BCB to welcome 8 new students in Fall 2017

February 26, 2017

The Bioinformatics and Computational Biology Graduate program will welcome 8 new students in Fall 2017.  Below are five of the 8 students joining the program.  Three others who are joining are featured here.


Sharmistha Chakrabortty

Toledo, OH

BS and MS in Biochem, Genetics and in Biotech from Bangalore Univ.

M.S. in Bioinformatics, Proteomics and Genomics from the Univ of Toledo

Photo of Shamistha Chakrabortty


She is interested in genomics, transcriptomics, non-coding RNA, Epigenetics, Stem Cells, Cancer, NGS, Biomarker Research

Her itinerary during her visit to Iowa State and BCB included meetings with BCB faculty members: Walter Moss, Geetu Tuteja, Don Sakaguchi, Chris Tuggle, Steven Cannon and Roger Wise.




M.S thesis project, Fedorov Lab , University of Toledo (2016 – 2017)

--Determination of correlation between the genetic diversity (density of SNPs) and recombination rate in Human Genome using GEMA (Genome Evolution and Matrix Algorithm) computational modelling program.

--Demonstration of effect of different parameters such as recombination rate, selection pressure (measured by number of offspring per couple per generation), Dominance coefficient of genes (co-dominant, recessive, and dominant mode of genes), and distribution of mutation in natural population by their effect (deleterious, beneficial and neutral mutation) on genetic diversity.

--Demonstration of the effect of two evolutionary selective forces namely Genetic Hitchhiking and Background Selection, on genetic diversity (through linked SNPs) under different experimental conditions.


Research project on population and evolutionary genetics, Fedorov Lab (2015 - 2016)

--SNP analysis, characterization of haplotypes and populations specific data from 1000 Genomes project, and Denisovan sequencing project for determination of origin of modern human population (using Perl scripts).

--Application of machine learning algorithms for classification, clustering, and pattern searching for reconstruction of ancient human lineages (using WEKA, Rapid Miner).


Research project on ultra-conserved region and non-coding RNA, Fedorov Lab (2016-2017)

--Analysis and characterization of tissue specific expression patterns of novel ultraconserved elements in human and other model organisms, and identification of putative non-coding RNA in human genome (using public available database, phylogenetic analysis, and sequence alignment algorithm).



--Microarray and RNA-Seq data analysis

--SNP data analysis.

--Pairwise-sequence and multiple sequence alignment.

--Gene expression and pathway analysis platforms.

--Experience with biological databases (1000 Genome, SRA, etc).

--Phylogenetic analysis (MUSCLE, CLUSTALW, MEGA).

--Machine learning algorithms (dimensionality reduction, classification, clustering and decision tree based approaches).

--Parametric and non-parametric statistical tests.



--Rajib Dutta; Joseph Mainsah; Yuriy Yatskiv; Sharmistha Chakrabortty; Basil Khuder; Patrick Brennan; Shuhao Qiu; Larisa Fedorova; Alexei Fedorov, Intricacies in arrangement of SNP haplotypes suggest "Great Admixture" that created modern human, BMC Genomics (In Review).

--Siva Koganti, Carissa Clark, Jizu Zhi, Xiaofan Li, Emily Chen, Sharmistha Chakrabortty, Erik Hill, and Sumita Bhaduri-McIntosh, Cellular STAT3 functions via PCBP2 to restrain EBV lytic activation in B lymphocytes, JVI. 2015 May;89(9):5002-11. doi: 10.1128/JVI.00121-15.

--Sharmistha Chakrabortty, Sourav Bhattacharya* and Arijit Das, Optimization of process of parameters for Chitinase production by a marine isolate of Serratia marcescens, IJPBS / Volume 2 / Issue 2 / APRIL-JUNE / 2012 / 08-20.

--Correlation between genetic diversity and recombination rate in natural human populations (MS thesis project, manuscript in preparation).



--Programming languages: Perl, R, C, C++, Java.

--Operating systems: Windows, Linux.

--Database management system: Oracle.



--Cell biology: animal and microbial cell culture, Flow-cytometry.

--Model organism: Drosophila handling and maintenance, breeding experiments.

--Microscopy: RNA-FISH, fluorescent and confocal microscopy.

