Emmanuel R. Yera

I haven’t posted in a while. But I finally joined a lab. Actually in July! I am joined Ajay Jain’s lab. So far it has been great. I am working on computational drug discovery. I spent the summer working on a project relating the 3D structure of small molecules and their corresponding biological activity patterns. Check out http://jainlab.org for more information.

I honestly can’t believe that my first year is coming to an end. It has been a difficult road but completely worth it. My knowledge has grown exponentially in every way. In this final quarter, I took three mini-course: statistical methods for micro-array analysis, statistical methods for genetics and macromolecular structure and function III. They were all interesting and I believe that I got exactly what I wanted out of them.

My rotation has been really interesting! I have been working on what Joe calls “Dark Matter”. I will have a lot of results which I hope will be interesting to the lab. I do have one more rotation with Ajay Jain. I will comment on that once I start. It will definitely be nice to just to research and not have to worry about classes and as many journal clubs!

My last quarter is underway! This quarter is different since I will be taking three mini-course that are 2-3 weeks long. They are ment to go deep into a specific area such as Statistical methods in microarray analysis and genome wide association studies. Each graduate program offers their own mini-courses that you can take.

I am also rotating in Joe Derisi’s lab. It will be my first time doing wet lab. So far I have been growing malaria in red blood cells. They are still alive after a few days, I wonder how long they will stay alive!

I am proud to announce that I finished my second quarter! This quarter was more managable since I had a better background in the topics being covered. But it was intense and very time consuming. I really enjoyed my rotation in Esteban’s lab. I definately got a good idea of the science he is working on and more importantly I know where I would fit  in the lab. I had a great conversation with him yesterday that will keep me thinking on what I want to persue in the future.

My first quarter is over and grades are in! I passed all my classes. It was a very crazy and busy quarter but my knowledge grew not exponentially but combinatorially.

I started my new rotation in Esteban Buchard’s Lab. I am going to be working on analyzing single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in minority populations. He is currently performing genome wide association studies to see if he can find genomic indicators of why drug response to asthma treatement vary between minority populations.

I haven’t posted in a while but a quick update! I am rotating in the McManus lab! I really like the work that they are doing and Michael is a awesome! I am very glad that I decided to rotate in his lab. I will post what I have done later after I have completed it. It has been really busy with classes, journal club and applying to fellowships. I can’t believe that the quarter is almost over (Nov. 26th).

I had a great time during my first lab rotation! Everyone in the lab is awsome. My knowledge of the subject grew exponentially. The problem is that I must now move on to the next rotation since the Bioinformatics program requires three rotations. I might do an extra rotation to become even more familiar with the research at UCSF but that is to be determined. I am trying to plan my next rotation and have talked to the following individuals:

Esteban González Burchard, he works on identifying racially-specific genetic and biologic risk factors for asthma and asthma severity among U.S. ethnic and racial minority groups.

Bruce R. Conklin, his lab has produced a free, publicly distributed software package, GenMAPP (Gene Map Annotator and Pathway Profiler).

Ajay Jain, he focuses on the discovery, characterization, and exploitation of genomic and molecular phenomena involved in cancer by predictive computational modeling.

Michael M. McManus, studies biological processes relating to RNA interference pathways.

Everyone is great and is doing exciting research! I have an idea who I want to rotate with in the fall quarter but it is not definate yet!

I started my first lab rotation here at UCSF in Patricia Babbit’s Lab. I have been performing research here almost three weeks. I have been directly working with Daniel Almonacid. Currently, I am working on building computational methods for finding enzymes which perform similar functions. More details to follow. Check out the research page for more a detailed description.

I am currently writing my thesis, which is titled “GenomExplorer: genomic cancer data visualization”. I have a lot written but am currently in the revising process. Hopefully it will not take many revisions but we will see. I start a summer rotation at UCSF in early June so I need to wrap this up. I will hopefully have a little more time soon to do some more restaurant reviews!

I just wanted to let everyone know what has been the outcome of my PhD applications. I was accepted to UC San Diego and UC Santa Cruz to the Bioinformatics PhD program. UCSD had a visiting weekend which was amazing. I really enjoyed hearing about the current research from faculty and students.

I interviewed at Stanford for the Biomedical Informatics PhD and after two rounds of interviews, I was rejected a month later. I also had intense interviews at UC San Francisco for the Biological and Medical Informatics PhD. I knew a lot about UCSF since I currently do research there but that doesn’t necessarily mean I would get accepted. A week after the UCSF interview I was accepted!

It was a difficult decision but after careful consideration, I will be starting my Biological and Medical Informatics PhD at the University of California, San Francisco. This summer will be spent learning lots of biology and possibly a summer research rotation! I can’t wait!