Kalyani Dhusia Ph.D.

Computational Biologist

**** * ******, *** #**, Little Rock, Arkansas

Tel: 517-***-**** Website LinkedIn Git

Computational biologist working as Assistant Staff Scientist at Bioinformatics Core with Dr. Stephanie Byrum at University of Arkansas Medical Sciences. My research interest includes cancer genomics, web development, database management, drug design, machine learning for sequence analysis, analysis of large biological data sets, using scikit-learn in python.

Professional Experience

Assistant Staff scientist Jan 1, 2022 – present

Assistant Staff Scientist (MMDB) position in the Department of Biochemistry and Molecular Biology (https://biochemistry.uams.edu/) at the University of Arkansas for Medical Sciences (UAMS) extracts and compiles medical research data from existing databases within the Winthrop P. Rockefeller Cancer Institute. This position works closely with CI faculty to perform targeted database queries and distribute requested data in compliance with IRB rules and regulation.

Along with this, I have formulated an collaboration with Nanome Inc. They have sponsored me with oculus quest 2 to visualize study and develop 3-D protein structures in virtual reality.

Tools used: MS access, MS-SQL, python, R

Research Fellow Dec 31, 2019 – Dec 31, 2021

Working as postdoc research associate at with Wu Lab at Albert Einstein College of Medicine. With Wu lab, I aim on constructing large scale database in structural bioinformatics and develop machine learning based computational algorithms to study the dynamics of protein protein interaction of membrane receptors in immune systems and their functional role in cell signal transduction. The Structure-based Online database constructed is EXCESP and is available at Home:EXCESP.

Tools used: MS-SQL, flask, python, R package, Skit-learn, jupyter notebook

Research Associate Jan 1, 2019 – Dec 30 2019

My first year of postdoc research work with Michigan State University with Bhattacharya Lab had focus on development of predictive models of genomic binding by the nuclear receptors, aryl hydrocarbon receptor (AHR) and nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This is where, I used transcription data of nrf2 from ENCODE and used machine learning to predict NFE2L2 binding sites models. In a collaborative project with Gilad Lab, we used the orphan aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor that upon activation binds to specific AHR response elements (AHRE) of the Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) promoter. Flavonoids have been identified as AHR ligands. Data generated with this project shows the successful creation of a synthetic gene “off” switch that can be monitored directly using an optical reporter gene.

Research Experience

Sam Higginbottom Institute of Agriculture, Technology and Sciences

Ph.D. scholar with Dr. Pramod W. Ramteke 2014- 2018

Research topic: Structural bioinformatics analysis of potential inhibitors against microbial pathogens

Studied and analyze the pathway for siderophore production in bacterial pathogens.

Examined, predicted and designed siderophore-antibiotic conjugates for specific drug delivery

Post Graduate Student with Dr. Pramod K. Yadav 2013-2014

Research topic: Prediction of T-cell and B-cell epitopes for msp119 protein in Plasmodium yeolii

Identified msp119 protein in Plasmodium yeolii as potential target for epitope prediction against malaria

The 3D structures of T-cell epitopes (MHC-I and MHC-II) were modeled and validated

The protein–protein docking of modeled epitopes with respective MHC molecules was performed

Six each for B-cell and T-cell epitopes were identified as potent candidate for vaccine development

Bio-Axis DNA Research Centre, Lucknow

Summer research graduate with Dr. Amita Kashyap 2013

Topic: In-silico approach towards designing exemestane against BAG1 protein for the treatment of Leukemia

• Studied BAG1 gene that causes most kinds of cancer especially Leukemia.

• Using computational tools predicted structure, performed molecular docking and identified 6-mecaptopurin as best drug candidate against BAG1.

Education:

Sam Higginbottom University of Agriculture, Technology and Sciences, Dec 11th, 2018

Allahabad, UP, India

Doctorate of Philosophy

Emphasis in Bioinformatics

Sam Higginbottom University of Agriculture, Technology and Sciences, July, 2014

Allahabad, UP, India

Master of Science

Emphasis in Bioinformatics

86 percentages with as first position holder with Silver medal.

