Posts Tagged bioinformatics

Immunotherapy, Bioinformatics, Devices: EPPICon 2017 Preview


One of the latest most talked about buzzwords in cancer treatment is “immunotherapy” where body’s immune system is used to wage a war against the cancer cells. Cancer cells divide rapidly than ordinary cells and manage to evade the immune system. The focus of a range of immunotherapies is to put body’s immune system on high alert so it can easily locate and destroy cancer cells.

Image result for immunotherapy, bioinformaticsThis year, EPPICon (annual flagship conference at eppicglobal at will focus on Immunotherapy, Bioinformatics, and Devices. Another recent buzzword, “bioinformatics” focuses on harnessing technological advances for management and analysis of data, for cancer immunology and immunotherapy.  The hope is that more reliable and comprehensive picture can emerge of tumor genomics landscape and that can point a way towards more effective personalized medicine.

Immunotherapy often involves delivery of a cocktail of immune drugs to awaken the body’s immune system and put it in a “ready” mode to get rid of the cancer cells. Implantable devices can be used to provide regular dosages of medication for several days or everyday for a few weeks and can be used to make localized delivery.  This convergence of technologies makes it an interesting time for treatment of cancer and other diseases.  

EPPICon, EPPIC’s all day conference will be held on Saturday, March, 25th at Crowne Plaza, Burlingame, CA and has a fabulous lineup of keynotes, speakers, and panels.

Image result for Ira Mellman, genentechMorning keynote, Ira Mellman is VP of Cancer Immunology at Genentech and has an illustrious career in solving most profound health problems with strong research, grounded in science.  He spent 20 years at Yale University School of Medicine, prior to joining Genentech in 2007.  After the keynote, the conference program will continue with excellent speakers and panels with a special speed pitch session thrown in, where startups looking for funding will have an opportunity to pitch to a panel of investors and receive critical feedback, in real time. At the end of the day, 2017 “EPPIC Eleven” awards will be given out to chosen startups, from around the globe.

To register for the conference, please go to .

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JOBS – December, 2013

For the opportunities below, please send resume at wd_darshana at hotmail dot com.  Please indicate in the email how closely the job description matches your background and identify gaps, if any.  Also, indicate your current compensation and compensation expectations.  Please note: All below opportunities require several years of industry experience and are only for local candidates, with valid US work visa (when need arises for applicants with other types of visas, I will mention that).  Also note, opportunities at the top are hot and the ones lower down may be at various stages of being filled or not burning needs.  I am awaiting more job descriptions and will keep adding.   Leads appreciated.

ios/ Android Developers – Bay Area, CA
Immediate need for health-IT company.

Senior and Junior Bioinformatics Scientists – San Ramon, CA

An organization near San Ramon, CA, dedicated to leveraging a range of transformational digital medical technologies in medical imaging and information technologies, medical diagnostics, patient monitoring, disease research, drug discovery & biopharmaceutical manufacturing technologies, has an immediate openings for Bioinformatics Scientists at Senior and Junior level.  Below description is for senior role.

Responsibilities: Bioinformatics developer will work with scientists & engineers for development of systems software within medical diagnostics. The position may also develop distributed software application for subsystems that enable the business strategic imperatives.  Essential functions: Develop robust bioinformatics software solutions to support company’s medical diagnostic activities; Work closely with systems teams in requirements gathering & software design; Interact with global teams to promote consistency & maximize synergies across common software platforms; Design & build strong testing infrastructure to minimize dependency on hardware availability; Leverage DFR for software, Agile & Lean software development methodologies to drive reliability upstream into the product development life cycle.

Requirements: MS or Ph.D. in Bioinformatics or Molecular Biology with a minor in Computer Science, Statistics or Computational Biology; 5+ years experience in combining knowledge of chemistry, physics, and/or biology with software engineering; 3+ years experience in programming using Pearl and/or Python; 2+ years experience with SQL, preferably MySQL; 2+ years experience with statistical programming (e.g. R, MATLAB).

Regulatory Affairs Director – Mount Laurel, NJ, & Orangeburg, New York (and another similar opening in Bay Area, CA)
(mention location preference when sending in the CV)

There is an immediate opening for Regulatory Affairs Director in a medical device company with innovative treatment of chronic heart failure built around CCM technology.  RA Director Will be responsible for RA and for Quality systems.

