Surrounded by geniuses- part 10 : Sal

Sal the professional…the professional integrated systems biology researcher

It’s easy to get the wrong impression of the Tough-looking, badass genius, and much harder to accurately portray him. Sure, the Tough-looking, badass genius bears an uncanny resemblence to Leon (the titular character from Leon, the Professional), which contributes to this impression, but partially because he objects strongly to being called a genius. See, the Tough-looking, badass genius, Salvatore Loguercio, worked really hard to become accomplished in his field, so he would prefer that the term genius be reserved for people like Maryam Mirzakhani, the indisputable intellectual who won a prestigious Fields Medal this year. No one disagrees that Maryam Mirzakhani’s brilliance is on a completely different level, but this post isn’t about Maryam Mirzakhani. It’s about Sal.

No one disputes the awesomeness that is Maryam Mirzakhani.

Sal’s journey into the Su lab began even before he realized it. He originally began working on a dataset generated by the genius-in-charge with insane mental organizational skills back when the genius-in-charge with insane mental organizational skills was still at GNF. The two finally met at the 2009 ISMB conference. While still a Research Associate at the Biotechnology Center of the Technische Universität Dresden (BIOTEC-TU) in Dresden, Germany, Sal began collaborating with the genius-in-charge with insane mental organizational skills on semantic web integration in Gene Wiki plus in 2010. They met again in 2010 at the ISMB conference, and the genius-in-charge with insane mental organizational skills searched exhaustively for ways to officially bring Sal into his team. Unfortunately, the hurdles to do so were high and could not be cleared until the genius-in-charge with insane mental organizational skills moved from GNF to The Scripps Research Institute. After moving, the genius-in-charge with insane mental organizational skills contacted Sal in September of 2011, and officially brought him into the Su Lab in January of 2012.

At first, Sal worked on games with a purpose. In particular, he helped develop Dizeez and GenESP and contributed to the data analysis of The Cure. Towards the end of the year, Sal began moving towards analysis, integration, and modeling of data from collaborators (Dr. Ann Feeney at TSRI) to generate new hypotheses which could then be tested by the Feeney group. Simultaneously, he collaborated with Dr. William E Balch and developed the Network-Augmented Genomic Analysis (NAGA) methodology to integrate and utilize two somewhat disparate datasets generated by the Balch lab: 1. RNAi functional screening data, and 2. protein interaction data from mass spectrometry. Sal’s work on NAGA enables researchers to discover and prioritize pathway proteins and is currently being applied in at least five different labs.

In addition to working hard at multiple projects, Sal has not neglected the importance of networking and attributes much of his success to the mentorship and networking opportunities provided by the San Diego Center for Systems Biology. As a testament to his productivity, Sal was awarded a fellowship from the Cystic Fibrosis Foundation in 2013, and a seed grant from the San Diego Center for Systems Biology. Don’t be fooled by his resemblance to Jean Reno, the Tough-looking, badass genius is pleasant, good-humored, and serious about doing great research.

Surrounded by geniuses- part 9 : Louis

Be ready for anything when working on thrilling research

Trail-mix-and-red-bull genius is a Graduate Student in the Kellogg School of Science and Technology at The Scripps Research Institute, which explains his ability to live off standard graduate student fare like Red Bull and trailmix. The Trail-mix-and-red-bull genius, Louis Gioia (pronounced loo-is joy-ah), joined the Su lab in January of 2014 during the great influx of 2014 (note- the year is not over yet, so it’s not too late join the deluge of new members). Since he joined the lab, the Trail-mix-and-red-bull genius has been strengthening his computational and analytical acumen by riding what can only be described as the roller-coaster of research programming, which looks something like this:

The research programming roller-coaster

In Louis’s case, he began working on snp annotations for the OncoRep project when he first joined as a rotation student, and then transitioned into working diligently on the Omics pipe project as he became an official member of the lab. As the Omics pipe project nears completion, the Trail-mix-and-red-bull genius has recently joined a new project on the meta transcriptomics of the microbiome (so you can imagine the ride he has ahead of him.)

Surrounded by geniuses- part 8 : Vyshakh

Around the time I joined the lab, a Fellow-new-person-but-smarter genius also joined as a summer intern. The Fellow-new-person-but-smarter genius, was once a Software engineer for Infosys Technologies Ltd where he developed the Java/J2EE based E-Commerce website Spring and Hibernate Web Application framework which included
• Designing proof of concept (PoC) for Warehouse Inventory Management using Sterling IBM Ecommerce Development tool for Distributed Order Management
• Working on Localization and Internationalization module for the website
• Integrating and testing Sterling OMS with Oracle SQL and JSP using Java, Hibernate and Spring MVC framework

The Fellow-new-person-but-smarter genius, Vyshakh Babji joined the Master’s program in Computer Science at San Diego State University and has taken part in several successful projects.