--Molecular biology: molecular cloning, transfection (siRNA, shRNA) PCR, qRT PCR, DNA and RNA isolation, gel electrophoresis, PAGE, Blotting techniques.


Yulu Chen

West Lafayette, IN


B.S. from China Ag Univ., Beijing, China in Forage and Grassland Science


M.S. from Purdue University, West Lafayette, IN, in Animal Science

Photo of Yulu Chen


She is interested in the transcriptome, sequencing analysis, develop statistical methods and bioinformatics methods to solve biology problem

During her visit, she met with BCB Faculty members: Julie Dickerson, Drena Dobbs, Jim Reecy, Chris Tuggle, Geetu Tuteja, Iddo Friedberg, and Karin Dorman.


Research Experience -- March 2016 – Present

Graduate Research Thesis

– Research on the effect of high fat diet on mouse mammary transcriptome during lactation.

– The objective in this study was to take advantage of using RNA-Seq and small RNA-seq high-throughput technology to provide a comprehensive transcriptome profiling of the mouse lactating mammary gland.

– Responsible for data processing and next generation sequencing (NGS) data analysis.


Graduate AGRY600 Genomics Course Project -- August 2016 – Present

– Analysis of M. roreri mitochondrial genome.

– Quality analysis and preprocessing of NGS data using FASTQC and TRIMMOMATIC, followed by K-mer size prediction and Genome Assembly to compare different assembly programs.

– Conduct transcriptome analysis: including data preprocessing, reference genome analysis, De novo transcriptome assembly, differential expression and KEGG Pathway and GO analysis.


Graduate STAT512 Applied Regression Analysis Course Project April 2016

– Worked on the effect of punishment regimes on crime rates using aggregate data on 47 states of the USA for 1960.

– Used SAS to develop a good model to analyze data collected to determine the effect of punishment regimes on crime rates.


Graduate Laboratory Research -- August 2015 – March 2016

– Investigated the role of the clock in regulation of growth and differentiation of the mammary gland. Publication resulted.  See below.


Graduate ANSC514 Animal Biotechnology Course Project -- August 2015 – December 2015

– Used Tophat, Cufflink and CummerBund to analyze and visualize the differential gene expression from the data set of

“Variation in the Ovine Abomasal Lymph Node Transcriptome between Breeds Known to Differ in Resistance to the

Gastrointestinal Nematode”.


Undergraduate Research Thesis -- August 2014 – April 2015

– Researched the selection and optimization of molecular markers for Melilotus.officinalis and M.alba.


Teaching Experience – Fall 2016

Teaching assistant for ANSC444 Dairy Management



– Co-authored publication: Casey, T*, Crodian, J, Suárez-Trujillo, A, Erickson, E, Weldon, B, Crow, K Cummings, S Chen, Y

Shamay, A, Mabjeesh, SJ and Plaut, K. 2016. CLOCK Regulates Mammary Epithelial Cell Growth and Differentiation.

American Journal of Physiology - Regulatory, Integrative and Comparative Physiology Published 5 October

2016 Vol. no., DOI: 10.1152/ajpregu.00032.2016

-- Chen, Y1., Yang, S1., Crodian, J1., Kuang, S1., Wang, J2., Gribskov, M2., Plaut, K1., and Casey, T1. Maternal high-fat diet significantly impacts milk miRNA and mRNA content of lactating mice. (in progress)




--JMP, SAS, SPSS, R, Unix commands, MS Office Suite

Biological experiment skills:

--Mammalian cell culture including routine passaging and growth curve analysis, PCR, q-PCR, ELISA, Western Blot analysis, Bradford assays; rodent handling including weighing, milking and injections.


Basil Khuder

Maumee, OH


B.A. in Psychology from the Univ. of Toledo


Certificate in Biostatistics and Epidemiology, The Univ of Toledo

M.S. in Bioinformatics/Proteomics, and Genomics from the Univ of Toledo

Photo of Basil Khuder

During his visit, Basil met with BCB faculty members: Walter Moss, Geetu Tuteja, Xiaoqiu Huang, Nicole Valenzuela, and Heike Hofmann.

Research Interests: Noncoding RNA, Genetics, Genomics and Epigenomics, Proteomics, Gene Regulation and Processing, Machine Learning and Artificial Intelligence.