Responsibilities: Domestic & international submissions & approvals for all new & existing products; Assuring compliance with domestic & international quality and regulatory requirements; Assistance with design & implementation of clinical trials to support new & existing products; Represent company with FDA, Notified Body &  international regulatory agencies regarding company’s regulatory strategies & submissions; Determine strategy, content & structure of domestic & international regulatory filings & quality assurance strategies; Maintain quality system & current product documentation & labeling in compliance with new standards, directives & requirements; Assist in design & implementation of clinical studies in support of new & existing products.  Act as liaison with clinical function; Represent the company with all domestic & international regulatory agencies including all verbal & written communication to & from the company; make all final decisions regarding all Quality System related activities; Review all product complaints & ensure timely reporting of those events to domestic & international regulatory agencies as necessary; Review & revise quality system documentations; Schedule, ensure completion of, manage & respond to all audits; Ensure training of employees on Quality Systems Regulation & key international regulations & standards; Manage the program for handling product returns, returned product evaluations (repair/rework, where applicable), complaints & customer feedback in accordance with internal policies and procedures; Maintain ISO 13485:2012 facility registration in accordance with applicable standards; Participate in product development teams on behalf of Regulatory & Quality Systems; Ensure that the Quality Systems function is carried out in accordance with GMP & ISO directives; Prepare &  submit regulatory submissions to obtain approval to conduct domestic & international clinical investigations & to seek regulatory approval to commercialize new & existing devices & their accessories.

Requirements: Bachelor in science / engineering with at least 5 years’ experience in Regulatory/Clinical/Quality area or related experience; Regulatory/Clinical/Quality experience with Class 3 medical device; Regulatory experience in the Implantable field – highly preferable; Excellent working knowledge of domestic & international requirements, regulations & standards applicable to medical electrical devices – highly desirable; Proven experience with at least one complete medical device submission to a EU Notified body and the US FDA involving a device subject to the 60601-1 3rd edition standard; Thorough understanding of the MDD (Medical Device Directive); Previous direct interaction with the FDA & an EU Notified Body; Excellent working understanding of requirements & implementation of Quality Systems compliant with US & international requirements for medical device manufacturers; Previous experience assuring that the Quality Systems function is carried out in accordance with GMP & ISO directives; Ability to analyze & perform commercial risk management in the context of regulatory & quality requirements.

Director of Quality Assurance – Palo Alto, CA

Details to follow.

Senior Manager/ Director of Mechanical Engineering – San Jose, CA

There is an immediate opening for hands-on Director of R&D Mechanical Engineering in an early stage company developing a novel approach for the oral delivery of large drug molecules.  This position will be responsible for building the team and effectively leading multi-project R&D efforts of the organization through technical expertise, interpersonal skills & a clear vision for execution.  Stock options and cutting edge technology makes it highly attractive opportunity for the right candidate.

Responsibilities: Manage resources to accomplish multi-project product research & development; Provide Mechanical Engineering support to meet R&D objectives; Remain current on developments in field(s) of expertise and industry trends; Actively pursue development of corporate IP; Identify future product opportunities; Develop plans & analyses for execution and review with leadership team; Maintain & update appropriate controlled documentation; Mentor junior staff members.

Skills & Experience: Demonstrated leadership of technical teams in medical device field; aptitude for & mastery of Mechanical Engineering principles; problem solving skills in a multidisciplinary environment; Proficient with statistical analysis for engineering and manufacturing; ability to work closely with team members across engineering & non-engineering disciplines such as biochemistry, physiology, pharmacology & chemistry; Knowledge of plastic manufacturing processes including injection molding, thermoforming, casting, machining, extrusion etc.; Knowledge of metals & alloys used in medical devices and processing techniques such as brazing, laser welding & cutting, electropolishing, electroplating, machining etc.; Deep experience in polymer processing, catheter design & fabrication, including knowledge of polymer joining, fusing, die cutting, adhesives etc.; Knowledge of biomaterials & coatings suitable for implantation; Knowledge of packaging & sterilization techniques; ability to interface effectively with professionals in the medical and biological sciences; knowledge of sound design principles, regulatory requirements, and product and process validation procedures; proficiency with computer aided design software & hardware. Formal training on systems & software is desired.

