Education

• B.Sc., Computer Engineering, 2021
  • Bilkent University, Ankara, Turkey

After Alkan Lab

Meryem Banu Cavlak is still a member of Alkan Lab in her heart and her spirit still wanders around the EA building. More formally though, she is an M.Sc. student in the SAFARI Research Group at ETH Zurich, advised by Prof. Onur Mutlu. Her current research interests span everything including bioinformatics and computer architecture.

Publications

• ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. 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, and Onur Mutlu. arXiv, 2207.09765, 2022.

• FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, and Onur Mutlu. Bioinformatics, btac554, 2022.

• SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie Kim, Nika Mansouri Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu. Proceedings of the 49th Annual International Symposium on Computer Architecture (ISCA), New York, NY, USA, June 2022.

• AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, and Onur Mutlu. bioRxiv, 2021.02.16.431517, 2021.