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Product Description
During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It is a valuable resource for statisticians and anyone interested in data mining in science or industry. The book’s coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting—the first comprehensive treatment of this topic in any book.
This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression & path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on methods for “wide” data (p bigger than n), including multiple testing and false discovery rates.
Trevor Hastie, Robert Tibshirani, and Jerome Friedman are professors of statistics at Stanford University. They are prominent researchers in this area: Hastie and Tibshirani developed generalized additive models and wrote a popular book of that title. Hastie co-developed much of the statistical modeling software and environment in R/S-PLUS and invented principal curves and surfaces. Tibshirani proposed the lasso and is co-author of the very successful An Introduction to the Bootstrap. Friedman is the co-inventor of many data-mining tools including CART, MARS, projection pursuit and gradient boosting.
About the Author
Trevor Hastie, Robert Tibshirani, and Jerome Friedman are professors of statistics at Stanford University. They are prominent researchers in this area: Hastie and Tibshirani developed generalized additive models and wrote a popular book of that title. Hastie co-developed much of the statistical modeling software and environment in R/S-PLUS and invented principal curves and surfaces. Tibshirani proposed the lasso and is co-author of the very successful An Introduction to the Bootstrap. Friedman is the co-inventor of many data-mining tools including CART, MARS, projection pursuit and gradient boosting.
Bioinformatics Scientist
Job #09-035
The Institute for Systems Biology (ISB) is an internationally renowned non-profit research institute dedicated to the study and application of systems biology. Founded in 2000 in Seattle, Washington, ISB’s goal is to unravel the mysteries of cellular networks and identify strategies that will usher in a new era of P4 Medicine (predictive, preventive, participatory and personalized medicine).
ISB is seeking a bioinformatics scientist for a multi-institution project which aims to uncover the mechanisms underlying AIDS vaccine immunogenicity. This project, funded by the Bill and Melinda Gates Foundation, employs systems biology and gene expression microarray approaches to identify novel genes and pathways which, when activated, lead to enhanced vaccine-induced immune responses.
This individual will be responsible for analyzing gene expression microarray and immunological datasets collected by our collaborators for human and NHP responses to model vaccines. A primary focus will be integrating the microarray data with the immunological measurements (such as percentage of antigen-specific responding CD8+ T-cells) to identify gene expression signatures for enhanced immune responses. Additional efforts will focus on identifying gene expression signatures that are consistent across vaccine models and experimental model systems, and interpreting the biological significance of the signatures.
The individual will be expected to perform analysis in a transparent manner and to clearly communicate analysis results to collaborating scientists. The individual will also be expected to develop tools and facilities to make data and analysis results easily accessible to other scientists. Finally, the individual is expected to take an active interest in the biology and to interpret analysis results in a biological context. While a strong background in Immunology is not required for this position, enthusiasm and interest in Immunology is required. We are seeking an individual who will independently dive into the biological literature to gain then necessary background knowledge as needed for the project.
Applicants must hold an MS or Ph.D. degree in Bioinformatics, Biology, Engineering, Physics, Computer Science, Mathematics, or a related scientific discipline pertinent to the position. Some experience working with microarrays or complex biological datasets is required, as is fluency with basic statistical methods. Applicants must also have experience with computational analysis frameworks such as R or MATLAB. Familiarity with bioinformatics tools like Bioconductor and Cytoscape is a bonus. A successful candidate will have demonstrated success in scientific creativity, collaboration, and independent thought.
ISB is an M/F/D/V/EOE.
Please visit the Careers page of our website at http://www.systemsbiology.org/careers for application instructions. Please include Job # 09-035 in all correspondence regarding this position.
BioNanomatrix seeks highly innovative and motivated individuals in the fields of cancer genomics, epigenetics, micro/nanotechnology, polymer/surface chemistry, optics, system automation engineering, software engineering, and bioinformatics. We are looking for talented, creative, results-driven individuals who enjoy being part of an interdisciplinary team.
BioNanomatrix is an equal opportunity employer. We offer a positive, diverse and exciting work environment with competitive salary and benefits and the potential for career growth.
The following full time software engineering position is currently available. If you are interested, please send a cover letter, resume and salary requirements to hr@bionanomatrix.com.