Master's Thesis: Analysis of Ultra-Conserved Intronic Regions of Mammalian Fat-Mass and Obesity Gene (FTO)


  • Constructed a model to define expression levels of FTO intronic elements across multiple tissues, sequencing libraries, and species.
  • Used publicly available databases to analyze a wide variety of sequencing data including SRA, FASTQ, and SAM/BAM.
  • Created PERL Scripts to identify specific nucleotides of interest within sequencing files.



Project in Laboratory of Dr. Robert Blumenthal:  Investigation of Specific DNA-Methylation Sites.


  • Analysed RNA-Seq and WGBS data from the ENCODE project to investigate methylation sites across endodermal and ectodermal tissue.
  • Using the Genome Analysis Toolkit, SAMTools and Picard Tools, raw sequencing reads were mapped/aligned, and variant-calling was then conducted to produce VCF files.
  • Variant annotation using the Variant Effect Predictor was then completed, and variants of interest were studied further.



Intricacies in Arrangement of SNP Haplotypes Suggest "Great Admixture" That Created Modern Humans

BMC Genomics (Under Review) Authors: Rajib Dutta; Joseph Mainsah; Yuriy Yatskiv; Sharmistha Chakrabortty; Basil Khuder; Patrick Brennan; Shuhao Qiu; Larisa Fedorova; Alexei Fedorov




Founder and Lead Director, Young Data Scientists of America (www.ydsoa.org)


--YDSOA is an online collaboration of young data scientists from around the United States. Our mission is to educate, empower and connect those new to data science and those looking to get immersed in this ever-evolving field.

Zachary Lozier

Jeffersonville, IN


B.S. in Secondary Ed and Life and Physical Science Education from Indiana Univ. Southeast


Photo of Zach Lozier

He is interested in biodiversity, genetics, genomics, evolution

During his visit, Zach met with BCB faculty members: Jonathan Wendel, Robert Jernigan, Erik Vollbrecht, Crystal Lu, Matt Hufford, and Alex Travesset.


Projects and Research

Spring 2017 -- Designing an introductory level bioinformatics course for college freshmen or AP high school students. Research into this topic has just begun, with a draft due to the professor on February 23rd 2017 and the final draft due on April 1st 2017.


Spring 2015 -- I worked with a professor as a student research assistant in a study aimed at estimating the population of two variants of the peppered moth: the white and black variant and the black variant. The study wished to assess the effects the local distilleries manufacturing processes had on the surrounding forests. During this time, I placed and retrieved moth traps and assisted in determining captured specimens’ species.

Designed an experiment to determine the effects of various wavelengths of light on Alaskan snow pea plant growth. Peas were imbibed under dark conditions and grown under specified light conditions. Measurements included plant length, leaf number, and leaf color.


Fall 2014 -- I assisted in conducting an ecological survey of Bear Grass Creek Greenway in Louisville, KY. The study focused on developing an estimate of the various species of trees present in the greenway, with information on their sizes and estimations of their ages. Additional information was gathered on the various animal species residing in the greenway, although far less extensive than the information gathered about the trees. I also conducted a water quality test quantifying the presence of E. coli.


Spring 2013 -- Successfully recombined the plasmid PBR322 within Escherichia coli with the pGFPuv gene while enrolled in a genetics course at Indiana University Southeast. The project involved analyzing the DNA sequence of PBR322 in order to insert pGFPuv gene into areas of antibiotic resistance within the PBR322 plasmid. The recombined plasmid was then cloned within a colony of E. coli. After having been cloned, the recombination was tested for success by swabbing colonies onto petri dishes infused with antibiotics. Out of 10 satellite sites swabbed and transferred, 9 were successful.


Professional Experience

Spring 2017 -- Plant Physiology Supplemental Instructor, Indiana University Southeast

Reinforces topics covered by the teaching professor for a Plant Physiology course. Works closely with the teaching professor to address student needs.


Winter 2016 – Present -- DNA Sequencing Technician, Eurofins Genomics, Louisville, KY

Processes incoming shipments per laboratory protocol. Enters necessary information into order tracking system. Maps and builds 96-well plates for DNA sequencing. Prepares stock reaction mixtures.


