Optimization algorithms for biological data

High-throughput techniques in biology have enabled the generation of enormous amount of data allowing researchers to reveal systems level information deciphering the underlying dynamics and mechanisms of the cell. In the last few decades, the immense databases containing DNA, RNA and protein sequences, structures and abundance estimates have been available to researchers. Research in bioinformatics necessitates the use of advanced efficient algorithms to analyze and interpret those biological data. A common characteristic of high-throughput biological data is that it is often incomplete, noisy and inconsistent due to the biases and inefficiencies induced by the laboratory methods. That is why several of the problems defined on biological data can be viewed as constrained optimization problems. In this dissertation, I address different optimization problems that arise in the analysis of biological data: RNA structural alignment, protein interaction network querying, micro-array expression data clustering, protein quantification and protein modification site assignment. The dissertation begins with an overview of the basic concepts of molecular biology and an introduction to the optimization problems to be addressed. Then, each problem is discussed in detail in a separate chapter along with our contribution in the solution of the problem and our results on biological data opening a way for biological discoverie

Structural Alignment Of Pseudoknotted Rna

In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs. © Mary Ann Liebert, Inc. 2008

S.: Structural alignment of pseudoknotted RNA

In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs. Key words: structure. dynamic programming, pseudoknotted RNA, RNA alignment, RNA secondary 1

Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes

ATM is a protein kinase that initiates a well-characterized signaling cascade in cells exposed to ionizing radiation (IR). However, the role for ATM in coordinating critical protein interactions and subsequent exchanges within DNA damage response (DDR) complexes is unknown. We combined SILAC-based tandem mass spectrometry and a subcellular fractionation protocol to interrogate the proteome of irradiated cells treated with or without the ATM kinase inhibitor KU55933. We developed an integrative network analysis to identify and prioritize proteins that were responsive to KU55933, specifically in chromatin, and that were also enriched for physical interactions with known DNA repair proteins. This analysis identified 53BP1 and annexin A1 (ANXA1) as strong candidates. Using fluorescence recovery after photobleaching, we found that the exchange of GFP-53BP1 in DDR complexes decreased with KU55933. Further, we found that ANXA1 knockdown sensitized cells to IR via a mechanism that was not potentiated by KU55933. Our study reveals a role for ATM kinase activity in the dynamic exchange of proteins in DDR complexes and identifies a role for ANXA1 in cellular radioprotection

Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes

ATM is a protein kinase that initiates a well-characterized signaling cascade in cells exposed to ionizing radiation (IR). However, the role for ATM in coordinating critical protein interactions and subsequent exchanges within DNA damage response (DDR) complexes is unknown. We combined SILAC-based tandem mass spectrometry and a subcellular fractionation protocol to interrogate the proteome of irradiated cells treated with or without the ATM kinase inhibitor KU55933. We developed an integrative network analysis to identify and prioritize proteins that were responsive to KU55933, specifically in chromatin, and that were also enriched for physical interactions with known DNA repair proteins. This analysis identified 53BP1 and annexin A1 (ANXA1) as strong candidates. Using fluorescence recovery after photobleaching, we found that the exchange of GFP-53BP1 in DDR complexes decreased with KU55933. Further, we found that ANXA1 knockdown sensitized cells to IR via a mechanism that was not potentiated by KU55933. Our study reveals a role for ATM kinase activity in the dynamic exchange of proteins in DDR complexes and identifies a role for ANXA1 in cellular radioprotection

Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes

ATM is a protein kinase that initiates a well-characterized signaling cascade in cells exposed to ionizing radiation (IR). However, the role for ATM in coordinating critical protein interactions and subsequent exchanges within DNA damage response (DDR) complexes is unknown. We combined SILAC-based tandem mass spectrometry and a subcellular fractionation protocol to interrogate the proteome of irradiated cells treated with or without the ATM kinase inhibitor KU55933. We developed an integrative network analysis to identify and prioritize proteins that were responsive to KU55933, specifically in chromatin, and that were also enriched for physical interactions with known DNA repair proteins. This analysis identified 53BP1 and annexin A1 (ANXA1) as strong candidates. Using fluorescence recovery after photobleaching, we found that the exchange of GFP-53BP1 in DDR complexes decreased with KU55933. Further, we found that ANXA1 knockdown sensitized cells to IR via a mechanism that was not potentiated by KU55933. Our study reveals a role for ATM kinase activity in the dynamic exchange of proteins in DDR complexes and identifies a role for ANXA1 in cellular radioprotection