 infection,” Cell Host Microbe. Submitted in
March 2011 (Under revision).
Impact Factor: 13.02
J8. Ali Bashashati, Ryan Brinkman, “A
survey of flow cytometry data analysis methods,” Advances in Bioinformatics, vol. 2009, Article ID 584603, pp.
1-19, Dec 2009.
Impact Factor: NA – first
issue 2008, Number of citations: 13
J9.
Florian Hahne, Alireza Hadj Khodabakhshi, Ali Bashashati, Chao-Jen Wong, Randy D. Gascoyne, Andrew P. Weng,
Robert Gentleman, and Ryan Brinkman, “Per-channel basis normalization methods
for flow cytometry,” Cytometry A
(Published online: Nov 2009).
Impact Factor: 3.03, Number of
citations: 7
J10.
Greg Finak, A. Bashashati, Ryan R.
Brinkman and Raphael Gottardo, “Merging mixture components for cell
population identification in flow cytometry”, Advances in Bioinformatics Article, vol. 2009, Article ID 247646,
pp. 1-12, Nov 2009.
Impact Factor: NA – first
issue 2008, Number of citations: 8
J11. Farshid Garmaroudi, David Marchant, Xiaoning
Si, Abbas Khalili, Ali Bashashati,
Brian Wong, Aline Tabet, Raymond Ng, Kevin Murphy, Honglin Luo, Kevin Janes,
Bruce McManus, “Pairwise network mechanisms in the host signaling response to
coxsackievirus B3 infection” Proceedings
of the National Academy of Sciences of USA (PNAS), 107(39):17053-8, Sep
2010.
Impact Factor: 9.43, Number of
citations: 3
J12. Golnaz Baghdadi, Ali M. Nasrabadi, Ali Bashashati, “A comparison between
left and right brain activity during hypnosis,” Medical Engineering & Physics (submitted in Dec 2010)
Impact Factor: 1.67
J13. Nathalie A. Johnson, Merrill Boyle, Ali Bashashati, Laurie Sehn, Mukesh
Chhanabhai, Ryan Brinkman, Joseph M. Connors, Andrew Weng, Randy D. Gascoyne,
“Dim CD20 and CD5 positive DLBCL are associated with an inferior survival in
CHOP+/- R treated patients,” Blood,
113(16):3773-80, Apr 2009.
Impact Factor: 10.56, Number of
citations: 38
J14. S.M. Vercauteren, A. Bashashati, D. Wu, R.R. Brinkman, C. Eaves, A. Eaves, and A.
Karsan, “Reduction in multi-lineage and erythroid progenitors distinguishes
myelodysplastic syndromes from non-malignant cytopenias,” Leukemia Research, vol. 33, no. 12,
pp. 1636-42, 2009.
Impact Factor: 2.36
J15. Nathalie A. Johnson, Stephen Leach, Bruce
Woolcock, Ron de Leew, Ali Bashashati,
Laurie Sehn, Joseph M. Connors, Angie Brooks-Wilson, Randy D. Gascoyne, “CD20
mutations involving the rituximab epitope in diffuse large B cell lymphomas
are rare and are not a significant cause of R-CHOP failure,” Haematologica, 94(3):423-427, Feb 2009.
Impact Factor: 6.41, Number of
citations: 12
J16. Ali
Bashashati, Rabab Ward, and Gary
Birch, “Towards development of a 3-state self-paced brain interface based on
hand extension movements,” J Computational Intelligence & Neuroscience, vol. 2007,
Article ID 84386, pp. 1-8, Sep 2007.
Impact Factor: NA – First
issue 2007, Number of citations: 14
J17. Ali Bashashati, Borna Noureddin,
Rabab Ward, Peter Lawrence, and Gary Birch, “Effects of eye blinks on the
performance of a self-paced brain interface,” Clinical Neurophysiology, vol. 118, no. 7, pp. 1639-47, Jul 2007.
