3 code implementations • 3 Nov 2023 • Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joel Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy.
1 code implementation • 25 Oct 2023 • Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joel Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses.
1 code implementation • 8 Oct 2023 • Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
mean) while improving accuracy by 1. 35$\times$ (1. 34$\times$) in terms of F-1 score on average (geo.
1 code implementation • 11 Sep 2023 • Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis.
1 code implementation • 22 Jan 2023 • Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value.
1 code implementation • 9 Dec 2022 • Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
However, for many applications, the majority of reads do no match the reference genome of interest (i. e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.
1 code implementation • 20 Jul 2022 • Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie Kim, Taha Shahroodi, Meryem Banu Cavlak, Joel Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, Onur Mutlu
We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs.
1 code implementation • 16 May 2022 • Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, Onur Mutlu
We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent.
no code implementations • 30 Mar 2022 • Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do, Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research.
1 code implementation • 17 Jan 2022 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Also available in Bioconda at: https://anaconda. org/bioconda/fastremap-bio.
1 code implementation • 16 Dec 2021 • Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu
We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches.
2 code implementations • 16 Sep 2020 • Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
Unfortunately, it is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems, as many of the steps in genome sequence analysis must process a large amount of data.
Hardware Architecture Genomics
1 code implementation • 18 Dec 2019 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
There are several tools that attempt to accelerate the process of updating a read data set from one reference to another (i. e., remapping).
1 code implementation • 12 Feb 2019 • Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, Onur Mutlu
Our experiments with real read sets demonstrate that Apollo is the only algorithm that 1) uses reads from any sequencing technology within a single run and 2) scales well to polish large assemblies without splitting the assembly into multiple parts.