Description
You will be responsible for providing support related to all aspects of software analysis, design, development, documentation, and configuration management of the software deployed with our product. You’ll be responsible for developing new functionality for a high throughput system, followed by upgrades, testing, debugging and enhancements to our deployed software applications.
The position also includes writing or reviewing specifications, analysis, testing and design of the software.
It requires the ability to work well with beta sites when providing support, and with our clinical consultants when writing or reviewing specifications.
Specific Duties:
• Participate in the preparation of system requirements and design specifications.
• Engineer software in C++, .NET environment, adhering to our software design specifications
• Apply software engineering skills and tool knowledge to produce a system that meets the stated requirements and controlled standards.
• Provide software engineering and product expertise throughout the lifecycle of assigned projects, including code optimization, documentation and testing.
• Adhere to configure management practices.
• Participate in the preparation of project plans, status and statistical reports, etc.
• Assist in the resolution of product issues escalated from alpha and beta sites, as required.
• Learn new skills as required, particularly moving in the direction of multiple device integration.
Required Education and/or Experience
• BS in Computer Science or 5 years of Software Engineering experience. Masters/PhD a plus.
• Experience in machine learning and statistical methods a plus.
• Minimum 3 years of software engineering experience required
• 1 year Microsoft Dot Net experience required
• 2 years MS Visual Studio experience required
• 1-2 years C++ experience required
• Microsoft Certified Engineer preferred
• Biological sequence analysis experience preferred
• Must have excellent communication skills
• Must be able to work in a team environment
• Must be able to adhere to deadlines
hr@bionanomatrix.com
DESCRIPTION:
Designing experiments, as well as optimizing and performing various assays including but not limited to: quantitative real-time PCR, siRNA /ShRNA/cDNA transfection and transduction, luciferase reporter assay, immunostaining.
Applying various genetic and chemical tools to dissect cancer and signal transduction pathways in different in vitro cancer models to elucidate drug mechanism of action and mechanisms of drug sensitivity and resistance.
Participating in the development of novel biological and chemical assays/screens to accelerate the current drug and biomarker discovery effort.
SKILLS
Expertise with basic molecular and cellular biology techniques such as molecular cloning, mammalian cell culture, compound efficacy profiling, viral based gene delivery, real-time qPCR and RNAi technology is required.
The ideal candidate will have excellent analytical and organizational skills as well as good oral and written communication skills. A familiarity with data analysis software and basic bioinformatics packages is expected.
Highly motivated, fast learner, ability to work independently and as a team member and ability to multi-task are key qualities.
EDUCATION
B.S. or M.S. in Cell/Molecular Biology, Biochemistry, Genetics, or a related field with at least three years of academic or industry lab experience.
Must be US Citizen or Green Card Holder and Live Local
Please submit resume as word attachment to jobs@cwsciences.com
Commonwealth Sciences, Inc.
http://www.cwsciences.com
The Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) is seeking a database administrator / programmer for several ongoing clinical research projects. This person will be responsible for independently learning clinical data models through data dictionaries and seeking data elements from VistA, the VA’s electronic medical record system, to support ongoing clinical research. Must be comfortable networking with other DBAs across the VA system to find data elements. The second primary role of this person will be participation in the development and implementation of a data model to support analysis across several ongoing clinical trials. This initial effort is part of a larger initiative to lay the foundation for the next generation of clinical research for the Veterans Administration Hospital System and its academic affiliates. This model and the development team will eventually scale to incorporate several different data types including electronic medical record data, biological specimen data, and genomic data.
Communication skills are very important for this position. Qualified candidates will have experience working directly with end users unfamiliar with database technologies and structures and be capable of translating their information needs into data extractions. Candidates must also have been part of a larger development team and responsible for creating or customizing relational databases.
The hired candidate will report to MAVERIC’s Associate Center Director of Biomedical Informatics and work on several ongoing projects with multidisciplinary teams of clinicians, informatics researchers, and IT staff to develop prototypes and solutions. Projects include funded informatics research projects as well as the development of solutions to streamline in-house research operations. The ability to work independently to meet multiple deadlines is essential.