Also required: Bachelor’s degree or higher in Mechanical Engineering; 10+ years experience in engineering and product development with demonstrated capability & thorough understanding of the medical device product development process; Three years minimum direct personnel management & related project leadership experience; ability to map task interdependencies, multi-task, prioritize such tasks, meet deadlines & develop, monitor and live within budgets as well as ability to forecast major milestones. Must be skilled at delegation, follow-up, and team building.

Director Quality Engineering – San Jose, CA

There is an exciting opportunity for Director Quality Engineering with strong capability and experience developing quality innovative medical devices.  This position is responsible for effectively leading multi-project quality engineering efforts of the organization through technical expertise, interpersonal skills and a clear vision for execution.

Responsibilities: Manage resources to accomplish multi-project product research, development and manufacturing; Contribute to strategy and management of GMP/GLP operation; Provide Quality Engineering support as necessary to meet organizational objectives; Maintain quality management systems necessary for development, including clinical evaluation; Develop quality plans and data analyses for execution and review with leadership team; Develop test strategies DOEs and test protocols to test developmental medical devices and manufacturing processes; Work with R & D and Operations to establish quality requirements at all phases of product/process development and manufacturing; Design, schedule, and if necessary, performs specific testing for existing and new products including supporting design and process validations, qualifications and first article inspections; Conducts supplier evaluations including supplier audits; Ensure that appropriate level of quality/reliability in purchased components is specified; Identify product/process problems and ensure appropriate corrective actions are taken and verified to be effective in eliminating problem; Remain current on developments in field(s) of expertise and industry trends; Mentor junior staff members

Skills Required: Demonstrated leadership of technical teams in medical device field; Demonstrated aptitude for and mastery of Quality Engineering principles; Demonstrated problem solving skills in a multidisciplinary environment; Exemplary analytical, organizational, written and oral communication skills; Proficient with statistical analysis for engineering and manufacturing; Strong ability to operate independently and as a team member; Teamwork: ability to work closely and effectively with team members and colleagues across engineering as well as non-engineering disciplines such as biochemistry, physiology, pharmacology and chemistry; Knowledge of implantable medical device design control and manufacturing processes ; Deep experience in safety standards for a variety of medical device types; Knowledge of biocompatibility, packaging and sterilization quality assurance; Demonstrated ability to interface effectively with professionals in the medical and biological sciences; Demonstrated knowledge of sound design principles, regulatory requirements, and product and process validation procedures; Demonstrated proficiency with computer aided design software and hardware familiarity. Formal training on systems and software is desired.

Also required: Bachelor’s degree or higher in Engineering; Ten years minimum experience in medical device engineering (Quality, R&D and Manufacturing) with demonstrated capability and thorough understanding of quality management; Three years minimum direct personnel management and related leadership experience; ASQ Certified Quality Engineer certification preferred; Must have experience in GMP electro-mechanical product design and manufacturing; Requires highly developed leadership skills and experience, including the ability to map task interdependencies, multi-task, prioritize such tasks, meet deadlines, and develop, monitor and live within budgets as well as the demonstrated ability to forecast major milestones.  Must be skilled at delegation, follow-up, and team building.

Patent Attorney – Sunnyvale, CA

Innovative medical device company with a broad line of product portfolio, has an opening for Senior Patent Attorney for VP level position.  Must have 15+ years of medical device and biotech patent prosecution experience in a law firm.

Research Engineer – San Francisco, CA

A company that has developed advanced consumer health sensing technology, has an immediate opening for research engineer.  Responsibilities include, research and implement cutting edge physiological sensors and algorithms and work closely with research and device teams to integrate research into company’s consumer product portfolio.