Impact Factor: 3.12, Number of citations: 1
J18. Ali Bashashati, Mehrdad
Fatourechi, Rabab K. Ward, and Gary E. Birch, “A survey of signal processing
algorithms in brain-computer interfaces based on electrical brain signals,” Journal of Neural engineering, vol. 4,
no. 2, pp. R35-57, Jun 2007.
Impact Factor: 3.74, Number of
citations: 169
J19. Ali Bashashati, S.G. Mason, Jaimie
Borisoff, Rabab K. Ward, and G. Birch, “A comparative study on generating
training-data for self-paced brain interfaces,” IEEE Trans. Neural Systems and Rehabilitation, vol. 15, no. 1,
pp. 59-66, Mar 2007.
Impact Factor: 2.42, Number of
citations: 6
J20.
Mehrdad Fatourechi, Ali Bashashati, Rabab K. Ward, and Gary E. Birch, “EMG and EOG artifacts in brain
interface systems: A Survey,” Clinical
Neurophysiology, vol. 118, no. 3, pp. 480-94, Mar 2007 (invited paper).
Impact Factor: 3.12, Number of
citations: 106
J21.
S.G. Mason, A. Bashashati, M.
Fatourechi, K.F. Navarro, and G.E. Birch, “A comprehensive survey of brain
interface technology designs,” Annals
of Biomedical Engineering, vol. 35, no. 2, pp. 137-69, Feb 2007.
Impact Factor: 2.40, Number of
citations: 138
J22.
M. Fatourechi, A. Bashashati, Gary
E. Birch, and Rabab K. Ward, “Automatic user customization for improving the
performance of a self-paced brain interface system,” IEE Journal of Medical & Biological Engineering and
Computing, vol. 44, no. 12, pp. 1093-104, Dec 2006.
Impact Factor: 1.76, Number of
citations: 5
J23. A. Bashashati, S.G. Mason, Rabab
K. Ward, and G. Birch, “An improved asynchronous brain interface:
making use of the temporal history of the LF-ASD feature vectors,” Journal of Neural Engineering, vol. 3,
no. 2, pp. 87-94, Jun 2006.
Impact Factor: 3.74, Number of
citations: 15
J24. A. Bashashati, M. Fatourechi, R.
Ward, and G. Birch, “User customization of the feature generator of an
asynchronous brain interface,” Annals of Biomedical Engineering, vol. 34, no. 6, pp. 1051-60, Jun 2006.
Impact Factor: 2.40, Number of
citations: 18
J25. A. Bashashati, B. Noureddin, R. Ward, P. Lawrence, and G. Birch,
“An experimental study to investigate the effects of a motion tracking
electromagnetic sensor during EEG data acquisition,” IEEE Trans. Biomed. Eng., vol. 53, no. 3, pp. 559-63, Mar 2006.
Impact Factor: 2.15, Number of
citations: 4
J26. J.
Borrisof, S. Mason, A. Bashashati,
and G. Birch, “Brain computer interface (BCI) design for asynchronous control
applications: improvements to the LF-ASD asynchronous brain switch,” IEEE Trans. Biomed. Eng., vol. 51, no.
6, pp. 985-92, Jun 2004.
Impact Factor: 2.15, Number of
citations: 71
Refereed Conference Proceddings
C1. Ali Bashashati, Kenneth Lo, Raphael Gottardo, Randy Gascoyne, Andrew Weng, Ryan Brinkman, “A pipeline for automated analysis of flow cytometry data: preliminary results on lymphoma sub-type diagnosis,” in proc. of the 31st Annual International IEEE Engineering in Medicine and Biology Society Conference, Minneapolis, Sep 2-6 2009, pp. 4945-8.
C2. Ali Bashashati, Rabab K. Ward,
and Gary E. Birch, “Recent advances in the design of a 3-state self-paced
(asynchronous) brain computer interface,” in proc. of the IEEE-EMB Society
Neural Eng. Conference, Hawaii, May 2-5 2007, pp. 188-91.