As part of the Su Lab, Vyshakh is working on an outgrowth of The Cure: Branch. The Cure was a challenging game which allowed players to help scientists to select genes for predicting breast cancer survival. See the recently released paper on The Cure here. As a game, The Cure was a quite challenging for players with no expertise in the field of breast cancer, but could be very powerful in the hands of experts. Why not give experts biologists more control in the process of selecting and organizing genes and their associated disease outcomes? Thus was the idea for Branch born, and researchers at the Su Lab like the Fellow-new-person-but-smarter genius, the Insanely-talented-undergrad-genius, and the Young-dad-in-charge-of-too-many-crazy-projects genius have been hard at work building Branch. As a tool, Branch will enable expert biologists to easily engage directly with high-throughput datasets without the need for a team of bioinformaticians. Using a tree building process, Branch allows researchers to rapidly test hypotheses about interactions between biological variables and phenotypes in ways that would otherwise require extensive computational sophistication. In so doing, this tool can both inform biological research and help to produce more accurate, more meaningful classifiers.

Contributing the development of Branch, Vyshakh has:
• Been involved in writing Application work flow both for front end and backend.
• Supported the team in understanding the work flow of the application.
• Developed the business logic using Java.
• Used spring and hibernate for backend development.
• Design & development of web-based programs using HTML, JavaScript and CSS.
• Implemented MYSQL/PostgreSQL queries and MYSQL/PostgreSQL stored procedures, and built-in functions to retrieve and update data from the databases.
• Followed Agile methodology for rapid application development
• Used Eclipse Kepler for Code Development and Apache Tomcat7 deployment of the Project.
• Used Groovy based Apache Gadle for building and project automation
• Followed Test driven developed (TDD) throughout the application.
• Performed regression test to check for unintended errors after enhancement.
• Transitioned from Apache Maven to Gradle for previous modules of the project.

Of course, it’s not sufficient to be called a genius simply based on his extensive skills in programming. Vyshakh is a genius because he’s also performed music in NGOs, blind schools, and taught music to poor children.

Surrounded by geniuses- part 7 : Adam

The Mysterious Genius of the Su Lab remained quite the mystery even after I’d been with the lab for a month. Where did he come from? Where does he vanish to? What is he working on? Given the extremely varied backgrounds of the other Su lab members, it would make sense if he was a member of a secret organization dedicated to liberating humans from machines hellbent on enslaving humanity. Were this the case…did I really write this post?

Fortunately, the Mysterious Genius, Adam Mark, doesn’t appear from and disappear into a higher plane of reality. He’s just making the painful commute between the Su lab at TSRI and San Diego State University, where he just completed his first year as an M.S. Candidate in Biomedical Informatics.

Enthusiastic about both bench work and programming, Adam would love to combine his two disparate skill sets to transcend the translational genomics and big data realm. The Mysterious Genius has been working on developing an R client for MyGene.info as well as MyVariant.info.

Don’t be fooled by the surfer dude vibe…Adam is unmistakably intelligent

An avid surfer and genuine connoisseur of ocean waves, the Mysterious Genius has traveled throughout Asia and the south pacific, and plans to make a trip to the Meditarranean soon. Not so mysterious, after all? Think again! The Mysterious Genius seems to be a beach-loving, wave-surfing, fun-in-the-sun, kind of genius, but further investigations reveal a colder, darker side to him.
 

Forget the hockey coach scouting Adam for his team, Adam became a coach himself

Throughout his undergrad, he played for SDSU’s ice hockey team and then went on to coach the sport for two years after graduating. After graduating, with a B.S. in biochemistry, Mysterious Genius joined Dr. Saloman’s lab at TSRI and even contributed to a publication in the prestigious journal, Science. Upon returning to SDSU for graduate studies, Mysterious Genius was recruited by the genius-in-charge with insane mental organizational skills to conduct his thesis research in Biomedical Informatics.

Surrounded by geniuses- part 5 : Toby

Unlike the other PhD in Friends, the Su lab’s friendly, pro-linux, sitcom-perfect genius is actually an expert in his field of study.