Requirements: MS or PhD in biomedical engineering, electrical engineering, or related discipline; Minimum of 2-4 years (or academic equivalent) experience in physiological data collection, interpretation and analysis; Proficient in common signal processing techniques including time series analysis, adaptive filters, and noise cancellation; Demonstrated ability in a scientific computing language (e.g. Python, R, Matlab).
Also preferred: Experience developing algorithms for  physiological signals such as heart rate, temperature, perspiration or body motion accelerometry; Proficiency with machine learning and statistical modeling; Experience with data handling and storage, e.g. NoSQL database systems

Software Developers – SF Bay Area (contract, part-time)

Big data and machines are revolutionizing the way we operate. A software company that provides innovative, modular, scalable and world class solutions, in this industrial-internet paradigm, by leveraging state of the art sensor technologies, cloud computing, big data analytics, and complex event processing, is now scaling in pre-funding stage. Some of the clients include Cisco Systems, Applied Mateirals, Huawei, Agilent, HP, Foxconn, Fletronics, and Sanmina that are using this software to transform their engineering and manufacturing operations. The company is expanding core engineering and product development team and looking for high caliber, senior software developers, with interest in working with cutting edge technologies in a high energy entrepreneurial environment.

Responsibilities include: Being involved in all stages of SDLC including analysis, design, implementation, testing, documentation, and release; Participate in multiple projects with changing requirements; and Maintain contact with clients/ partners to provide solution support and updates.

Requirements include: 4-6 years of software development experience; Software Development experience; ASP.NET with MVC, JQuery; Comfortable in data modeling, developing stored procedures, and triggers; and Readiness to learn new technologies quickly. Windows Workflow Communication Foundation 4.0; Biztalk RFID server skills; Windows Mobile Development experience; and Exposure to Windows Azure.

The position is located in the San Francisco Bay Area. Telecommute is okay but may need to attend client team meetings. Duration: 6-12 months to full-time. Terms: 1099, corp-to-corp, contract-to-hire, no visa sponsorships but OPT visa may be ok. Pay: rate negotiable. Open to considering excellent part-time candidates.


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CellWorks & BioImagene – Successfully bringing IT innovation to Life Sciences

With technology advancement and ability for wider application, interesting things are happening on the boundaries of disciplines, rather than within a given discipline.  Internet and Sofware technology advancement along with fresh “can do” attitude, has infused new energy into Biotech.  CellWorks and BioImagene are two examples, where software stalwarts and serial entrepreneurs like Pradeep Fernandes and Mohan Uttarwar brought innovation to be applied to the healthcare industry.

At event on August 5, 2013, Fernandes and Uttarwar discussed what motivated them to gravitate towards life sciences, after a career in IT and software, the opportunities and challenges in making this transition, and the lessons learned in the process.  They both said, their ignorance about regulatory challenges was a bliss because had they been previously aware of the regulatory hurdles, they might have doubted the whole enterprise.  Both of them encountered a problem in healthcare and realized there was a hole in the market, in addressing the problem.

Fernandes’s wife got thyroid cancer and while making the rounds of the hospitals and doctors, they came to realize that despite existence of huge amount of big data and large quantities of freely available published data, few people were connecting the dots for efficient diagnosis and treatment. Serendipitous discussions with his good friend and colleague (an engineer) and his wife, a PhD in biology, led them to investigate whether modeling can be used to connect the dots and predict biological effects computationally, bridging two disciplines. R&D costs in big pharma are skyrocketing and it costs about $1to $4 B per drug, before it is available for commercial use.  During the development stage, 40% of drugs fail due to lack of efficiency (that is, they simply do not work), and other 40% fail due to toxicity (bad side effects), said Fernandes.  In the long chain of drug development, Fernandes focused on Biology.  “If the biology is wrong, no amount of chemistry is going to make it safe or potent”, said Fernandes.  The challenge is that despite technology advancement, drug development process remains unchanged and key decisions regarding validation of drugs happen very late in clinical trials.   Bringing the advancement in computational algorithms and informatics, his company, CellWorks extracts information from large data sets and also predicts information through abstraction modeling and simulation.  With an ability to model how pathways interact to represent disease phenotypes, CellWorks has further refined their approach to design therapies with novel mechanism of actions.  Greatly reduced cost and time for drug development has enabled CellWorks to advance their lead candidates for several indications from early design stage to validated animal efficacy studies in very short time period.  CellWorks closed $10M Series B round, at the end of 2012.