C3. Ali Bashashati, Rabab K. Ward,
and Gary E. Birch, “Comparison of using monopolar and bipolar
electroencephalogram (EEG) electrodes for detection of right and left hand
movements in a self-paced brain computer interface (BCI),” in proc. of the
IEEE Canadian Conf. on Electrical and Computer Engineering, Vancouver,
Canada, Apr 22-26 2007, pp. 725-8.
C4. Ali Bashashati, Rabab K. Ward,
and Gary E. Birch, “Detection of hand extension movements in the context of a
3-state asynchronous brain interface,” in proc. of the IEEE Inter. Conf. on
Acoustics, Speech, and Signal Proc. (ICASSP), Toulouse, France, May 15-19
2006.
C5. A. Bashashati, R. Ward, and G.
Birch, “A new design of the asynchronous brain computer interface using the
knowledge of the path of features,” in proc. of the IEEE-EMB Society Neural
Eng. Conference, Arlington, VA, Mar 16-19 2005, pp.101-4.
C6. M.
Fatourechi, A. Bashashati,
R. Ward, and G. Birch, “A hybrid genetic algorithm approach for improving the
performance of the LF-ASD brain computer interface,” in proc. of the
IEEE-ICASSP, Philadelphia, Mar 2005, pp. 345-8.
C7. A. Bashashati, S. Mason, R. Ward,
and G. Birch, “An automatic method to generate ensemble averages of
movement-related potentials for individuals with spinal cord injuries,” in
proc. of the 26th Inter. Conf. of the IEEE Eng. in Medicine and Biology (EMB)
Society, San Francisco, CA, Sep 1-5 2004, pp. 4529-32.
C8. M.
Fatourechi, A. Bashashati,
R. Ward, and G. Birch, “Improving the performance of the LF-ASD brain
computer interface by means of genetic algorithm,” in proc. of the IEEE
Symposium on Signal Processing and Information Technology (ISSPIT), Italy,
Dec 18-21 2004, pp. 38-41.
C9. A. Bashashati, R. Ward, G. Birch,
M. Hashemi, and M. Khalilzadeh, “Fractal dimension-based EEG biofeedback
system,” in proc. of the 25th Inter. Conf. of the IEEE-EMB Society, Mexico,
Sep 17-20 2003, pp. 2220-3.
Abstracts
A1. A. Bashashati, A.
Hadj-Khodabakhshi, K. Lo, N. Johnson, R. Gascoyne, R. Gottardo, A. Weng, and
R. Brinkman, “Identifying a group of diffuse large B-cell lymphoma patients
with inferior survival using automated analysis of flow cytometry data,”
International Society for Analytical Cytology (ISAC) Annual Conference,
Seattle WA, May 8-12 2010 (submitted in Dec 2009).
A2. H.
Zare, A. Bashashati,
A. Weng, R. Gascoyne, A. Gupta, and R. Brinkman, “Diagnosis of lymphoma based
on automated analysis of flow cytometry data,” International Society for
Analytical Cytology (ISAC) Annual Conference, Seattle WA, May 8-12 2010
(submitted in Dec 2009).
A3.
Farshid S. Garmaroudi, David Marchant, Ali
Bashashati, Mitra Esfandiarei, Raymond T. Ng, Kevin Murphy,
Honglin Luo, and Bruce M. McManus, “Functional properties of signaling
networks in enteroviral myocarditis,” The 10th International Conference on
Systems Biology, Stanford, California, Aug30-Sep4 2009.
A4.
Farshid S. Garmaroudi, David Marchant, Ali
Bashashati, Abbas Khalili, Brian Wong, Raymond T. Ng, Kevin
Murphy, Honglin Luo, and Bruce M. McManus, “Partial correlation signaling
networks in virus-infected cardiomyocytes,” The 10th International Conference
on Systems Biology, Stanford, California, Aug30-Sep4 2009.