In theory Toby would fit right in with the rest of the Big Bang Theory group

When seeing how well the friendly, pro-linux, sitcom-perfect genius would fit on a television show, it’s easy to think that this descriptor does him some measure of justice…well, in theory anyway.

Unfortunately, it does not.

Is he friendly? Yes! Does he favor linux? Yes! Does he look like he could be a character in a very popular sitcom or TV series? You decide! Is that all? Heck no!

The truth is out there!

In truth, there is much more to Dr. Tobias Meissner than meets the eye. Toby is a bona fide bioinformatician with experience in gene expression profiling for the purposes of developing personalized medical prognoses and treatment strategies in multiple myeloma patients. Fluent in both German and English, the friendly, pro-linux, sitcom-perfect genius has a knack for language acquisition–especially programming languages! As a testament to his genius, Toby can code in R, C/C++, Java, Perl, Python, and SQL. He also has a working knowledge of PLINK and is fairly handy with a number of next-gen sequencing tools such as BWA, GATK, STAR, DESeq, and ANNOVAR. Make no mistake, though, friendly, pro-linux, sitcom-perfect genius is not just another genius programmer, he is a bioinformatician…which is like a super-charged genius programmer spanning multiple disciplines. Toby’s expertise with analyzing next-gen sequencing data; mRNA and miRNA profiling data; and GWAS and eQTL data makes him an ideal researcher for the Su Lab.

Now what exactly has friendly, pro-linux, sitcom-perfect genius been working on since he was recruited by the genius-in-charge with insane mental organizational skills?

Many things. Like many of the other geniuses in the Su Lab, friendly, pro-linux, sitcom-perfect genius, works on multiple projects which help to drive personalized cancer diagnostics forward such as: the Omics Pipe and OncoRep. Toby also works on analyzing metatranscriptomics data and gene markers associated with quantitative transcriptional levels of multiple myeloma transcripts. If that isn’t mind-blowing enough, friendly, pro-linux, sitcom-perfect genius has an impressive publication record of over twelve publications in academic journals and more than 300 citations to his published work, considering the fact that it has only been three years since he completed his PhD. At this rate, one can’t help but to expect great things out of the friendly, pro-linux, sitcom-perfect genius.

Unlike the other scrubs, Dr. Toby has been working on advancing the application of medical genomics

Surrounded by geniuses- part 4 : Chunlei

Remember Last week when I confessed to posting my second impressions of two of the geniuses from the Su Lab? Though I had a chance to more accurately portray one of the two aforementioned geniuses, I didn’t have a chance to explain the other one…the hard-working, friendly, go-to-for-help genius.

It turns out, hard-working, friendly, go-to-for-help genius is a grossly inept description Dr. Chunlei Wu. Chunlei earned his PhD in Biomathematics and biostatistics and previously worked on the integrating large-scale multi-omics datasets (such as gene expression, copy number variations, genome-wide associations, proteomics, and next-gen sequencing data) for biomedical discovery. If that sounded impressive, it’s because it IS IMPRESSIVE! That’s a lot of inconsistent data from a lot of different sources to be put together in a useful manner. Hence the reason why the development of software packages for these disparate datasets is impressive and important.

In addition to integrating datasets, Chunlei has also been collaborating with Dr. Dennis Burton’s group on the Antibodyome project which aims to profile all antibodies from patient or animal’s B cells and then make these profiles available via an Antibodyome web portal. While companies have been trying to catalog all commercially available antibodies for awhile, these antibodies are typically limited to antigens of commercial interest. In contrast, the Antibodyome project will focus on clinically relevant antibodies as the profiles are derived from antibodies in patients and determining the genetic sequences (ie- VDJ recombinations) needed to create these antibodies.

Hard-working, friendly, go-to-for-help genius has been working tirelessly to make data more accessible and more useful with his involvement in scientific methodologies and tools such as HAM (for GWAS analysis), GEA (for stepwise gene-set enrichment analysis), BioGPS (the one-stop shop for gene information), and MyGene.info. If you do biomedical research but have never tried using BioGPS to learn more about a gene, I encourage you to try it. BioGPS provides one of the most comprehensive reports about a given gene of interest for biomedical research and has the potential to be even more powerful since the users can contribute their own plugins to further extend the capabilities of the tool. BioGPS is pretty much powered by the MyGene.info service that Mr. hard-working, friendly, go-to-for-help genius has been working tirelessly on as he prepares to make the leap forward and delve into more complex and less organized data types: genetic variant information. As a co-investigator on NIH grant: R01GM083924 (Props to the NIH for supporting the development of MyGene.info and BioGPS), hard-working, friendly, go-to-for-help genius is poised to develop the next logical bioinformatics service: MyVariant.info. Just as how MyGene.info is a high performance, scalable, and extensible research tool for gene annotation data, MyVariant.info will be a useful tool for genetic variant annotation data.

