A brand new version of our Coriolis metagenomic classifier is out! This release (0.2.1) brings new task scheduler that significantly improves classification throughput. Coriolis can perform real-time classification while running alongside a basecaller (e.g., dorado).

09/27/2024, 01:24 PM

For the second time, I have been recognized with the IEEE Transactions on Parallel and Distributed Systems Award for Editorial Excellence.

04/08/2024, 10:18 AM

We have released a new version of our Coriolis metagenomic classifier and its accompanying frameworks. The classifier is specifically designed to operate efficiently on portable devices with limited main memory. Its primary use case is for mobile metagenomics, particularly with MinION DNA sequencers. Coriolis can perform real-time classification while running alongside a basecaller (e.g., dorado).

12/07/2023, 09:24 AM

I am on the program committee of CCGRID 2024.

09/11/2023, 03:06 AM

I am on the program committee of ICPP 2023.

04/03/2023, 03:06 AM

I am on the program committee of IPDPS 2023.

10/18/2022, 06:40 AM

Starting Fall 2022 I am on sabbatical leave, hanging out in Europe (till Summer 2023). As I seem to have some free time ;-) do not hesitate to ping me if you would like to meet!

10/18/2022, 06:40 AM

I am on the program committee of IPDPS 2022. This time the conference will be held in Lyon, France. It seems that the conference will be in person. Lyon is one amazing city which has plenty to offer, so you definitely should join us there!

10/19/2021, 10:58 AM

I am on the program committee of ACM BCB 2021. The conference is virtual this year. Please consider submitting your best work! The submission deadline is April 1, 2021.

03/16/2021, 01:15 PM

I am deeply honored to be recognized with the 2020-2021 President Emeritus and Mrs. Meyerson Award for Distinguished Undergraduate Teaching and Mentoring. Thank you to all amazing undergraduate students I was privileged to work with!

01/07/2021, 04:26 PM

I am on the program committee of ICPP 2021 (Algorithms Track). This is special year for ICPP – 50th Anniversary! Consider submitting your best work! The submission deadline is April 16, 2021.

01/07/2021, 04:26 PM

I am on the program committee of HiCOMB 2021. Submissions deadline: January 29, 2021.

01/05/2021, 12:01 AM

I am excited to join IEEE Transactions on Parallel and Distributed Systems as an Associate Editor.

08/13/2020, 11:25 AM

I have been invited to join the Editorial Board of the Journal of Parallel and Distributed Processing in the role of Associate Editor.

04/23/2020, 01:38 PM

I have been recognized with the 2019 Early Career Teacher of the Year Award by the UB School of Engineering and Applied Sciences.

02/28/2020, 10:17 PM

Here is a short blog post summarizing the setup I use for delivering and recording lectures.

01/22/2020, 11:24 AM

We released SABNA 3.001, our end-to-end Bayesian network learning platform. In this release, we add fully parallel network structure search capability. We also migrated from OMP to Intel TBB (better performance!).

01/22/2020, 11:24 AM

I have open PhD position in the domain of parallel and distributed computing with applications to data analytics.

09/06/2019, 01:55 PM

I am on the programming committee of ICPP 2020. Abstracts are due March 2, 2020, the full papers deadline is March 9, 2020.

09/06/2019, 01:54 PM

I am giving invited talk during the Workshop on Microbiomics, Metagenomics, and Metabolomics (MMM), which is hosted together with the ACM-BCB 2019.

09/06/2019, 01:50 PM

I have been awarded NSF CNS Core grant to work on new solutions for fully-mobile DNA analytics (based on ONT MinION portable DNA sequencer). This is amazing collaborative effort with Steve Ko (UB CSE) and Lou Sassoubre (UB CSEE). The project code name is SMARTEn.

06/18/2019, 12:22 PM

Together with my collaborator Olga Wodo (PI), we have been awarded NSF CMMI grant to continue and expand our work on data analytics for materials science. This project is a joint effort with Baskar Ganapathysubramanian from Iowa State University.

06/18/2019, 12:16 PM

Together with my collaborators Varun Chandola (PI), Nils Napp (Co-PI) and Olga Wodo (Co-PI) we have been awarded NSF OAC Core grant to continue and expand our work on non-linear spectral dimensionality reduction methods.

04/23/2019, 10:53 PM

I have been awarded NSF CAREER grant to continue work on scalable probabilistic graphical modeling with applications to biomedical informatics.

02/06/2019, 01:35 PM

I have been recognized with Early Career Faculty Teaching Award by the Department of Computer Science and Engineering at UB.