Required Experience
• Microsoft SQLServer (3+ years)
• Database design (3+ years)
• Report development (3+ years)
• Work directly with end-users to translate needs into data pulls
Preferred Experience
• Data warehouse development
• Business intelligence / OLAP software (Cognos, SAS BI, Sybase, SQLServer Analysis Services)
• Intersystems Cache
• MUMPS
• Fileman
• Healthcare data
• Clinical trials operations
• CDISC
• Creation and use of data cubes
• Familiarity with biological data (genomic, proteomics, bioinformatics, etc)
Candidates must be U.S. citizens
About MAVERIC
The Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) is comprised of four scientific divisions; clinical trials, epidemiology, bio-specimen laboratory, and biomedical informatics. MAVERIC is an independent entity with 10,000 square feet of newly renovated space located on the 13th & 14th floors, C & D wings of the VA Boston Healthcare System (VABHCS) and an additional 8,000 sq. ft. for our bio-specimen lab in the basement of the Research Building. The MAVERIC staff includes project managers, biostatisticians, informatics researchers, computer programmers, database managers, program and staff assistants, career development awardees, fellows, physicians, a quality assurance officer, and administrative personnel.
MAVERIC is affiliated with the following academic and hospital institutions:
Harvard School of Public Health Boston University School of Public Health
Harvard Medical School Boston University School of Medicine
Brigham and Women’s Center for Surgery and Public Health Brigham and Women’s Hospital Channing Laboratory
Northeastern University’s Graduate Program in Health Informatics
Interested candidates should send a cover letter and résumé to:
Shalena Robinson at:
Shalena.Robinson@va.gov
The Broad Institute was launched to pioneer a new model of collaborative biomedical science that would transform medicine. To accomplish these goals, we have built an amazing team of talented “Broadies” who work together to realize this transformation.
We are always looking for new Broadies to join our team and help us tackle important problems at the cutting edge of science.
RESEARCH TECHNICIAN at the Broad Institute, Cancer Program, to assist in the discovery of new human oncogenes and therapeutic targets for cancer using RNA interference and cDNA screening approaches as part of a multidisciplinary team of scientists in a leading program in integrated functional cancer genomics. Will work closely with project leaders and serve as a key player in the molecular analysis of new therapeutic targets for cancer. May also assist in the development of bioinformatic and database tools to streamline this project. Will coordinate oncogene screening project including the design, construction, and inventory of libraries of cDNA clones of human genes and execute genetic screens using these libraries; validate discoveries from a genome-scale RNAi screening project aimed at finding new molecular targets for novel cancer therapies; confirm phenotypes in cell-culture model systems of cancer; perform diverse molecular biological techniques including RNAi, PCR, DNA subcloning and viral gene-transfer; conduct cell-culture and animal-based experiments; document, compile, and analyze experimental data; attend team meetings to share results and plan projects and experiments; maintain, order, and stock supplies, reagents, and solutions for the laboratory; and interact with collaborators within the Broad Cancer Program and RNAi platform and the Center for Cancer Systems Biology at the Dana-Farber Cancer Institute.
A bachelor’s or master’s degree in biology or comparable area; research experience in molecular biology, cell biology, or similar field; strong interpersonal, communication, and organizational skills; and attention to detail. Solid knowledge of computers and experience with bioinformatics and/or databases desired. A two-year commitment is required
The Broad community
The Broad community includes professional scientists from many disciplines, administrative staff, and students. We seek to cultivate an interdisciplinary, goal-oriented work environment that unleashes scientific creativity and empowers our people to pursue ambitious and critical projects.
Our work transcends traditional academic boundaries, giving Broad employees and affiliates access to an unparalleled biomedical research community across the Harvard and MIT communities and beyond.
Benefits of working at Broad
The Broad Institute is committed to providing its employees with a competitive compensation and benefits package. We recognize the need for our employees to have a balance between work and personal life. To that end, our benefit plans and options reflect our desire to promote an environment that supports the health, diversity, and general wellbeing of our employees.
All Broadies also have access to world-class research and state of the art technology and are fully supported in their professional development, pushing the envelope for further growth.