Ewing Christian College, University of Allahabad, Uttar Pradesh, India July, 2012

Bachelor of Science

Emphasis in Zoology and Chemistry

50 percentages

St. Mary’s Covent School, Ghoorpur, Allahabad, India May, 2008

Intermediate (Central Board of Secondary Education)

Emphasis in Biology, Chemistry, Physics, English and Information Practices

69.3 percentages

St. Mary’s Covent School, Ghoorpur, Allahabad, India May, 2006

High School (Central Board of Secondary Education)

Emphasis in Science

82.5 percentages

KEY SKILLS

Bioinformatics skills

Computational skills

Sequence analysis

Operating Systems

Machine learning and NLP

GNU/Linux[advanced]

Evolutionary trace analysis

Windows [advanced]

NGS: Fastx, Bowtie, Samtools, Bedtools

Mac OS [advanced]

Structural informatics

Web development

Protein interface analysis

MS-SQL, flask, MS-Access db

HM, Modeller, SpringDB

AutoDock Vina and Schrӧdinger

Cluster and parallel computing

High Performance Computing

Molecular dynamics simulations

Grid and Cloud Computing

Gromacs

Protein in water/membrane simulation

Programming language

Protein and Protein-ligand simulation

BioPerl

Ambertools

Python

Protein-ion simulation

R

Membership in international societies

1.International Society of Computational biology (ISCB)

2.The Protein Society

3.Society of Bioinformatics and Biological Sciences (SBBS)

4.Asian PGPR Society

Journal’s reviewer:

Scientific Reports, Nature

Biology, MDPI

Journal of structural Biology, Elsevier

Network Modeling Analysis in Health Informatics and Bioinformatic, Springer

Journal of Biomolecular Structure & Dynamics

Computers in Biology and Medicine

PUBLICATIONS PUBMED GOOGLE_SCHOLAR

[1].Dhusia, K., Madrid-Aliste C., Su, Z., Wu Y., (2022) EXCESP: A Structure-based Online Database for Extracellular Interactome of Cell Surface Proteins in Human link. Journal of Proteome Research 10.1021/acs.jproteome.1c00612

[2].Dhusia, K., Su, Z., Wu Y., (2021) A Structural-based Machine Learning Method to Classify Binding Affinities between TCR and peptide-MHC Complexes. Molecular Immunology. https://doi.org/10.1016/j.molimm.2021.07.020

[3]. Su Z, Dhusia K, Wu Y (2021) Coarse-grained simulations of phase separation driven by DNA and its sensor protein cGAS. Archives of Biochemistry and Biophysics. 710-109001 https://doi.org/10.1016/j.abb.2021.109001

[4].Wu Y., Dhusia K., Su Z., (2021) Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations, Integrative Biology, Apr 24; zyab006 https://doi.org/10.1093/intbio/zyab006

[5].Su Z, Dhusia K, Wu Y (2021) A Multiscale Study on the Mechanisms of Spatial Organization in Ligand-receptor Interactions on Cell Surfaces. Computational and Structural Biotechnology Journal https://doi.org/10.1016/j.csbj.2021.03.024

[6].Su Z, Dhusia K, Wu Y (2021) A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells. PLoS Computational Biology 17(3): e1008825. https://doi.org/10.1371/journal.pcbi.1008825

[7].Su, Z., Dhusia, K., Wu Y., (2021) Understanding the impacts of cellular environments on ligand binding of membrane receptors by computational simulations. J. Chem. Phys. 154, 055101 (2021); https://doi.org/10.1063/5.0035970