Spring 2016 -- Student Teacher, New Albany High School

Completed 10 weeks of student teaching in a high school classroom where I was assigned to teach biology, chemistry, and physics to high school students. Work primarily consisted of planning lessons, units, designing coursework, writing quizzes and tests, and grading papers.


Spring 2015 – Fall 2015  -- Molecular Biology Supplemental Instructor, Indiana University Southeast

Reinforced topics covered by the teaching professor for a Molecular Biology course. Presented information in a variety of ways to students, gathering information from personal experience with the course as well as outside sources.


Technical Skills

I have had extensive training and education in the field of biology. I have taken courses involving lab and field work including General Biology 1 & 2, Genetics, General Chemistry, Organic Chemistry 1 & 2, Evolution, Plant Physiology, Ecology, and Entomology. I understand standard lab and field procedures, disposal protocol, and safety measures. Additionally, during my classes at Indiana University Southeast, I have acquired experience with the following equipment and techniques:


--Micropipetting (specifically with the P20 and P200)

--Primer design




--DNA extraction and purification



--Vortex mixer

--Gel electrophoresis

--Southern blotting

--DNA recombination

--Tree age estimation

--Population estimates of different species

--Water testing

--Research writing

--Python programming language

--MS Access SQL



Paul Villanueva

Costa Mesa, CA


B.S. from CA State Univ, Long Beach in Mathematics with a minor in ComS


Photo of Paul Villanueva

He is interested in genomics, machine learning but open to many research projects

BCB Faculty he met with during his visit to Iowa State include: David Fernandez-Baca, Xiaoqiu Huang, Eric Henderson, and Robert Jernigan.


Research and Teaching Experience

Researcher, California State University, Long Beach, January 2016.

Research conducted in knot theory with Dr. Ryan Blair. Created a novel definition of bridge number and used it to investigate the meridional rank conjecture and other results in the field. Used computer aided computations to investigate open problems in knot theory. Funded by the PUMP URG Grant.


Research Assistant, California State University, Long Beach, Fall, 2016.

Research conducted with Dr. Vennila Krishnan and Dr. Shadnaz Asgari. Analyzed motion capture data, EMG signals, and accelerometer readings for patterns which would enable an earlier diagnosis of, among other neurological diseases, multiple sclerosis. Assisted in data collection and signal processing. Will later assist with writing machine learning code.


Instructional Student Assistant, California State University, Long Beach, Fall, 2016.

Graded homework assignments, projects, and tests (both written and coded) for CECS 328: Data Structures and Algorithms.


Work History

Summer 2016 -- Informatics Intern, IIHR - Hydroscience and Engineering, Iowa City, Iowa.

Created a novel method of collecting stream level readings using smartphone sensors. Reviewed current stream level monitoring technologies. Researched image recognition, machine learning, and multiple view geometry techniques for possible applications to stream level monitoring. Developed a phone application to measure river gage height

for use in conjunction with Iowa Flood Information System. Gave a presentation sharing results.


2010 – 2013 Assistant General Manager, Bank of America, Westminster, CA.

Managed the day-to-day operations and long-term planning for the Westminster banking center.

Duties:  Managed a staff of ~30 associates. Interviewed, hired, and trained associates in all roles. Led weekly and daily meetings to deliver company news, refocus banking center performance, and celebrate associate success. Wrote weekly and monthly schedules to meet customer volume, labor targets, and associate availabilities. Led training sessions whenever a new product was launched or a new system was implemented. Managed banking center reserve cash supply of ~$1,000,000. Created long-term development plans for associates in all roles. Responsible for obtaining outside sales.



8/2016 -- Virtual Stream Monitoring via Crowdsourcing, IIHR Weekly meeting, Iowa City, IA                                                                                                                                                                            



2013 – Alpha Gamma Sigma Honor Society, Orange Coast College Chapter.

2015 – National Alliance for Doctoral Studies in the Mathematical Sciences.

The Alliance is an "NSF funded community of math sciences faculty and students" whose goal is to "increase the number of doctoral degrees in the mathematical sciences among groups that have been traditionally underrepresented."

2015 – American Mathematical Society.

2016 – American Geophysical Union.



Programming Languges: C++, Java, Python, SQL, MATLAB

Typesetting: LATEX

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