The Broad Benefits Program includes:
• Medical
• Dental
• Basic Life Insurance, Accidental Death & Dismemberment, Business Travel and Supplemental
Life Insurance
• Short-Term and Long-Term Disability
• Flexible Spending Accounts
• 401(K) Plan w/Competitive Employer Match
• 4 Weeks of Vacation after 1 Year
• Tuition Reimbursement
• Identity Theft Prevention and Insurance
• Estate Planning
• Adoption Assistance
• Employee Assistance Program (EAP)
• MBTA Commuter Transportation Subsidies
• Parents in a Pinch Back Up Child Care
• Credit Union
The Broad Institute is an equal opportunity employer.
To learn more about the Broad’s job opportunities, visit our Career Center at: https://www.broadinstitute.org/careers/career-center
If interested, please apply online at http://track.tmpservice.com/ApplyClick.aspx?id=809063-1857-5339
The Broad Institute was launched to pioneer a new model of collaborative biomedical science that would transform medicine. To accomplish these goals, we have built an amazing team of talented “Broadies” who work together to realize this transformation.
We are always looking for new Broadies to join our team and help us tackle important problems at the cutting edge of science.
Desktop Support Specialist II at the Broad Institute – Under the direction of the Team Leader for Desktop Support, the Desktop Support Specialist is responsible for hands-on, enterprise level desktop support for the desktop computing environment at the Broad Institute. Desktop Support Specialists focus on providing tier-2 technical support and participate in projects that shape and effectively manage the scaling of the desktop computing environment.
Provide effective community relations by ensuring appropriate and timely responses to desktop computing issues and Desktop Support projects. Prioritize daily workload effectively and ensure that the member community is regularly updated on the status of their outstanding support issues. Troubleshoot issues related to the software applications, desktops, laptops, printers, and related peripherals provided by Desktop Support to the Broad member community. Maintain community satisfaction with the desktop computing environment through continued education about issues and services provided (and periodic liaison with community members). Process and manage the daily operations workload for the desktop computing environment by assessing the priority and level of urgency and ensuring that all incoming issues receive an appropriate, timely and completed response. Provide internal escalation support to all members of the Desktop Support Team, documenting the best practices for processing the escalated issue and educating the rest of the team accordingly. Develop skills that involve understanding the support trends at the institute and addressing them more holistically. Participate in Desktop Support Team community outreach by developing training courses involving proper usage of hardware and software applications and leading them accordingly. Showing proficiency with the supported operating systems provided by Desktop Support including Windows and Mac OSX (as well as the current supported Linux distribution Ubuntu).
Degree in Computer Science or other technical discipline with an in-depth and broad understanding of modern computing technology, systems architecture, or equivalent training and experience. Minimum of 3.5 years related experience. Experience with hands-on, enterprise-level, technical support. Experience with tier-2 practices and effectively managing internal technical escalations. Experience with imaging, post-configuration, deployment and administration desktop computing hardware. Excellent understanding of Windows, Mac, and linux environments and support requirements. –Excellent communication skills suited to a large professional service-oriented organization. A basic understanding of genomics/bioinformatics is highly desired.
The Broad community
The Broad community includes professional scientists from many disciplines, administrative staff, and students. We seek to cultivate an interdisciplinary, goal-oriented work environment that unleashes scientific creativity and empowers our people to pursue ambitious and critical projects.
Our work transcends traditional academic boundaries, giving Broad employees and affiliates access to an unparalleled biomedical research community across the Harvard and MIT communities and beyond.
Benefits of working at Broad
The Broad Institute is committed to providing its employees with a competitive compensation and benefits package. We recognize the need for our employees to have a balance between work and personal life. To that end, our benefit plans and options reflect our desire to promote an environment that supports the health, diversity, and general wellbeing of our employees.
All Broadies also have access to world-class research and state of the art technology and are fully supported in their professional development, pushing the envelope for further growth.
The Broad Benefits Program includes:
• Medical
• Dental
• Basic Life Insurance, Accidental Death & Dismemberment, Business Travel and Supplemental
Life Insurance
• Short-Term and Long-Term Disability
• Flexible Spending Accounts
• 401(K) Plan w/Competitive Employer Match
• 4 Weeks of Vacation after 1 Year
• Tuition Reimbursement
• Identity Theft Prevention and Insurance
• Estate Planning
• Adoption Assistance
• Employee Assistance Program (EAP)
• MBTA Commuter Transportation Subsidies
• Parents in a Pinch Back Up Child Care
• Credit Union
The Broad Institute is an equal opportunity employer.