02/06/2019, 01:33 PM

I am a Workshops Vice-Chair for IPDPS 2019.

08/18/2018, 04:23 AM

I am on the program committee of SBAC-PAD 2018.

05/22/2018, 06:00 PM

I am on the program committee of HiPC 2018. Paper submission deadline June 15, 2018.

05/22/2018, 06:00 PM

SCoRe group and I have moved to new location in Capen Hall. My new office is Capen 209 (enter through Capen 212).

02/19/2018, 10:08 AM

I have several open positions for UTAs in CSE250 "Data Structures" in Spring 2018. If you are interested, please send me email or stop by my office!

12/11/2017, 10:27 AM

Our paper on Applications and Challenges of Real-time Mobile DNA Analysis in now available in arXiv.

11/21/2017, 10:51 AM

UB SEAS News has a nice summary of the "I Can!" program run by the UB's Liberty Partnership Program. Together with Oliver Kennedy from CSE@UB I have been participating in the program as an instructor.

08/21/2017, 03:07 PM

I am a Workshops Vice-Chair for IPDPS 2018. The deadline for workshop proposals and renewal requests is September 1, 2017.

07/17/2017, 05:41 PM

I am on the programming committee of HiPC 2017. Abstracts are due June 5, the full papers deadline is June 15.

06/02/2017, 12:59 PM

I am on the programming committee of SBAC-PAD 2017.

05/30/2017, 02:14 AM

I am now serving as a Director of Web Communications for the ACM SIGBio, the ACM's special interest group focusing on research in bioinformatics and biological and biomedical data, knowledge, and information management.

01/12/2017, 10:30 AM

I am serving as a co-chair of the "Advancing Algorithms and Methods" track of ACM-BCB 2017. Papers submissions deadline: April 10, 2017.

01/09/2017, 11:09 AM

I am on the program committee of HiCOMB 2017. Submissions deadline, January 30, 2017.

11/16/2016, 08:29 PM

I am on the program committee of the 12th International Conference on Parallel Processing and Applied Mathematics (PPAM).

11/03/2016, 12:11 AM

I will be serving as the Student Travel Awards Chair for the IEEE Technical Committee on Parallel Processing (TCPP). Currently, IEEE TCPP sponsors several conferences including IPDPS, the flagship conference of IEEE on parallel and distributed processing.

11/03/2016, 12:11 AM

My student, Subhadeep Karan, and I have released SABNA – our software toolkit for exact Bayesian networks structure learning. The source code and documentation are available from https://gitlab.com/SCoRe-Group/SABNA-Release. The accompanying preprint describing the optimal path extension technique, which is at the core of SABNA, is available from arXiv: http://arxiv.org/abs/1608.02682. Enjoy!

08/10/2016, 11:44 AM

I have been awarded a small seed grant from the UB Innovative Micro-Programs Accelerating Collaboration in Themes (IMPACT). Together with Tevfik Kosar and Michael Buck we will be working on OneBioStore, a distributed smart storage and scalable algorithms for collaborative biomedical discovery.

07/11/2016, 11:37 AM

Thanks to the support from the NSF, the ACM International Workshop on Big Data in Life Sciences (BigLS) offers travel grants for students and postdocs from US academic institutions! Application deadline August 5, 2016.

06/30/2016, 02:11 PM

On June 29, I am giving a talk during the Eric Pitman Annual Summer Workshop in Computational Science organized by the Center for Computational Research at the University at Buffalo.

06/29/2016, 03:04 PM

The Biomedical Informatics Department at UB moved to a new location on Goodell St. (UB Gateway). My office is on 5th floor (suite 540B).

05/12/2016, 10:07 AM

I am on the program committee of the Workshop on Accelerator-Enabled Algorithms and Applications in Bioinformatics (WACEBI 2016). Papers submission deadline is October 9, 2016.

05/10/2016, 10:16 AM

I am on the program committee of ACM-BCB 2016. Papers submission deadline is May 20, 2016.

04/26/2016, 11:15 PM

I have been awarded by Amazon $10,000 in AWS cloud credits for research on cloud software for long reads analysis.

04/11/2016, 11:05 PM

On March 23, 12pm I will be presenting at the Biomedical Informatics Grand Rounds. Title: "Parallel Computing and Bioinformatics — Practitioner's Point of View". The talk will be in UB's CTRC 5019A.

03/21/2016, 12:23 PM

On March 9, 7pm in the Ninth Ward at Babeville in Buffalo I will be talking about "Signal of Life: DNA and Computers" during the Science and Art Cabaret 17.0. Come and enjoy!

