Laptop backup week 10? (for safety reasons)

8th-Semester-Spring-2025/frontiers/references/10.1038_s41467-017-01104-3-citation.ris

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+TY  - JOUR
+AU  - Al Ouahabi, Abdelaziz
+AU  - Amalian, Jean-Arthur
+AU  - Charles, Laurence
+AU  - Lutz, Jean-François
+PY  - 2017
+DA  - 2017/10/17
+TI  - Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
+JO  - Nature Communications
+SP  - 967
+VL  - 8
+IS  - 1
+AB  - In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.
+SN  - 2041-1723
+UR  - https://doi.org/10.1038/s41467-017-01104-3
+DO  - 10.1038/s41467-017-01104-3
+ID  - Al Ouahabi2017
+ER  - 

8th-Semester-Spring-2025/frontiers/references/achs_jacsat137_5629.bib

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+@article{doi:10.1021/jacs.5b02639,
+author = {Al Ouahabi, Abdelaziz and Charles, Laurence and Lutz, Jean-Fran{\c{c}}ois},
+title = {Synthesis of Non-Natural Sequence-Encoded Polymers Using Phosphoramidite Chemistry},
+journal = {Journal of the American Chemical Society},
+volume = {137},
+number = {16},
+pages = {5629-5635},
+year = {2015},
+doi = {10.1021/jacs.5b02639},
+    note ={PMID: 25851514},
+
+URL = { 
+    
+        https://doi.org/10.1021/jacs.5b02639
+    
+    
+
+},
+eprint = { 
+    
+        https://doi.org/10.1021/jacs.5b02639
+    
+    
+
+}
+
+}
+
+

8th-Semester-Spring-2025/frontiers/references/acs.macromol.5b00890.ris

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+TY  - JOUR
+T1  - Coding Macromolecules: Inputting Information in Polymers Using Monomer-Based Alphabets
+AU  - Lutz, Jean-François
+Y1  - 2015/07/28
+PY  - 2015
+DA  - 2015/07/28
+N1  - doi: 10.1021/acs.macromol.5b00890
+DO  - 10.1021/acs.macromol.5b00890
+T2  - Macromolecules
+JF  - Macromolecules
+JO  - Macromolecules
+SP  - 4759
+EP  - 4767
+VL  - 48
+IS  - 14
+PB  - American Chemical Society
+SN  - 0024-9297
+M3  - doi: 10.1021/acs.macromol.5b00890
+UR  - https://doi.org/10.1021/acs.macromol.5b00890
+ER  - 

8th-Semester-Spring-2025/frontiers/references/siam_140962486.bib

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+@article{doi:10.1137/140962486,
+author = {Acharya, Jayadev and Das, Hirakendu and Milenkovic, Olgica and Orlitsky, Alon and Pan, Shengjun},
+title = {String Reconstruction from Substring Compositions},
+journal = {SIAM Journal on Discrete Mathematics},
+volume = {29},
+number = {3},
+pages = {1340-1371},
+year = {2015},
+doi = {10.1137/140962486},
+
+URL = { 
+    
+        https://doi.org/10.1137/140962486
+    
+    
+
+},
+eprint = { 
+    
+        https://doi.org/10.1137/140962486
+    
+    
+
+}
+,
+    abstract = { Motivated by mass-spectrometry protein sequencing, we consider the problem of reconstructing a string from the multisets of its substring composition. We show that all strings of length 7, one less than a prime and one less than twice a prime, can be reconstructed uniquely up to reversal. For all other lengths, we show that unique reconstruction is not always possible and provide sometimes-tight bounds on the largest number of strings with given substring compositions. The lower bounds are derived by combinatorial arguments, while the upper bounds follow from algebraic approaches that lead to precise characterizations of the sets of strings with the same substring compositions in terms of the factorization properties of bivariate polynomials. Using results on the transience of multidimensional random walks, we also provide a reconstruction algorithm that recovers random strings over alphabets of size \$\ge4\$ from their substring compositions in optimal near-quadratic time. The problem considered is related to the well-known turnpike problem, and its solution may hence shed light on this longstanding open problem as well. }
+}
+
+