If you’ve used BioGPS or MyGene.info, drop him a note and let him know how useful these tools have been for you. He’s a hard-working, friendly, go-to-for-help kind of guy, so he’ll definitely appreciate the encouragement.

Surrounded by geniuses- part 3 : Ben

As we’ve seen so far, the short descriptors really did not do my brilliant colleagues any justice and fail miserably to convey the sheer volume of awesome concentrated into each of the geniuses found in the Su lab.

To be honest, I lied about two of the first-impression descriptors. See, those were actually second-impression descriptors. The first lie was about Young-dad-in-charge-of-too-many-crazy-projects genius. The truth is that Young-dad-in-charge-of-too-many-crazy-projects genius was actually one of the two brilliant people I got to meet after my interview with genius-in-charge with insane mental organizational skills. At the time of our first meeting, I overlooked the ‘child-wrangler’ part inYoung-dad-in-charge-of-too-many-crazy-projects genius’s profile. My impression of him had primarily been based on a blog entry he posted around the time I was investigating the Su lab. Thus, the true first impression was that he was just one of those humorous-dude-in-charge-of-too-many-crazy-projects type of genius. My apologies for the deception caused by my attempts to simplify my blog entries.

Aside from having a name with great revenue and licensing potential, Young-dad-in-charge-of-too-many-crazy-projects genius AKA Dr. Benjamin Good, is a senior staff scientist in the Su lab. Now, you would think that you could get a good idea of what he works on looking at his profile on the Su Lab site. Ha ha! Think again!

Not. Remotely. Sufficient.

Ben’s Gene Wiki efforts extend beyond that which has been described in his profile. Did you know that he and Andrew have partnered with the journal Gene so that authors writing review articles for Gene also submit updates to Gene Wiki to help build the knowledge base available to the public? How’s that for awesome? If you are an expert on a certain gene, you could write a review for the journal Gene and then ensure that people will read your review (or at least know where to find it) by linking it as a reference when you update the Gene Wiki entry for that gene. Benefits everyone!

But the most awesome projects that Ben manages (at least in my opinion of awesome) are the Su lab games with a purpose. Ben has been working on Mark2Cure with Quirky, artistic, rock star programming genius with awesome hair, which will hopefully allow ANYONE WHO CAN READ to contribute to the progress of scientific research. (Ad alert) If you can read, you can help, join the Mark2cure mailing list to receive alerts on the progress of this project (end of Ad).

Ben has also been working on the The Cure along with Insanely talented undergrad genius which uses the collective wisdom of game players in order to build predictions regarding how certain variables (like genes) can affect tumor metastasis.

In addition to spearheading many of these crowd sourcing projects, Ben can be found injecting useful input into a variety of projects in the lab. He contributes his expertise to the knowledge management of several of the Integrative Structural Biology projects. Plus he’s just a helpful person in general. In fact, he is involved in so many projects around the lab that he can generally answer any question you may have. Further, he’s done so much research in the field of crowdsourcing and mining crowd data that he’ll be joining Andrew, Robert, and Zhiyong in chairing the Crowdsourcing and Mining Crowd Data session at the Pacific Symposium for Biocomputing. If you are also an expert in this field, you should submit an abstract and help blow the mind of Young-dad-in-charge-of-too-many-crazy-projects genius.

Surrounded by geniuses – part 2: Max

My first impression of Quirky, artistic genius with awesome hair was really based on nothing but a couple of pictures. First is the little thumbnail of a picture on the Su Lab’s main site: which clearly displays his awesome hair, and also an interesting background which looks like a blue screen and a studio spotlight, or a supernova on the beach (who knows, it’s too tiny to tell, leaving the viewer plenty of room to speculate.) Next is the profile pic from his website: which conveys a quirky sense of humor in addition to showcasing his awesome hair. Sadly, these pictures do not adequately convey the programming genius that is Max Nanis. Did you know that rock star genius programmers can actually get an agent and be managed by a talent agency? It’s true! Combine those crazy programming skills with artistic talent that gets exhibited in places like the Smithsonian Institution National Museum of Natural History and San Diego International Airport, and you finally get a sense of Max’s sheer brilliance.

