From 3f095d59f9e5ede3ba7d840fa073eb6987fa89be Mon Sep 17 00:00:00 2001 From: calkan Date: Mon, 16 Dec 2024 11:27:15 +0300 Subject: [PATCH] pubs update, software update --- papers/index.html | 30 ++++++++++++------- software/index.html | 4 +++ team/_posts/2013-09-01-azita-nouri.md | 4 +-- .../_posts/2021-02-01-nermin-\303\247elik.md" | 1 + team/_posts/2023-12-07-sila-ozel.md | 1 + 5 files changed, 28 insertions(+), 12 deletions(-) diff --git a/papers/index.html b/papers/index.html index 6e9a7ec..6459fca 100644 --- a/papers/index.html +++ b/papers/index.html @@ -9,6 +9,26 @@ first or last authors are marked with * in case of equal contribution) +

+
+ +
Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data. + + Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, Ekin Sağlıcan, N. Ezgi Altınışık, Anna-Sapfo Malaspinas, Can + Alkan, Mehmet Somel. + Genome Biology, published online, Dec xx, 2024.
+
+ +

+
+ +
AirLift: a fast and comprehensive technique for remapping alignments between reference genomes. + Jeremie S Kim, Can Firtina, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can + Alkan, Onur Mutlu. + IEEE Transactions on Computational Biology and Bioinformatics, published online, Aug 19, 2024.
+
presented + at the 21st Asia Pacific Bioinformatics Conference (APBC 2023), Changsha, Hunan, China, April 14-16, 2023.
+

@@ -49,16 +69,6 @@ Bioinformatics, 39(4): btad175, 2023.
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-
- -
AirLift: a fast and comprehensive technique for translating alignments between reference -genomes. - Jeremie S Kim, Can Firtina, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can - Alkan, Onur Mutlu. - Proceedings of the 21st Asia -Pacific Bioinformatics Conference (APBC 2023), Changsha, Hunan, China, April 14-16, 2023.
-

diff --git a/software/index.html b/software/index.html index ac266c0..3d83007 100644 --- a/software/index.html +++ b/software/index.html @@ -90,6 +90,10 @@

Others

Tool to perform pairwise sequence alignment using block edits and rearrangements.
  • Linden: Alternating Lyndon Factorization Tree data structure and its application to whole-genome alignments.
    • +
  • LCPtools: + Implementation of the Locally Consistent Parsing (LCP) algorithm for string processing as an API.
    • +
  • GenCore: + Fast alignment-free genomic distance estimation using LCP.

    • Deprecated Tools

    diff --git a/team/_posts/2013-09-01-azita-nouri.md b/team/_posts/2013-09-01-azita-nouri.md index f0534a0..2c5e04c 100644 --- a/team/_posts/2013-09-01-azita-nouri.md +++ b/team/_posts/2013-09-01-azita-nouri.md @@ -19,7 +19,7 @@ alumni: true ### Education -- Ph.D. Computer Science, 2017 - present +- Ph.D. Computer Science, 2017 - 2024 - [Rutgers University](https://www.cs.rutgers.edu/), Piscataway, NJ, United States - M.Sc. Computer Engineering, Spring 2016 @@ -31,4 +31,4 @@ alumni: true ### After Alkan Lab -Azita is now a Ph.D. Candidate at Rutgers University. +Azita obtained her Ph.D. at Rutgers University. She now works at the [NEC Research Lab](https://www.nec-labs.com/research/optical-networking-sensing/people/). diff --git "a/team/_posts/2021-02-01-nermin-\303\247elik.md" "b/team/_posts/2021-02-01-nermin-\303\247elik.md" index 765bcd1..26d7c7d 100644 --- "a/team/_posts/2021-02-01-nermin-\303\247elik.md" +++ "b/team/_posts/2021-02-01-nermin-\303\247elik.md" @@ -9,6 +9,7 @@ scholar: image: /images/team/stickfig.png cv: https://github.com/_cv.pdf email: nermin.celik@gmail.com +alumni: true --- I am a postdoc working on sepsis detection. diff --git a/team/_posts/2023-12-07-sila-ozel.md b/team/_posts/2023-12-07-sila-ozel.md index d490da5..616f404 100644 --- a/team/_posts/2023-12-07-sila-ozel.md +++ b/team/_posts/2023-12-07-sila-ozel.md @@ -7,6 +7,7 @@ linkedin: sıla-özel-0b9625242/ instagram: email: sila.ozel@ug.bilkent.edu.tr image: /images/team/sila.jpeg +alumni: true --- I am a Computer Science student at Bilkent University.