[8].Desmet, Nicole M., Dhusia K, Qi W, Doseff A., Bhattacharya S., and Gilad A. (2021) Bioengineering of Genetically Encoded Gene Promoter Repressed by the Flavonoid Apigenin for Constructing Intracellular Sensor for Molecular Events Biosensors 11, no. 5: 137. https://doi.org/10.3390/bios11050137

[9].Su, Z., Dhusia, K., Wu Y., (2020) Understand the Functions of Scaffold Proteins in Cell Signaling by a Mesoscopic Simulation Method. Biophysical Journal. 119 (10) 2116 – 2126 https://doi.org/10.1016/j.bpj.2020.10.002 [I.F. 3.665]

[10].Dhusia, K., Su, Z., Wu Y., (2020) Using Coarse Grained Simulations to Characterize the Mechanisms of Protein–Protein Association. Biomolecules. 15;10(7): 1056-1077. http://doi.org/10.3390/biom10071056 [I.F. 4.082]

[11].Dhusia, K., Su, Z., Wu Y., (2020) Understand the Impacts of Conformational Dynamics on the Regulation of Protein-protein Association by a Multiscale Simulation Method. Journal of Chemical Theory and Computation. http://doi.org/10.1021/acs.jctc.0c00439 [I.F. 5.011]

[12].Rizvi, Z. A., and Dhusia, K., (2019) Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea. bioRxiv https://doi.org/10.1101/724674

[13].Pandey S., Dhusia K., Katara P., Singh S., Gautam B., (2019) A comprehensive insilico analysis of deleterious SNPs and molecular dynamics simulation of disease linked mutations in gene responsible for neurodegenerative disorder. Journal of Biomolecular Structure & Dynamics 37, 1–14. doi:10.1080/07391102.2019.1682047 [I.F. 3.3]

[14].Agnihotri S, Dhusia K, Srivastav A.K., Upadhyay J., Verma V., Shukla P.K., Ramteke P.W., and Gautam B., (2019) Biochemical properties and regulation of copper-transporting ATPase in a human hepatoma cell line, J Cell Biochem. 1 19. https://doi.org/10.1002/jcb.29199 [I.F. 3.4]

[15].Dhusia, K., Yadav, P. K., Raja K. and Ramteke, P. W., (2019) Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcenses. Journal of Infection, Genetics and Evolution. (65)101-111 https://doi.org/10.1016/j.meegid.2018.11.001 [I.F. 2.5].

[16].Dhusia, K., Rizvi, Z. A., Rai, S. and Ramteke P.W., (2018) Structural and functional characterization for interaction of silver nanoparticles with ergostrol in Trichoderma harzianum. Microbial Pathogenesis. 318-324. https://doi.org/10.1016/j.micpath.2018.09.039 [I.F. 2.33]

[17].Dhusia, K., Yadav, P. K., Farmer R. and Ramteke, P. W., (2018) Inhibition of Polyamine biosynthesis for toxicity control in Serratia marcescens strain WW4 by targeting ornithine decarboxylase: A structure-based virtual screening study, International Journal of Computational Biology and Drug Design, 11(1/2), 114-134.doi 10.1504/IJCBDD.2018.090837

[18].Alka Sagar, Dhusia K, Pradeep K Shukla, Atul Singh, Rubina Lawrence, and Pramod W Ramteke, (2018) Comparative analysis of Production of Hydrogen Cyanide with Production of siderophore and phosphate solubilization activity in Plant Growth Promoting Bacteria. Vegetos 31(2):130-135, 2018 Doi:10.5958/2229-4473.2018.00064.2

[19].Sajjan B., Dhusia, K., Saxena S., et. al. (2017) Nicotinic acetylcholine receptor alpha 1(nAChRα1) subunit peptides as potential antiviral agents against rabies virus, International Journal of Biological Macromolecules, 140:180-188. doi: 10.1016/j.ijbiomac.2017.05.179. [IF: 3.671]

[20].Singh, R. Chandra, S. Dhusia, K. and Sharma, G. (2017) "Capacitating surveillance and situational awareness with measure of visual engagement using eye-tracker,"International Conference on Computing, Communication and Automation (ICCCA), 1161-1165. doi: 10.1109/CCAA.2016.7813892

[21].Dhusia, K., Kesarwani P. and Yadav, P. K. (2016) Epitope prediction for msp119 protein in Plasmodium yeolii using computational techniques. Network Modeling Analysis in Health Informatics and Bioinformatics, 5(1), 5: 19. doi 10.1007/s13721-016-0127-4 [Springer].