A5. A. Bashashati, K. Lo, R.
Gottardo, R. Gascoyne, A. Weng, and R. Brinkman, “An automatic pipeline for
the analysis of flow cytometry data: preliminary results on lymphoma,”
International Society for Analytical Cytology (ISAC) Annual Conference,
Hungary, May 17-21 2008.
A6. P.
Shooshtari, A. Bashashati,
I. Vulto, P. Lansdorp, A. Gupta, and R. Brinkman, “An automated method for
measuring average telomere length using flow-FISH data,” International
Society for Analytical Cytology (ISAC) Annual Conference, Hungary, May 17-21
2008.
Posters
P1.
Farshid S. Garmaroudi, David Marchant, Ali
Bashashati, Mitra Esfandiarei, Raymond T. Ng, Kevin Murphy,
Honglin Luo, and Bruce M. McManus, “Functional properties of signaling
networks in enteroviral myocarditis,” The 10th International Conference on
Systems Biology, Stanford, California, Aug30-Sep4 2009.
P2. Farshid S. Garmaroudi, David Marchant, Ali Bashashati, Abbas Khalili, Brian Wong, Raymond T. Ng, Kevin Murphy, Honglin Luo, and Bruce M. McManus, “Partial correlation signaling networks in virus-infected cardiomyocytes,” The 10th International Conference on Systems Biology, Stanford, California, Aug30-Sep4 2009.
P3-
Parisa Shooshtari, Ali Bashashati,
Irma Vulto, Peter Lansdorp, Arvind Gupta, Ryan Brinkman, “An automated method
for measuring average telomere length using flow-FISH data,” International
Society for Advancement of Cytometry Annual Conference, Budapest, Hungary,
17-21 May 2008.
P4-
Parisa Shooshtari, Ali Bashashati,
Irma Vulto, Peter Lansdorp, Arvind Gupta, Ryan Brinkman, “An automated method
for measuring average telomere length using flow-FISH data,” Student
Biotechnology Network (SBN) Research Exchange, Vancouver, Canada, April 2008.
Invited Talks
IT1- “Automated analysis of flow cytometry data: identifying a group of diffuse large B-cell lymphoma patients with inferior survival,” Flow Informatics and Computational Cytometry Society Meeting, Seattle, WA, March 2009.
IT2-
“New flow cytometry data standards and data analysis with Bioconductor,”
Danish Society for Flow Cytometry Annual Meeting, August 2008.
IT3-
“Flow cytometry data classification,” Department of Statistics, University of
British Columbia, March 2008.
IT4-
“Automated analysis of flow cytometry data,” British Columbia Cancer Research
Center (Work in Progress Talk Series), February 2008.
Conference Talks
CT1. “An
automatic pipeline for the analysis of flow cytometry data: preliminary
results on lymphoma,” International Society for Analytical Cytology (ISAC)
Annual Conference, Hungary, May 17-21 2008.
CT2.
“Recent advances in the design of a 3-state self-paced (asynchronous) brain
computer interface,” IEEE-EMB Society Neural Eng. Conference, Hawaii, May 2-5
2007.
CT3.
“Comparison of using monopolar and bipolar electroencephalogram (EEG)
electrodes for detection of right and left hand movements in a self-paced
brain computer interface (BCI),” IEEE Canadian Conf. on Electrical and
Computer Engineering, Vancouver, Canada, Apr 22-26 2007.
CT4. “A
new design of the asynchronous brain computer interface using the knowledge
of the path of features,” IEEE-EMB Society Neural Eng. Conference, Arlington,
VA, Mar 16-19 2005.
CT5. “Fractal dimension-based EEG biofeedback system,”
25th Inter. Conf. of the IEEE-EMB Society, Cancun, Mexico, Sep 17-20 2003.
© Copyright
2005. Ali Bashashati
Last updated: March 2012