To learn more about the Broad’s job opportunities, visit our Career Center at: https://www.broadinstitute.org/careers/career-center
Job Description:
The DNA Medicine Institute is seeking a Bioinformatics Scientist or Consultant to analyze next-generation sequencing data. This individual will modify, add, and enhance next-generation open source software for DNA sequence assembly. Examples of some of these programs include: ABySS, AMOS, MIRA, , SHARCGS, SSAKE, VCAKE, and Velvet. In addition, this scientist will analyze next-generation sequencing data and present them in a coherent manner. The successful candidate will also be able to keep accurate records and have superb programming skills. This individual will contribute to making important advancements in the DNA sequencing field.
Requirements:
A minimum of a Bachelors Degree or equivalent is required, preferably in Bioinformatics or equivalent field. The individual should have good references. The ideal candidate should be motivated, detail driven, and intellectually curious.
Company:
The mission of The DNA Medicine Institute (DMI) is to advance the diagnosis and treatment of human diseases through the use of nanotechnology, genomics, advanced engineering and information technology. DMI leverages interdisciplinary science to advance fundamental research in genomics and human diseases. The Institute has substantial expertise in a breadth of fields, leveraging these to solve challenging problems. The integration of disparate fields is a core focus, as it provides the basis for new insights and discovery. As a result, the environment is dynamic, energetic, and thought-provoking. DMI encourages innovation and bold vision in this setting.
Details:
Please send resume to info@dnamedinstitute.com
Our client is a rapidly growing software company building a modeling product related to the biotech industry. They have a smart team of scientists and developers already in place and are looking to hire a computer scientists with knowledge of bioinformatics, AI, and data-mining to help design and improve their knowledge repository.
This person will be working as the intermediary between the scientists and software engineers and should be able to do hands on software development with Java and Oracle 50% of the time.
Please send your resume for immediate, confidential consideration. We promise we won’t circulate it before speaking with you. Please note our client companies will only consider candidates who are authorized to work in the US.
Lynx stands out as one of New England’s leading search and placement firms in the software technology sector. Our team can open the door to job opportunities not available from other agencies, as we have spent the last two decades building relationships, trust and access with key software decision-makers.
Please call us at (781) 274-6400 , or visit www.lynxinc.com, where you can receive hot job alerts for your specific interests and location, search our current job listings, and find exclusive interviewing and hiring tips.
At the J. Craig Venter Institute (JCVI), teams of scientists, engineers, and bioinformatics professionals are making some of the most exciting scientific discoveries in the world. We recently uncovered more than six million new genes by sampling life forms across the world’s oceans, and are making steady progress in our quest to create synthetic organisms to serve as sources of renewable energy. These are just a few of the many research areas our teams are tackling as we seek to make a worldwide impact with our science. The Annotation Engineering Group, in which this position resides, is the central nexus of bioinformatics activities within the institute, and provides both services and tools for both our own internal research and for the scientific community as a whole.
We are searching for experienced and well qualified candidates for the position of Bioinformatics Engineer. The successful candidate will have a BS or MS degree in biology, bioinformatics, computer science, or related technical field, and 3+ years of related professional experience.
Looking to take the next step in your bioinformatics career? Apply today!
Qualifications:
- Significant, demonstrable skills in Perl/BioPerl required.
- In-depth knowledge of relational databases, schemas, and SQL queries required.
- Excellent communications, teamwork, and time management skills required. We have a strong preference for candidates who have previous experience on software project teams with successful projects.
- Deep and broad understanding of biological concepts preferred; minimum requirement is a basic understanding of genomics and general biology.
- Strong HTML skills strongly preferred. Flash skills desirable.
- Working experiences with bioinformatics sequence analysis tools such as BLAST and phylogenetic analysis tools such as PHYLIP strongly preferred.
- Experience with large biological datasets such as NCBI and/or UCSC genome databases strongly preferred.
- Experience with statistics or algorithm development desirable.
- Experience with JAVA or other object-oriented software technologies desirable.
JCVI offers an excellent working environment and a competitive benefits package. For more info or to apply, visit our web site at www.jcvi.org. Equal Opportunity Employer M/F/D/V
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