Book Chapters:

[1].S. Ashraf, K. Dhusia, and S. Verma, (2021) Siderophores -Mediated Iron Acquisition and Virulence of brown rot disease in Stone Fruits caused by Monilinia fructicola in Jammu & Kashmir. . In: Dhusia K., Raja K., Ramteke P. (eds) Fungal Siderophores. From Mineral-Microbe interactions to anti-pathogenicity. Fungal Biology. Springer Nature https://doi.org/10.1007/978-3-030-53077-8_4

[2].S Rai, PW Ramteke, A Sagar, K Dhusia, S.K. Kesari (2019) Diversity Assessment of Antagonistic Trichoderma Species by Comparative Analysis of Microsatellites Plant Growth Promoting Rhizobacteria (PGPR): Prospects for Sustainable Agriculture. 233-254. Springer, Singapore https://doi.org/10.1007/978-***-**-****-8_20

Book Editor:

[1].Kalyani Dhusia, Kalpana Raja, Pramod W. Ramteke (2021) Fungal Siderophores: From Mineral-Microbe interactions to anti-pathogenicity. Springer Nature. https://doi.org/10.1007/978-3-030-53077-8

Additional Experience:

I have also initiated a collaboration with Nanome Inc. to explore proteins under study at our lab under virtual reality environment. Nanome sponsored with a $399 worth oculus quest 2 headset and the work is being streamed on my YouTube channel Camarada.

•Mentor high school volunteer Mr. Sasiru Pathiranage with Wu Lab on virtual screening of nsp2 of Covid-19 project, 2021

•Founder, Kalyani Welfare Association (Non-profit) since 2021 to channelize humanitarian initiatives, facilitating revenue increase and spread scientific awareness against COVID-19 pandemic in India.

•Manager, CompBio Discussion Group an initiative by Regional Student Group-INDIA, International Society for Computational Biology. For details visit: http://rsg-india.iscbsc.org/team.html .

•Teaching assignments as a part of Ph. D. Scholar to Undergraduate and Postgraduate students at Department of Biological Sciences, 2015-2018.

•Conducted and regulated the lunch hour programming class (lhpc) for perl and R programming languages 2016-2018

Achievements:

•Talk on Inclusion of diversity in academia by Triple101 radio on June 26th 2021 available at link

•Instructor, International e-workshop on Machine learning applications in Drug discovery: basic to advanced " from May 17, 2021, to May 31, 2021 link.

•Invited, Intelligent Systems for Molecular Biology (ISMB-2018), 6th July to 10th July, 2018 in Chicago, Illinois, United States.

•Young Science Scholar, Society of Bioinformatics and Biological Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST) - Jammu, 12-13 Oct 2017.

•Scientific Visit at the Department of Plant Biology, University of Szeged, Szeged, Hungary between 7th August to 11th August, 2017.

•Visiting Researcher at the Laboratoire de Mycologie et de Phytopathologie, Institut Jules Guyot, Universite de Bourgogne, France from 25th July to 30th August, 2017.

•Attended, Intelligent Systems for Molecular Biology (ISMB-2017) to present work on “Siderophores and its drug conjugates”, 21st July to 25th July, 2017 in Prague, Czech Republic.

•Travel award by Sysmod, ISCB to attend ISMB-2017, 21st July to 25th July, 2017 in Prague, Czech Republic.

•Visiting Researcher at the University of Missouri, Columbia, USA 11th to 14th December, 2016.

