Jainab Khatun
115 Christine ct, Chapel Hill, North Carolina-27516
khatun@email.unc.edu
Telephone: (919)-932-5972 (Home), (919)-843-3512 (Work).
Education:
Ph. D in Science (1998):
Indian Association for the Cultivation of Science, Jadavpur
University, Calcutta, India. Title of the
Thesis: Ò Theoretical Study on Multiphoton
Ionization of Small Diatomic GassesÓ
Masters Degree in physics (1991):
Nuclear physics as special paper, First Class, Calcutta University, Calcutta,
India.
Bachelor Degree in physics (1988): Mathematics and
Chemistry as subsidiary subject, First Class, Calcutta University, Calcutta,
India.
Professional
Experience:
UNC at Chapel Hill, Postdoctoral
Fellow; 2004-Present
Currently
I am working on annotating Human Genome using proteo-genomic
mapping. We started large-scale analysis of proteomics data sets to map
translation across the human genome. Recently, I developed a hidden Markov
model for improved peptide identification of MS/MS spectra by applying statistical
machine learning approaches. The developed algorithm shows better performance
from many of existing identification algorithms. I also performed statistical
analysis of mass spectrometry data derived from MALDI TOF/TOF instrument.
UNC at Chapel Hill, Postdoctoral
Fellow; 2003-2004
Developed
a new methodology to determine the contact potentials in proteins. I applied
this methodology to derive sets of contact interaction parameters for a
hierarchy of interaction models including solvation
and multi-body contact interaction parameters and determined the maximum
accuracy of predictions and the transferability of parameters obtained by using
contact models potentials.
UNC at Chapel Hill,
Postdoctoral Fellow; 2001-2002
Developed
a user interface for a scientific (molecular dynamics simulation) program using
CGI, PERL, and XML. Designed and developed more sophisticated and advanced
generic user interface implementing JAVA and XML. The developed interface
promises to lead to generally applicable method for any of a large number of
existing and yet-to-be-written complex programs.
Indian Association
for the Cultivation of Science, Ph.
D student; 91 - 98
Studied resonance enhanced multi-photon
ionization (REMPI) of small diatomic molecules, such as hydrogen, deuterium and
HD molecule. We have shown that total photoelectron
angular distribution and vibrationally resolved angular distribution vary with
laser intensity. In addition, we have shown that the tendency for a
non-Frank-Condon vibrational distribution and the
degree of deviation of vibrationally resolved photoelectron angular
distribution from the usual nature increases for heavier isotopes.
Professional Memberships
Honors
and Awards:
1983, National Scholarship for Madhyamik examination, Govt. of West Bengal.
1985, National Scholarship for
H.S. (+2) examination, Govt. of West Bengal.
1988, National Scholarship for
B.Sc. examination, Govt. of West Bengal.
1991, Qualified Graduate Aptitude Test
in Engineering (GATE), Govt. of India.
1994, Awarded Senior Research
fellowship by Council and Scientific Industrial Research (CSIR), Govt.
of India.
Skills Summary:
Five years experience in modeling and computational biology.
Two years experience in GUI development.
Five years experience in computational
physics with quantum mechanical calculations.
More than five years experience in
scientific programming. Object-oriented programming and
design.
Environments
-Mac OS, UNIX, Windows 95/98, Windows NT,
MS-DOS, VAX-VMS, SUN.
Languages
-C++,
Objective-C, Java GUI and Java Application.
PERL/CGI, HTML, XML, FORTRAN.
List of Publications:
1. ÒIn
response to Ô On E-values for Tandem MS scoringÕ Ò Jainab Khatun and
Morgan C Giddings, Bioinformatics, doi-10.1093/bioinformatics/btn252 (Letter to the editor, 2008)
2.
"Incorporating sequence
information into the scoring function: A hidden Markov model for improved
peptide identification." Jainab Khatun, Eric Hamlett
and Morgan C. Giddings, Bioinformatics, doi:10.1093/bioinformatics/btn011
(2008).
3.
"Fragmentation
Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass
Spectrometry." Jainab Khatun,
Kevin Ramkissoon and Morgan C Giddings, Anal. Chem. 79, 3032 (2007).
4. ÒComputational methods enabling
genome-based protein identification from large, complex genomes using mass
spectrometry data. Third IEEE Workshop on Genomic Signal Processing and
StatisticsÓ Mike Wisz, Jainab Khatun and Morgan C Giddings; GENSIPS, Newport Rohde Island; (2005)
5. ÒCan contact potentials reliably predict stability of
proteins?" Jainab Khatun, Sagar D. Khare & Nikolay V. Dokholyan, Journal
of Molecular Biology, 334, 1223(2004).
6. "The effect of electronic auto-ionization on vibrational branching ratio in (1+1)-photon resonance
enhanced multi-photon ionization of H2 molecules: dependence on laser intensity", Jainab
Khatun and Krishna Rai Dastidar,
J. Phys. B, vol. 32, 373(1999).
7.
"Theoretical study of vibrational branching ratio and photoelectron angular
distribution in (1+1')-photon resonance-enhanced multi-photon ionization of HD
and D2 molecules" Jainab Khatun and
Krishna Rai Dastidar; Phys.Rev.A, vol.53, 4326(1996).
8.
"Theoretical study of
photoelectron angular distribution in (1+1')-photon resonance-enhanced multiphoton ionization of H2 molecule", Jainab Khatun and Krishna Rai Dastidar, Phys.Rev.A,
vol.52, 2971(1995).
9. "Non-Franck-Condon vibrational
distribution in the (1+1')-photon resonance-enhanced multiphoton
ionization of H2",
Jainab Khatun, S. Sanyal and Krishna Rai
Dastidar, Phys.Rev.A,
vol.49, 4765(1994).