02/11/2016, 09:20 PM

I am on the program committee of IPDPS 2016. Submission deadline is October 16, 2015.

09/17/2015, 10:51 PM

I am a program co-chair of HiCOMB 2015. Submission deadline is December 18, 2015 - this is great workshop, consider submitting a paper!

09/17/2015, 10:47 PM

I have been invited to present during the pSALSA Workshop hosted in conjunction with the ACM BCB conference.

08/20/2015, 08:25 PM

Thanks to the support from NSF, BigLS 2015 offers travel grants for students and postdocs from US academic institutions.

08/04/2015, 09:56 PM

Eva K. Lee from Georgia Tech will deliver this year keynote presentation at BigLS 2015! Prof. Lee is well known for her outstanding contributions to Operations Research in medicine and health care.

07/16/2015, 04:28 PM

I am co-organizing a half-day workshop on "Computational and Data Challenges in Genomic Sequencing" during the ACM/IEEE Supercomputing 2015. We lined up some outstanding speakers -- you should attend!

07/16/2015, 04:21 PM

On June 2, I am giving a talk "Decoding DNA mysteries with Supercomputers" during the Eric Pitman Annual Summer Workshop in Computational Science organized by the Center for Computational Research at the University at Buffalo. The workshop is a great K-12 outreach activity. Stop by if you are in the area :)

06/25/2015, 09:57 AM

I have been invited to the AAAS-FBI roundtable on enhancing the research and educational environment at U.S. universities.

06/22/2015, 09:33 AM

I am on the program committee of the IEEE High Performance Computing for Big Data Computational Biology Workshop (IEEE HPC-BCB) 2015. This is a new, hopefully interesting, workshop. The paper submission deadline is September 10, 2015.

06/22/2015, 09:28 AM

I am on the program committee of HiPC 2015. The paper submission deadline is June 5, 2015.

05/04/2015, 11:51 PM

The call for papers of BigLS 2015, the workshop devoted to Big Data in life sciences that I am co-organizing, has been posted. Papers submission deadline is June 19.

04/30/2015, 09:01 AM

I am on the program committee of the 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). This the flagship conference of the ACM SIGBio. The submission deadline is May 8, 2015.

03/10/2015, 08:52 PM

UB Reporter has a short story on my involvement in the AAAS/FBI Working Group on Big Data in Life Sciences and National Security.

01/20/2015, 06:47 PM

I have been granted resource allocation on the ALCF Mira IBM Blue Gene/Q supercomputer - the 5th fastest supercomputer in the world. Together with the Argonne team I will be working on extending ELaSTIC.

11/25/2014, 08:46 PM

AAAS and FBI published a joint report on "National and Transnational Security Implications of Big Data in the Life Sciences." To prepare the project AAAS involved a working group of experts in which I participated. On December 11, AAAS will hold a public discussion on the report.

11/25/2014, 08:39 PM

I am serving as a co-chair of the Algorithms track for IC3 2015.

11/24/2014, 09:33 PM

I am looking for a graduate student to work on a collaborative project with Argonne Leadership Computing Facility, home to the 5th fastest supercomputer in the world. This position is available immediately! Visit http://www.score-group.org/doku.php?id=opportunities for more details.

09/25/2014, 10:45 PM

After two years with the Rutgers Discovery Informatics Institute I am moving to an assistant professor position in the Department of Computer Science and Engineering at the SUNY at Buffalo. I will be also working in the Department of Biomedical Informatics in the School of Medicine and Biomedical Sciences. Do not hesitate to contact me if you would like to join my research group!

07/23/2014, 02:35 PM

Thanks to the support from the NSF the ACM BigLS offers travel grants for students and postdoctoral researchers from US academic institutions. You can learn more at http://www.bigls.org/.

07/23/2014, 02:35 PM

Science Magazine has a brief story on how Big Data impacts life sciences, featuring my comments on the topic.

06/13/2014, 12:10 PM

I am happy to annouce that the ELaSTIC tool for large-scale similarity graphs construction from biological sequences is now available!

06/10/2014, 02:12 PM

I am very excited to announce that Larry Smarr will deliver this year's BigLS keynote address. Larry Smarr is a terrific speaker and a luminary in using high performance computing in life sciences.

05/29/2014, 04:03 PM

I am serving on the program committee of IC3 2014.

05/29/2014, 08:58 AM

I will be giving this year tutorial for DIMACS REU students. Title: "How to Find Who Lives on Your Belly Button: Not Too Short Introduction to Metagenomics." The focus of the tutorial is on computer science problems in metagenomics. Date: June 4th, 10am-12am and 1pm-2pm in CoRE 431.