•Oral Presentation in International Conference on Intelligent Biology and Medicine (ICIBM 2016) to present research work, 8th to 10th December, 2016 at Houston, Texas, USA

•Partial Travel award by Department of Biotechnology (DBT), Government of India for attending International Conference on Intelligent Biology and Medicine (ICIBM 2016) to present research work, 8th to 10th December, 2016 at Houston, Texas, USA.

•Partial Travel award by National Science Foundation (NSF) and ICIBM travel committee to present research work in International Conference on Intelligent Biology and Medicine, 8th to 10th December, 2016 at Houston, Texas, USA

•Best Oral Presentation in National Sympossium on Natural Resource Management for Sustainable Agriculture by Society of Biological Sciences and Rural Development, Nov 5th-6th 2016.

•Organizing secretory, Webinar on KALEIDOSCOPE OF COMPUTATION IN BIOLOGY (KCB2016), 20th April, 2016, Department of Biological Sciences in collaboration with RSG-ISCB India (https://www.youtube.com/watch?v=dzaLrfi_nE4).

•Selected for ICGEB Course “Bioinformatics: Computer Methods in Molecular and Systems Biology”, 23rd May to 27th May, Trieste, Italy.

•Awardee of Rajiv Gandhi National Fellowship to pursue Doctoral studies, by University Grants Commission (UGC), India.

•Member in the core committee of Regional Students Group (RSG)-India of International Society of Computational Biology(ISCB).

•Participated in ICAR Winter School training programme on: Bioinformatics and High Dimensional Genome Data Analysis, 25 Nov 2015 to 15 Dec 2015, Centre for Agricultural Bioinformatics (CABin) ICAR-IASRI, Library Avenue, Pusa, New Delhi, India.

•Selected in One-week International Field Biology Course 2015 organized by DIWPA: DIVERSITAS in the Western Pacific and Asia (under Future Earth), Nov 08-15, Mae-Klong-Thailand.

•Awarded Best volunteer Recognition in National Conference on Bioinformatics Panorama in Agriculture and Health (NCBPAH-2015), Sam Higginbottom Institute of Agriculture Technology and Sciences (Deemed to-be University), 5th-6th October, 2015.

•Graduated as First-ranking student in M. Sc. (Bioinformatics) with silver medal in March, 2015.

•Vice President, Society of Bioinformatics (SOBI) at Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, India (2013-2014).

•Elected President, Zoological Society at Ewing Christian College, Allahabad, India (2010-2011).

•Awarded First prize in Oral Presentation on “Bioinformatics & its applications”, Ewing Christian College, 2nd May, 2011.

•Awarded certificate for six months course in “Analytical techniques in chemical Analysis”, Ewing Christian College, 9th March, 2011.

•Awarded First prize for paper presentation on the topic “Environmental pollution by Anthropogenic sources”, Inter-institutional competition, 4th March, 2011.

References

Dr. Yinghao Wu

Department of Systems and Computational Biology

Albert Einstein College of Medicine

Price Center, Rm 553

1301 Morris Park Ave,

Bronx, New York, 10461

adzekg@r.postjobfree.com

Tel: +1-718-***-****

Web:http://www.einstein.yu.edu/labs/yinghao-wu/

Dr. Sudin Bhattacharya

Center for Research on Ingredient Safety, Institute for Quantitative Health Science & Engineering,

Michigan State University

Room 1313, 775 woodlot drive,

East Lansing, MI, 48824

adzekg@r.postjobfree.com

Tel : +1-517-***-****

Web:http://www.egr.msu.edu/people/profile/sbhattac

Prof. Pramod W. Ramteke

FNABS, FNAAS, FLS

Dean, Post Graduate Studies

Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad,

Uttar Pradesh 211007, India

adzekg@r.postjobfree.com,

Tel: +91-941*******

Web:http://www.nabsindia.org/profiles/ramteke.html

Contact this candidate