pubs update, software update

BilkentCompGen · Dec 16, 2024 · 3f095d5 · 3f095d5
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diff --git a/papers/index.html b/papers/index.html
@@ -9,6 +9,26 @@
             first or last authors are marked with * in case of equal
             contribution)</span></div>
 
+         <div style="margin-left: 20px;"><span style="font-style: italic;"><br />
+          </span></div>
+
+        <div style="margin-left: 20px;"><strong><a href="https://www.biorxiv.org/content/10.1101/2023.11.11.566695v1">Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data.</a> 
+        </strong>
+        Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, Ekin Sağlıcan, N. Ezgi Altınışık, Anna-Sapfo Malaspinas, <strong style="color: #000100;">Can
+            Alkan</strong>, Mehmet Somel.
+	<em>Genome Biology</em>, published online, Dec xx, 2024. <strong><br />
+          </strong></div>
+
+       <div style="margin-left: 20px;"><span style="font-style: italic;"><br />
+          </span></div>
+
+        <div style="margin-left: 20px;"><strong><a href="https://pubmed.ncbi.nlm.nih.gov/39159015/">AirLift: a fast and comprehensive technique for remapping alignments between reference genomes.</a> </strong>
+         Jeremie S Kim, Can Firtina, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, <strong style="color: #000100;">Can
+            Alkan</strong>, Onur Mutlu.
+            <em>IEEE Transactions on Computational Biology and Bioinformatics</em>, published online, Aug 19, 2024.<br /></div>
+        <div style="margin-left: 20px;"><em><a href="http://bioinformatics.csu.edu.cn/APBC2023/">presented
+              at</a> the 21st Asia Pacific Bioinformatics Conference (APBC 2023)</em>, Changsha, Hunan, China, April 14-16, 2023.<br /></div>
+
        <div style="margin-left: 20px;"><span style="font-style: italic;"><br />
           </span></div>
 
@@ -49,16 +69,6 @@
 	<em>Bioinformatics</em>, 39(4): btad175, 2023. <strong><br />
           </strong></div>
 
-                 <div style="margin-left: 20px;"><span style="font-style: italic;"><br />
-          </span></div>
-
-        <div style="margin-left: 20px;"><strong><a href="https://arxiv.org/abs/1912.08735">AirLift: a fast and comprehensive technique for translating alignments between reference
-genomes.</a> </strong>
-         Jeremie S Kim, Can Firtina, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, <strong style="color: #000100;">Can
-            Alkan</strong>, Onur Mutlu.
-	<em>Proceedings of the 21st Asia
-Pacific Bioinformatics Conference (APBC 2023)</em>, Changsha, Hunan, China, April 14-16, 2023. <strong><br />
-          </strong></div>
 
                  <div style="margin-left: 20px;"><span style="font-style: italic;"><br />
           </span></div>

diff --git a/software/index.html b/software/index.html
@@ -90,6 +90,10 @@ <h3>Others</h3>
             Tool to perform pairwise sequence alignment using block edits and rearrangements.</li>
 	    <li><a href="https://github.com/BilkentCompGen/linden"><strong>Linden</strong></a>:
             Alternating Lyndon Factorization Tree data structure and its application to whole-genome alignments.</li>
+	    <li><a href="https://github.com/BilkentCompGen/lcptools"><strong>LCPtools</strong></a>:
+            Implementation of the Locally Consistent Parsing (LCP) algorithm for string processing as an API.</li>
+	    <li><a href="https://github.com/BilkentCompGen/gencore"><strong>GenCore</strong></a>:
+            Fast alignment-free genomic distance estimation using LCP.</li>
         </ul>
 
         <h3>Deprecated Tools</h3>

diff --git 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-çelik.md b/team/_posts/2021-02-01-nermin-çelik.md
@@ -9,6 +9,7 @@ scholar:
 image: /images/team/stickfig.png
 cv: https://github.com/_cv.pdf
 email: [email protected]
+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
@@ -7,6 +7,7 @@ linkedin: sıla-özel-0b9625242/
 instagram: 
 email: [email protected]
 image: /images/team/sila.jpeg
+alumni: true
 ---
 
 I am a Computer Science student at Bilkent University.