05/08/2014, 09:50 AM

AAAS published a summary of the "Big Data, Life Sciences and National Security" event hosted in D.C. by the AAAS Center for Science, Technology and Security Policy and the Biological Countermeasures Unit of the FBI Weapons of Mass Destruction Directorate. This event is one of the outcomes of the AAAS and FBI working group I participate in.

04/28/2014, 03:42 AM

The 2nd ACM International Workshop on Big Data in Life Sciences will be held in conjunction with the ACM BCB in Newport Beach, CA on Saturday, September 20, 2014. The call for papers is now posted! Please, visit http://www.bigls.org/ and help us spread the news :-)

03/31/2014, 10:52 PM

I have been invited to participate in a joint AAAS and FBI working group on Big Data in Life Sciences and National Security. The group brings together experts in technology, science, and security to review the current scientific and technological advancements in Big Data analytics in life sciences, and their impact on national security.

01/09/2014, 03:42 PM

I have been awarded an NSF STTR Phase I grant to work with our small business partner on using Big Data to support supply chain analytics and optimization. A brief summary of the proposal is available from the NSF web page.

12/30/2013, 09:35 AM

I am currently looking for a higly motivated individual to fill in a position of Research Associate or Postdoctoral Associate in Big Data analytics. The focus of this position is on using Big Data for supply chain management, and it involves a close collaboration with industry partners. Please contact me if you want to learn more or are interested.

12/13/2013, 10:03 AM

I am a publicity chair of the 4th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). This time we are going to Miami, Florida. The submission deadline is March 1, 2014.

12/13/2013, 10:03 AM

I am on the program committee of the 2nd IEEE/ASE International Conference on Big Data Science and Computing. This quite competitive conference (the acceptance rate in 2013 was 8.5%) focuses on very broadly defined Big Data challanges. The submission deadline is March 1, 2014.

12/13/2013, 10:03 AM

I am on the program committee of the 43rd International Conference on Parallel Processing (ICPP 2014). The conference will be in Minneapolis, MN. The submission deadline is March 1, 2014.

10/07/2013, 02:55 PM

The Quanta magazine published a story on Big Data in life sciences, featuring some of my comments on the topic.

10/07/2013, 11:52 AM

I released a new slightly updated version of Faster2. Enjoy!

09/09/2013, 09:31 PM

I have been awarded a small grant to work with B. Ganapathysubramanian (ISU) and D. DiCarlo (UCLA) on a very exciting project in CFD. I will be looking into underlying optimization questions. A brief summary of the proposal is available from the NSF web page.

09/02/2013, 10:26 PM

I am on program committes of ACM-BCB 2013 and SBAC-PAD 2013. In the meantime we are working to prepare a summary of the BigLS meeting, which was a clear success!

06/30/2013, 09:19 PM

The joint team from RDI2 and Iowa State University, which I led, participated recently in the UberCloud experiment. We executed some amazing computational work. You can find more details at http://nsfcac.rutgers.edu/uff/.

06/30/2013, 09:16 PM

Together with Ananth Kalyanaraman we are starting a new workshop dedicated to theory and practice of Big Data in life sciences. BigLS, pronounced "Beagles", will be inaugurated on Thursday, June 13, 2013, and will consist of a set of invited presentations, followed by a joint panel discussion. You are highly welcome to participate!

05/10/2013, 01:27 AM

I am a publicity chair for the 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). This fairly new conference supported by IEEE is becoming a very interesting venue to present all types of computational biology, bioinformatics and life sciences oriented research. The paper submission deadline is April 5, 2013. The conference will be held in New Orleans, LA, June 12-14, 2013.

03/12/2013, 03:49 PM

I am on the program committee of 2013 ASE/IEEE International Conference on Big Data. Washington D.C., September 8-14, 2013.

02/11/2013, 12:06 PM

Together with Bertil Schmidt and David Bader we are organizing the Fifth Workshop on Parallel Computational Biology. As usually we welcome all papers that are balancing on a thine line between HPC and biology ;-) PBC is held in conjunction with the PPAM.

01/24/2013, 01:22 PM

I am on the program committee of the 10th International Conference on Parallel Processing and Applied Mathematics (PPAM). PPAM is organized every two years in different parts of Poland. It is really fun conference to attend! This time it will be held in Warsaw.

11/02/2012, 07:34 PM

The BIGDATA collaborative proposal by Srinivas Aluru (PI), Charles Sing, Patrick Schanble, Wu Feng, Kunle Olukotun and me, got awarded by NSF! NSF/NIH and Iowa State posted related press releases.

10/03/2012, 10:42 AM