New BCB Students - Fall 2016

Page

Ten Students will Join BCB in Fall 2016

We are glad to welcome the following students to BCB this fall:

Sagnik Banerjee

Sagnik Banerjee

sagnik@iastate.edu

Alpine Manor Apartments

1209 North Dakota Ave. 
Ames, IA 50014 
Phone: (515) 268-1559 
Fax: (515) 268-8933
alpine.apts.ames@gmail.com

I am currently employed as an assistant professor in Institute of Engineering & Management, Kolkata, India. I completed my Masters in Engineering in 2014 and since then I have been associated with research and teaching.

 

I was born on 15th April 1990 in Kolkata. I graduated from Bharatiya Vidya Bhavan and joined the Institute of Engineering & Management (IEM) in 2008 to realize my dream of becoming a Computer Science Engineer. After finishing my BTech from IEM, in 2012, I joined the prestigious Jadavpur University to pursue my Masters in Engineering.

 

In the latter half of 2014 I got the opportunity to work as a researcher in CMATER labs at Jadavpur University. During this time I extended on my research conducted during my masters. From the beginning of 2015 I have been actively involved in teaching as well. During this time I have also presented my research at three conferences in India.

 

My first breakthrough came when I was given the responsibility to guide students pursue research at IEM. The institute boasts of hosting an international conference at Vancouver, Canada on 15th Oct 2015. As a mentor I took the charge of channelizing the talents of students and pave their career in active research. Being the Program chair of the said conference I also reviewed a myriad of research papers.

 

As a person I am very approachable and very friendly with my students whose company I utterly enjoy. In free time I love listening to music. I am an avid admirer of Rabindrasangeet which happens to be one of the most celebrated genres of Indian music.

Ian Braun

 

I’m twenty-two years old and completed my BS in Biochemistry at North Central College in Naperville, IL. Upper-level courses that I took for this degree included Biochemistry, Microbiology, and Molecular Biology topics. In addition to majoring in Biochemistry, I also minored in Computer Science and Bioinformatics, learning how to program in Java and Python, and taking courses on algorithms, data structures, and discrete math. I worked as a software engineering intern at Informatica in Naperville, IL for one summer, working primarily in Java.

Additionally, I participated in an undergraduate summer research program in the department of Microbiology and Immunology at Loyola University in Maywood, IL, working with Dr. Richard Schultz. We investigated the regulatory role of isomerization of a linker-region proline in the E. coli transcription factor RcsB.

As a separate research project, I also completed an honors thesis at North Central College working with Dr. Caroline St. Clair and Dr. Jonathan Visick. My aim for this thesis was to create a computational method for predicting proteins’ susceptibility to isoaspartyl formation given only their amino-acid sequence. My work on this project consisted of collecting a training set of proteins in which isoaspartyl formation has been experimentally observed, and developing an algorithm to predict susceptibility of new proteins based off these data.

Ames Address:

1201 Florida Ave, Ames, IA 50014

Alvin Chon

In college I was fascinated when I heard about the Human Genome Project. What intrigued me is the fact that we are trying to understand ourselves and nature through identifying
our genetic code, 3 billion bases, by assembling short sequences. The question is why did this impact me so much, but truthfully the answer is simple: understanding ourselves through computation. The more and more I read about the Human Genome Project, the challenges, future promises, and the field it ushered in, I knew this is it. I switched my major to Bioinformatics and after graduation took a job in Neuroscience to understand how our brain works. I haven’t looked back and in 2006, I became fascinated with the problem of Non Invasive Prenatal Diagnostics (NIPD ).

At the beginning I focused mostly on NIPD and Genomics as I worked in industry. Early on I realized that I didn’t have enough knowledge and skills to solve these problems computationally. Thus, I went back for a MS while working at precursors and an eventual startup, Diagnomics. While I was overzealous to do both at the same time, the most valuable takeaway is actually not an algorithm, but the ability to model complex biological problems of disparate data in a mathematical manner that lends themselves to be solved computationally. Thus, in 2014 after nearly a decade long endeavor trying to solve the associated challenges, I completed a full NIPT solution at EoneDiagnomics, a joint venture between Diagnomics and Eone (clinical lab testing company in South Korea). This solution incorporated state of the art lab techniques, protocols, and a custom informatics solution along with reporting. EoneDiagnomics now offers a NICE test in the cloud through the USA with Bioinformatics CLIA approval.

