Jainab Khatun

Can Contact Potentials Reliably Predict Stability of Proteins?

Jainab Khatun, Sagar D. Khare, Nikolay V. Dokholyan

The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting …

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Landscape of transcription in human cells

Joel Rozowsky, Sudipto K. Chakrabortty, Carrie Davis, Xian Chen et autres

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellular localizations are also poorly understood. Since …

Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development

Hsun-Cheng Su, Dona Kanavy, Jainab Khatun, Morgan C. Giddings

The alarming rise of ciprofloxacin-resistant Pseudomonas aeruginosa has been reported in several clinical studies. Though the mutation of resistance genes and their role in drug resistance has been researched, the process by which the bacterium acquires high-level resistance is still not well …

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification

Jainab Khatun, Eric D. Hamlett, Morgan C. Giddings

The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of …

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Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry

Kevin Ramkissoon, Jainab Khatun, Morgan C. Giddings

The identification of proteins by tandem mass spectrometry relies on knowledge of the products produced by collision-induced dissociation of peptide ions. Most previous work has focused on fragmentation statistics for ion trap systems. We analyzed fragmentation in MALDI TOF/TOF mass spectrometry, collecting …

Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development

Hsun-Cheng Su, Jainab Khatun, Dona Kanavy, Morgan C. Giddings

The alarming rise of ciprofloxacin-resistant Pseudomonas aeruginosa has been reported in several clinical studies. Though the mutation of resistance genes and their role in drug resistance has been researched, the process by which the bacterium acquires high-level resistance is still not well …

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Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

Jainab Khatun, Yanbao Yu, John A. Wrobel, Brian A. Risk et autres

BACKGROUND: Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the ENcyclopedia of DNA Elements (ENCODE) project, we applied proteogenomic …

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GOFAST: An Integrated Approach for Efficient and Comprehensive Membrane Proteome Analysis

Yanbao Yu, Ling Xie, Harsha P. Gunawardena, Jainab Khatun et autres

Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and resistance to proteolysis, both of which could lead to low recovery and low identification rates of membrane proteins. Here, we introduce a …

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Long noncoding RNAs are rarely translated in two human cell lines

Balázs Bánfai, Hui Jia, Jainab Khatun, Emily J. Wood et autres

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these …

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Landscape of transcription in human cells

Sarah Djebali, Carrie Davis, Angelika Merkel, Alexander Dobin et autres

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because …

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An integrated encyclopedia of DNA elements in the human genome

Ian Dunham, Ewan Birney, Javier Herrero, Steven P. Wilder et autres

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and …

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An integrated encyclopedia of DNA elements in the human genome

Ian Dunham, Anshul Kundaje, Shelley Force Aldred, Patrick Collins et autres

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and …