Chapter in Book:
10. Krishna Rai Dastidar, Jainab Khatun and T.K. Rai
Dastidar: "Multiphoton
absorption to and from autoionizing states and
ionizing continuum": ATOMIC MOLECULAR AND CLUSTER PHYSICS, eds. S.A. Ahmed, Narosa Publishing
House, page 158, 1997.
Papers presented
(selected) in Symposia/Conferences:
Talk presented in
Conferences:
11. ÒProteogenomic Mapping for the Human Genome to Identify Protein-Coding
SequencesÓ, Jainab Khatun, Jameson Miller, Mark Holmes
and Morgan Giddings, ÒInstitute of
Biological Engineering, 2008 Annual Conference, (2008), Chapel Hill, North
Carolina.
12. ÒProteogenomic Mapping for the Human Genome: Technologies
and Challenges for Identifying Protein-Coding Sequences; Jainab Khatun; Christopher
Maier; Morgan Giddings; U.S. HUPO Fourth Annual
Conference( 2008). Bethesda, MD.
13. "Proteogenomic mapping for the human
genome—Identifying protein-coding sequences", Jainab Khatun, Christopher
Maier, Jameson Miller and Morgan C Giddings, Genome Informatics, 2007, Cold
Spring Harbor Laboratory, NewYork.
14.
"Incoroporating
sequence information into the scoring function: a hidden Markov model for improved
peptide identification". Jainab Khatun and Morgan
C. Giddings, Human Proteome Organization
(HUPO) 5th Annual World
Congress, 2006, Long Beach, CA.
15. ÒA Machine
Learning Model for de novo Sequencing
of Peptides from Tandem Mass Spectrometry DataÓ, Jainab Khatun and Morgan C. Giddings; Scientific Retreat @ the Beach, September 16-18, 2005, Writesville Beach, North Carolina.
Poster
presented in Conferences (selected):
16. Jainab Khatun,
Jameson Miller, Mike Wisz, Dongmei
Yang, Atul Shah, Kristen Dang, Mark Holmes, Melissa Suarez,
and Morgan C. Giddings: Genome-Based Peptide
Fingerprint Scanning: A
Comprehensive Open Source Software System for Protein IdentiÞcation
Using Unannotated Genome Sequence Data, Version 2. Worldwide
Developers Conference (WWDC), June, 2007, Sanfrancisco,
CA.
17. Jainab Khatun, Jameson Miller, Mike Wisz,
Dongmei Yang, Atul Shah,
Kristen Dang, Mark Holmes, Melissa Suarez,
and Morgan C. Giddings: ÒGFS Version 2: A Comprehensive Open Source Software
System for Protein Identification Using Unannotated
Genome Sequence DataÓ, Poster presented in ÔHuman Proteome
Organization (HUPO) 5th Annual World Congress, Nov, 2006, Long Beach, CA.
18. Jainab Khatun, Sagar Khare & Nikolay Dokholyan: Ò A new method
for estimating contact interactions in proteinsÓ, Poster presented in ÔStructural
Biology Symposium at NIEHSÕ Sep. 23, 2003, NIEHS, RTP, North Carolina.
19. Jainab Khatun and Krishna Rai Dastidar: " The effect
of autoionization on (1+1')-photon resonance enhanced
Multiphoton ionization (REMPI) of H2 molecules" presented in International
Conference on the Physics of Electronic and Atomic and Collision, July
23-29, 1997, Vienna, Austria.
20.
Jainab Khatun and Krishna Rai Dastidar: "Resonance
enhanced multiphoton ionization of two isotopes of H2 molecules: Vibrational
branching ratio and photoelectron angular distribution": Presented poster in the
7-th International Conference on Multiphoton
Process, Sept.30-Oct.4, 1996, Max-Planck-Institute fur Quantenoptik,
Germany.
21. Jainab Khatun and Krishna Rai Dastidar: Proceeding of
the Second Euro Physics Conference on Photon and Electron Collisions with Atoms,
page 124, July 23-26, 1996, Queen's University, Belfast, N. Ireland, UK.
22. Jainab Khatun and Krishna Rai Dastidar: " Theoretical
study of photoelectron angular distribution in (1+1)-photon ionization of H2 molecule": XIX International
Conference on the Physics of Electronic and Atomic Collision, page 663,
July 26- August 1, 1995, British Columbia, Canada.
23. Jainab Khatun, S. Sanyal, Krishna Rai Dastidar and T.K. Rai Dastidar: "Effect of autoionization
on (1+1)-photon resonance enhanced multiphoton
ionization of H2,
7th International Symposium on Resonance Ionization Spectroscopy and Its
Applications (RIS-1994), Institute fur physik, Universitat Mainz, D-55029 Mainz, Bernkastel-kues,
Germany.
24. Jainab Khatun, S. Sanyal and K. Rai Dastidar: "(1+1)-photon REMPI of H2 via B1Su state:
Effect of near resonant channel via C1Pu state on the vibrational branching of the H2+ ion". Proceeding of National Laser Symposium,
page 267, Feb. 17-19, 1993, I.I.T. Madras.
References:
1. Dr. Morgan
C. Giddings
Department of Microbiology and
Immunology
University of North Carolina at
Chapel Hill
Phone: 919 843-3513, Email:giddings@unc.edu
2. Dr. Nikolay V. Dokholyan
Department of Biochemistry and
Biophysics
University of North Carolina at
Chapel Hill
Phone: 919 843-2513, Email:dokh@med.unc.edu
3. Prof. Krishna Rai
Dastidar, Department of Spectroscopy,
Indian Association for the
Cultivation of Science, Calcutta, India
Phone: 91 33 473-4971, E-mail: spkrd@mahendra.iacs.res.in