Interests
● Models → Probability Models especially for Biological problems
● Statistical Modeling and Inference
● Algorithms
● Programming
● Big Data
● Machine Learning
● Bioinformatics
● Genomics
● Next Generation Sequencing Technologies, Applications, Tools
● Personalized Medicine

 

Avani Khadilkar

509 N Hyland, Ames Iowa

 avani2311@gmail.com23rd November 1992

 

Education

2013 – 2015 Master of Science in Bioinformatics; University of Pune,

2010 – 2013 Bachelor of Science in Biotechnology; University of Pune,

 

Professional Experience

January 2016 – March 2016

Project Trainee at Bioinformatics Centre, University of Pune

Description: Research Project employing the use of molecular modeling, simulations and docking.

 

June 2015 – August 2015

Project Trainee at Persistent Systems Limited, Pune

Description: Worked in the quality assurance team for a bioinformatics software of a major life-science organization. Handled the domain related data analysis and testing. Also worked on improving the application with respect to usability for domain sector.

 

Master’s Thesis Research Project

Title: QM/MM studies of GFP-like chromophore in RNA environment and use of Genetic Algorithms to simplify large molecular systems

Conducted at CSIR National Chemical Laboratory, Pune

Description: This project required the basic knowledge of quantum mechanics and molecular mechanics concepts. The QChem software was used for the theoretical calculations. Also, as a spin-off from this project, genetic algorithm, a machine learning algorithm, for 1D and 2D Ising Models in Python was developed. Genetic Algorithm is a search heuristic that is inspired from the concepts of natural selection and evolution. Hence, concepts from Machine Learning were also put to use.

 

Bachelor’s Thesis Research Project

Title: Bioremediation approach for hydrocarbon degradation using bacterial isolates – its quantification and effect of isolates and consortium on seed germination and PGP (Plant Growth Promotion)

Conducted at MES Abasaheb Garware College, Pune affiliated to University of Pune

Description: The project required a fair knowledge of microbiological as well as molecular biology techniques. Also, it proved to be a major learning step with respect to development of ethical and logical research approaches.

 

Awards and Fellowships

 

  • Department of Biotechnology (DBT) Fellowship, Granted by University of Pune.
  • G.N. Ramachandran (GNR) Fellowship, Granted by DBT, Government of India.

 

Wet lab skills

  • Spectrophotometry, Colorimetry, Electrophoresis, Chromatography
  • Molecular Biology Techniques
  • Microbiological Techniques
  • Tissue Culture Techniques

Dry lab skills

Bioinformatics skills:

  • Databases: Nucleotide, Protein structure and sequence
  • Sequence analysis methods & tools: Sequence databases retrieval, sequence alignment, protein function prediction and annotation, BLAST suite, FASTA, ClustalW, gene finding & prediction Tools, T cell and B cell epitope prediction tools.
  • Structure analysis & tools: Protein structure prediction, Homology modeling, MODELLER
  • Visualization Tools: SwissPDB Viewer, Rasmol, Pymol, Accelrys (Discovery studio), VMD

Computer Science Skills:

  • Operating Systems: Windows, Linux
  • Programming Languages: Perl, C, Java, R, Python
  • Database Technologies: MySQL
  • Web Technologies: HTML

 

Ambuj Kumar's Biography and Photo are here:  Kumar,Ambuj-Bio.pdf

 

Devin Molnau

 

Education

University of St. Thomas, St. Paul, Minnesota                                                                                                        Graduation: May 2015

Bachelor of Science, Biochemistry with an English Minor

Honors and Awards: Magna Cum Laude, Dean’s list: Spring 2011-Spring 2015, Omicron Delta Kappa Honor Society member

Coursework included Biochemistry, Bioinformatics, Organic Chemistry, Physical Chemistry: Thermodynamics, Quantitative analysis, Statistics, Calculus, Physics, Neurobiology, and Genetics. Taking Introduction to Computer Science and Programming as well as Introduction to Algorithms through MIT OpenCourseWare (Spring 2016). 

GRE scores: Verbal Reasoning 160, Quantitative Reasoning 150, Writing 3.5.

