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Hire Dr. Swapna S.

Canada

USD 30 /hr

Bioinformatician with 10+ years of experience in sequence analysis, structural bioinformatics, genomics, transcriptomics

Profile Summary

I have >10 years’ experience in analyzing diverse biological datasets, and communicating the learnings to the community in written and presentation format, while mentoring younger students during the process, in which I have published >20 peer-reviewed publications. I have experience in analysing bulk RNAseq and single cell RNAseq data, and in the genome-wide prediction of protein-protein interaction networks and metabolic pathways. Further, I have experience in the area of structural bioinformatics i.e. in the analysis and modelling of protein structures and various aspects of sequence analysis - homology searches, multiple sequence alignments, phylogenetic analysis. My publications can be viewed at: https://www.ncbi.nlm.nih.gov/pubmed/?term=Swapna+LS%5BAuthor%5D

Subject Matter Expertise

• ★ Biochemistry
• ★ Bioinformatics

Services

• Writing
• Research
• Data & AI

Writing Technical Writing

Research Systematic Literature Review, Secondary Data Collection

Data & AI Statistical Analysis, Data Visualization

Work Experience

Postdoctoral research fellow

Hospital for Sick Children

May 2013 - April 2019

Postdoctoral research fellow

Hospital for Sick Children

May 2013 - April 2019

Education

PhD

Indian Institute of Science

August 2004 - July 2012

PhD (Molecular Biophysics)

Indian Institute of Science

July 2004 - June 2012

MSc (Biochemistry)

University of Mysore

July 2002 - May 2004

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

International Helminth Genomes Consortium(2018). Comparative genomics of the major parasitic worms . Nature genetics.

Swapna LS, Molinaro AM, Lindsay-Mosher N, Pearson BJ, Parkinson J(2018). Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation . Genome biology.

Swapna LS, Parkinson J(2017). Genomics of apicomplexan parasites . Critical reviews in biochemistry and molecular biology.

Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, et al.(2016). The genome of Onchocerca volvulus, agent of river blindness . Nature microbiology.

Joseph AP, Swapna LS, Rakesh R, Srinivasan N(2016). Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting . Journal of structural biology.

Cromar GL, Zhao A, Xiong X, Swapna LS, Loughran N, Song H, Parkinson J(2016). PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya . Database : the journal of biological databases and curation.

Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, et al.(2016). Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes . Nature communications.

Sudha G, Singh P, Swapna LS, Srinivasan N(2015). Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes . Protein science : a publication of the Protein Society.

Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, et al.(2015). Protein flexibility in the light of structural alphabets . Frontiers in molecular biosciences.

Blazejewski T, Nursimulu N, Pszenny V, Dangoudoubiyam S, Namasivayam S, Chiasson MA, Chessman K, Tonkin M, Swapna LS, Hung SS, et al.(2015). Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle . mBio.

Wetzel J, Herrmann S, Swapna LS, Prusty D, John Peter AT, Kono M, Saini S, Nellimarla S, Wong TW, Wilcke L, et al.(2014). The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite . The Journal of biological chemistry.

Swapna LS, Srinivasan N, Robertson DL, Lovell SC(2012). The origins of the evolutionary signal used to predict protein-protein interactions . BMC evolutionary biology.

Swapna LS, Mahajan S, de Brevern AG, Srinivasan N(2012). Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins . BMC structural biology.

Swapna LS, Srikeerthana K, Srinivasan N(2012). Extent of structural asymmetry in homodimeric proteins: prevalence and relevance . PloS one.

Swapna LS, Bhaskara RM, Sharma J, Srinivasan N(2012). Roles of residues in the interface of transient protein-protein complexes before complexation . Scientific reports.

Swapna LS, Rekha N, Srinivasan N(2012). Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly . Bioinformation.

Joseph AP, Agarwal G, Mahajan S, Gelly JC, Swapna LS, Offmann B, Cadet F, Bornot A, Tyagi M, Valadié H, et al.(2010). A short survey on protein blocks . Biophysical reviews.

Tyagi N, Swapna LS, Mohanty S, Agarwal G, Gowri VS, Anamika K, Priya ML, Krishnadev O, Srinivasan N(2009). Evolutionary divergence of Plasmodium falciparum: sequences, protein-protein interactions, pathways and processes . Infectious disorders drug targets.

Pantakani DV, Swapna LS, Srinivasan N, Mannan AU(2008). Spastin oligomerizes into a hexamer and the mutant spastin (E442Q) redistribute the wild-type spastin into filamentous microtubule . Journal of neurochemistry.

Krishnadev O, Rekha N, Pandit SB, Abhiman S, Mohanty S, Swapna LS, Gore S, Srinivasan N(2005). PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families . Nucleic acids research.

OTHER

L. S. Swapna, B. Offmann, N. Srinivasan Evolutionary Dynamics of Protein–Protein Interactions . Knowledge Discovery in Bioinformatics. p. 209--231. John Wiley {\&} Sons, Inc.