Since joining the Su lab in June of 2012, Quirky, artistic genius with awesome hair has been contributing to a variety of projects such as:

• The proteinboxbot

– A bot which created wiki entries for genes lacking representation in wikipedia and seeded them with information from public databases. Currently, the ProteinBoxBot automatically updates protein infoboxes across the nearly 10,500 gene pages on the Gene Wiki

• DataChart Browser

– A visualization tool for gene expression data currently available for use on its own or as a plugin in conjunction with BioGPS

• The Cure

– An online game which uses the collective knowledge of the players in order to find new gene/disease association patterns from very large datasets.

• Mark2Cure

– An online game using crowdsourced microtask methods to annotate biomedical literature in order to make current and future bodies of biomedical research literature more useful to biomedical researchers.

• JS Decision Tree viewer

– A simple SVG based decision tree viewer to show a visually intuitive decision tree visualization

At a glance it is hard to comprehend how an unusually artistic programming genius ended up joining the Su lab. Then again, given that Quirky, artistic genius with awesome hair is represented by a talent agency, and that the genius-in-charge with insane mental organizational skills has an ability for spotting and recruiting talent, it makes perfect sense.

Surrounded by geniuses – part 1: Katie

Since my first impressions are probably highly inaccurate, I should at least post corrections about my colleagues. Of course, the ‘genius’ part is 100% true. The rest is probably far too simplified, so I am compelled to introduce the members of the Su Lab who have not been adequately represented in my short first impression descriptions. Today, I will start with the Cool, friendly, adventurous genius: Katie Fisch.
I’m starting with Katie because I’ve been given the freedom to write about my colleagues in no particular order, and well, because she’s just so cool!
Prior to joining the Su Lab, Dr. Kathleen Fisch studied…fish!!! In particular, she investigated the historical population genetics of delta smelt and developed/implemented the delta smelt hatchery genetic management and monitoring plan as a post-doc at UC Davis. She then joined the San Diego Zoo’s Institute for Conservation Research as a Post-doc fellow creating individual-based forward-time computer simulations in Python and R to model population dynamics and genomics.

For anyone who was confused by that, it just means that she’s…a genius!

Need proof of her genius? Just take a look at the grants she was awarded:

• California Sea Grant Delta Science Program, Principal Investigator, “Saving San Francisco Bay-Delta native fishes: Hatchery management and reintroduction strategies.” Awarded $167,739 for 2011-2013.
• US Bureau of Reclamation, Co-Principal Investigator “Delta smelt refugial population genetic management and monitoring.” (Co-P.I. B. May) Awarded $771,599 for 2010-2015.
• US Fish and Wildlife Service, Principal Writer

If she’s such a genius, why is she in the Su Lab? That’s probably because the genius-in-charge with insane mental organizational skills has a knack for collecting geniuses in order to work on his insanely complicated and multidisciplinary projects. Katie is currently trying to use her computational genomics and systems biology skills in order to identify drug therapies targeting aberrant gene expression, tumor mutations, and dysregulated pathways using the molecular profile of a patient’s tumor. In other words, personalized medicine!

Katie is also working on applying systems biology approaches to build a multidimensional molecular profile of osteoarthritis and aging; as well as, developing the Next generation sequencing analysis pipeline (‘omics pipe’).

To top it off, she is friendly and helpful, and when she’s not avidly working at her computer, you might find her in the great outdoors hiking, rock climbing, or sky diving.

Verdict: First impression description is not too far off. Katie really is a Cool, friendly, adventurous genius.

In the midsts of talent

Starting a new job can be both thrilling and worrisome–especially if the new job is at a place full of brilliant people. Working with geniuses is sort of intimidating. First impression descriptions of a few of my colleagues:

• Insanely talented undergrad genius
• Quirky, artistic genius with awesome hair
• Cool, friendly, adventurous genius
• Young-dad-in-charge-of-too-many-crazy-projects genius
• friendly, pro-linux, sitcom-perfect genius
• Tough, bad-ass genius
• hard-working, friendly, go-to-for-help genius
• Trail-mix-and-red-bull genius
• Fellow-new-person-but-smarter genius
• Mysterious genius
• genius-in-charge with insane mental organizational skills

Of course, first impressions (especially mine) can be about as accurate as identifying the eye color of the driver of an inconspicuous vehicle from a bird’s-eye view on a cloudy day–in an unforgiving Sierra point-and-click game. It’s probably best, if you don’t know what I’m talking about.