 

Research Experience

University of St. Thomas, Research Assistant, St. Paul, MN                                                                                                    Summer 2013, 2014

  • Collaborated with Dr. Justin Donato to research the mechanism of the Tri1 protein in triclosan resistance
  • Cloned the tri1 and mutant tri1 K244A gene into pET-28b vector
  • Cultured and then purified Tri1 and Tri1 K244A proteins
  • Ran and analyzed kinetic tests of Tri1 and mutant Tri1 K244A proteins

 

Publications

Fischer, T.L., White, R.J., Mares, K. F. K., Molnau, D. E., and Donato, J.D. (In Press).ucFabV requires functional reductase activity to confer reduced triclosan susceptibility in E. coli. The Journal of Molecular Microbiology and Biotechnology

 

Presentations

Molnau, D.E., Lemma, E., Anderson, K., Sophy, T., and Ditty, J. Annotation of the Cytosolic Chemotaxis and Flagellar Motor Switch Proteins in the Methylobacterium extorquens AM1 Genome. Poster presented at the University of St. Thomas Biology Department Spring Poster Session, May 2015. St. Paul, MN.

Molnau, D.E., Donato, J.J. Characterization of the Function of Non-Enoyl Reductases in Triclosan Resistance. Poster presented at the University of St. Thomas Chemistry Department summer poster session, August 2014. St. Paul, MN.

Molnau, D.E. Fischer, T.L., Mares, K. F. K., and Donato, J.D. Exploring the Function of the Novel Tri1 Enzyme in Triclosan Resistance. Poster presented at the University of St. Thomas Chemistry Department summer poster session, August 2013. St. Paul, MN.

 

Skills

DNA isolation, Molecular cloning, Gel electrophoresis, SDS-PAGE, Restriction digest, Ligation, Restriction Mapping, PCR, Spectrophotometry, Western Blot, Affinity  chromatography, Thin Layer chromatography, Immunoprecipitation, Spectroscopy, Extractions, pH meter, Titration, Distillation, Calibration, Cell Culture, DNA sequencing, Kinetic Assays, Enzyme Activity Analysis, Hazardous chemicals use and disposal, Plasmid prep, Transforming E. coli, PCR mutagenesis, Isolating colonies, Screening, Preparing media and buffer, Autoclaving, Microsoft Windows, Igor, Bioinformatics, and Scientific Writing

 

Other Work Experience

Metropolitan Dermatology and Cutaneous Surgery, Medical Record Supervisor, Wayzata, MN                                May 2015-October 2015

  • Acted as a project supervisor to train and manage a team to copy and send medical records to desired location
  • Led the team in moving all active charts into long term storage as well as recording them for a closing medical practice within an extremely limited time frame.
  • Located, organized, and prepped patient files prior to appointments for each doctor daily
  • Made reminder calls to patients two days prior to appointment

University of St. Thomas: Disability services, Scribe, St. Paul, MN                                                    February 2012-December 2014

  • Read and recorded tests, essays, and quizzes of students with disabilities
  • Delivered confidential documents from Disability services directly to professors
  • Scanned and uploaded textbooks for students using the program Kurzweil

 

 

Teaching Experience

University of St. Thomas, Teaching assistant, St. Paul, MN                                                                                                 February 2015- May 2015

  • Assisted in the teaching lab for the course CHEM109, General Chemistry for Engineers

 

Writing Experience

Domestic Abuse Project, Volunteer, Minneapolis, MN                                                                                              February 2014 -May 2014

  • Wrote a professional profile for the men’s supervisor of the Domestic Abuse Project (DAP)
  • Wrote a short inspirational story based on an interview with the men’s supervisor

University of St. Thomas, Blog Writer, St. Paul MN                                                                                                            August 2014-May 2015

  • Wrote severalshort articles about enzymes of interest for the University of St. Thomas Biochemistry page

 

Volunteer Experience

N.C. Little Hospice, Floor volunteer, Edina, MN                                                                                                           June 2014-present 

Children’s Hospitals and Clinics of Minnesota, Floor volunteer, St. Paul, MN                                                      May 2014- December 2014

Metropolitan Dermatology and Cutaneous Surgery, Volunteer, Wayzata, MN                                                              June 2014- August 2014

 

Interests

  • I thrive on new experiences and have recently picked up competitive sailing. As a member of a of a 3 person sailing team, we won the Wayzata yacht club’s 50th anniversary fall regatta for the MORC III fleet.
  • I have trained in three martial arts and acquired my black belt in an American Tae Kwon Do form in 2011.
  • I have a deep love of cooking and go into N.C. Little Hospice to prepare meals and bake every other Saturday morning.
  • In my free time, I fence, cook, draw, read, or volunteer.