Origins of Mohan Uttarwar’s company BioImagene also lie in his keen notice of a problem in the market place that was not addressed.  One of the close family friends had cancer and in accompanying the individual to the medical facilities, he noticed that the medical establishment used glass slides to analyze, store, and share critical information.  This made it costly and challenging to share tissue samples and other information, critical for timely and effective diagnosis and to discuss treatment options.  BioImagene addressed the need by creating a suite of dynamic, image-based technologies that enable image capture, information management, image analysis and virtual sharing of patients’ tissue samples from glass microscope slides.  Their unique software, iScan, enabled viewing, analysis, and managing of tissue images, using a computer.  Emphasizing the need to adapt and change, Uttarwar said, the pivotal moment in the history of the company was when they made the decision to go into hardware.  They built a unique image viewing input device called the iSlide, and a high performance workstation called Crescendo.  Together their products greatly improved workflow efficiency in image archiving and retrieval, remote viewing, and turnaround time and made them an attractive target and the company was acquired for $100M by Roche, in August, 2010.

Both Uttarwar and Fernandes credited their team and EPPIC for their success.  EPPIC was started with a vision to promote networking, entrepreneurship, and mentoring for life science professionals, by a handful of people of Indian origin and has since vastly expanded.  Uttarwar and Fernandes shared about how they received significant coaching and guidance from prominent EPPIC members and veterans like Nagesh Mhatre, at critical periods.  Additionally, through EPPIC, they connected with Artiman Ventures and received funding as well.  With such a strong community to support and energize, “if I can do it, you can do it”, said Uttarwar.  Mohan Uttarwar is the guest speaker on October, 29 at event, in Sunnyvale, and will be speaking about one of his new ventures.   These are free events and all are welcome.

Please note down following dates (September, 18 and October, 26) for upcoming EPPIC events and register at

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Bits, Bytes and Biology: A new paradigm for designing therapies

Pradeep Fernades, co-founder and President of Cellworks Group (, discussed new derisked and innovative approach to developing therapies with enhanced probability of success at .


This new approach based on integrating biology and computing, enables a new paradigm that dramatically can reduce spending for developing new therapies.  Currently $100B is spent globally, each year for pharmaceutical R&D.  The cost for development of each new drug is estimated to be between $1 to $4B, depending on how the math is done.  While published research and data is exploding, the overload of information makes it increasingly challenging to meaningfully use the information.  The pharmaceutical industry is pouring more and more money into the R&D and increasingly has lesser probability of success.  Problem is that despite the technology advancement, the drug development process remains fundamentally unchanged and drug development is validated very late in clinical trials.  Real understanding of drugs is only possible during clinicals and even then the underlying mechanism of action if frequently unclear.


Informatics can bridge the gap and improve the outcomes, both better consumer oriented information that include monitoring of patient, drug, and trends as well as development oriented information that includes information about genomics, proteomics, biology etc.  Cellworks Group is focused on development oriented informatics, which have traditionally been aimed at leveraging information technology and software algorithms to help manage large data sets, extract information from large data sets, and allow visualization of data.  Their engineering model further goes from analyzing and extracting information to predicting information through abstraction modeling, simulation, and synthesis.  This is contrary to traditional model where biologist begins at the lab, puts the drug in and if there is expected effect, then the initial hypothesis is confirmed which does not frequently happen.  In this model, based on mathematical modeling, equation at each interaction within the cell, is analyzed and understood.  This is a predictive computational disease model based on integrating insights of thousands of scientists, research data, experimental protocols, and clinical trends, that is mathematically observed at cellular level.  Fernandes shared several ongoing collaborations and validations in oncology, rheumatoid arthritis, and anti-infection that are under way.


Essentially this is a process for finding innovative new therapies that begins with very explicit assumptions. It is based on leveraging functional representation of biology using mathematics.  Relationship of each interaction is represented using differential equations.  It emulates human disease physiology computationally and integrates it with understanding biological efficacy and toxicity.  The process enables prediction of clinical outcomes as well as novel non-obvious insights and is many times speedier than wet approaches.  It is about time that these new approaches be explored so that drug development process goes through an overhaul rather than small, incremental enhancements to make it more cost-effective.

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