Fahad Ullah

Bio: Fahad Ullah is an academic researcher from Colorado State University. The author has contributed to research in topics: Bandwidth allocation & Chromatin. The author has an hindex of 6, co-authored 16 publications receiving 142 citations. Previous affiliations of Fahad Ullah include University of Engineering and Technology, Peshawar & University of Engineering and Technology, Lahore.

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress.

Abstract: Drought is a major limiting factor of crop yields. In response to drought, plants reprogram their gene expression, which ultimately regulates a multitude of biochemical and physiological processes. The timing of this reprogramming and the nature of the drought-regulated genes in different genotypes are thought to confer differential tolerance to drought stress. Sorghum is a highly drought-tolerant crop and has been increasingly used as a model cereal to identify genes that confer tolerance. Also, there is considerable natural variation in resistance to drought in different sorghum genotypes. Here, we evaluated drought resistance in four genotypes to polyethylene glycol (PEG)-induced drought stress at the seedling stage and performed transcriptome analysis in seedlings of sorghum genotypes that are either drought-resistant or drought-sensitive to identify drought-regulated changes in gene expression that are unique to drought-resistant genotypes of sorghum. Our analysis revealed that about 180 genes are differentially regulated in response to drought stress only in drought-resistant genotypes and most of these (over 70%) are up-regulated in response to drought. Among these, about 70 genes are novel with no known function and the remaining are transcription factors, signaling and stress-related proteins implicated in drought tolerance in other crops. This study revealed a set of drought-regulated genes, including many genes encoding uncharacterized proteins that are associated with drought tolerance at the seedling stage.

Exploring the relationship between intron retention and chromatin accessibility in plants

Abstract: Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular. In this study we use publicly available DNase I-seq data in arabidopsis and rice to investigate the relationship between IR and chromatin structure. We find that IR events are highly enriched in DHSs in both species. This implies that chromatin is more open in retained introns, which is consistent with a kinetic model of the process whereby higher speeds of transcription in those regions give less time for the spliceosomal machinery to recognize and splice out those introns co-transcriptionally. The more open chromatin in IR can also be the result of regulation mediated by DNA-binding proteins. To test this, we performed an exhaustive search for footprints left by DNA-binding proteins that are associated with IR. We identified several hundred short sequence elements that exhibit footprints in their DNase I-seq coverage, the telltale sign for binding events of a regulatory protein, protecting its binding site from cleavage by DNase I. A highly significant fraction of those sequence elements are conserved between arabidopsis and rice, a strong indication of their functional importance. In this study we have established an association between IR and chromatin accessibility, and presented a mechanistic hypothesis that explains the observed association from the perspective of the co-transcriptional nature of splicing. Furthermore, we identified conserved sequence elements for DNA-binding proteins that affect splicing.

Short-term daily peak load forecasting using fast learning neural network

Abstract: Load forecasting has been an inevitable issue in electric power supply in past. It is always desired to predict the load requirements in order to generate and supply electric power efficiently. In this research, a neuro-evolutionary technique known as Cartesian Genetic Algorithm evolved Artificial Neural Network (CGPANN) has been deployed to develop a peak load forecasting model for the prediction of peak loads 24 hours ahead. The proposed model presents the training of all the parameters of Artificial Neural Network (ANN) including: weights, topology and functionality of individual nodes. The network is trained both on annual as well as quarterly bases, thus obtaining a unique model for each season.

A close look at protein function prediction evaluation protocols

Abstract: The recently held Critical Assessment of Function Annotation challenge (CAFA2) required its participants to submit predictions for a large number of target proteins regardless of whether they have previous annotations or not. This is in contrast to the original CAFA challenge in which participants were asked to submit predictions for proteins with no existing annotations. The CAFA2 task is more realistic, in that it more closely mimics the accumulation of annotations over time. In this study we compare these tasks in terms of their difficulty, and determine whether cross-validation provides a good estimate of performance. The CAFA2 task is a combination of two subtasks: making predictions on annotated proteins and making predictions on previously unannotated proteins. In this study we analyze the performance of several function prediction methods in these two scenarios. Our results show that several methods (structured support vector machine, binary support vector machines and guilt-by-association methods) do not usually achieve the same level of accuracy on these two tasks as that achieved by cross-validation, and that predicting novel annotations for previously annotated proteins is a harder problem than predicting annotations for uncharacterized proteins. We also find that different methods have different performance characteristics in these tasks, and that cross-validation is not adequate at estimating performance and ranking methods. These results have implications for the design of computational experiments in the area of automated function prediction and can provide useful insight for the understanding and design of future CAFA competitions.

A self-attention model for inferring cooperativity between regulatory features.

Abstract: Deep learning has demonstrated its predictive power in modeling complex biological phenomena such as gene expression. The value of these models hinges not only on their accuracy, but also on the ability to extract biologically relevant information from the trained models. While there has been much recent work on developing feature attribution methods that discover the most important features for a given sequence, inferring cooperativity between regulatory elements, which is the hallmark of phenomena such as gene expression, remains an open problem. We present SATORI, a Self-ATtentiOn based model to detect Regulatory element Interactions. Our approach combines convolutional layers with a self-attention mechanism that helps us capture a global view of the landscape of interactions between regulatory elements in a sequence. A comprehensive evaluation demonstrates the ability of SATORI to identify numerous statistically significant TF-TF interactions, many of which have been previously reported. Our method is able to detect higher numbers of experimentally verified TF-TF interactions than existing methods, and has the advantage of not requiring a computationally expensive post-processing step. Finally, SATORI can be used for detection of any type of feature interaction in models that use a similar attention mechanism, and is not limited to the detection of TF-TF interactions.

Alternative Splicing and Protein Diversity: Plants Versus Animals.

Abstract: Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.

Predicting network attack patterns in SDN using machine learning approach

Abstract: An experimental setup of 32 honeypots reported 17M login attempts originating from 112 different countries and over 6000 distinct source IP addresses. Due to decoupled control and data plane, Software Defined Networks (SDN) can handle these increasing number of attacks by blocking those network connections at the switch level. However, the challenge lies in defining the set of rules on the SDN controller to block malicious network connections. Historical network attack data can be used to automatically identify and block the malicious connections. There are a few existing open-source software tools to monitor and limit the number of login attempts per source IP address one-by-one. However, these solutions cannot efficiently act against a chain of attacks that comprises multiple IP addresses used by each attacker. In this paper, we propose using machine learning algorithms, trained on historical network attack data, to identify the potential malicious connections and potential attack destinations. We use four widely-known machine learning algorithms: C4.5, Bayesian Network (BayesNet), Decision Table (DT), and Naive-Bayes to predict the host that will be attacked based on the historical data. Experimental results show that average prediction accuracy of 91.68% is attained using Bayesian Networks.

The changing paradigm of intron retention: regulation, ramifications and recipes

Abstract: Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.

Kuhn–Munkres Parallel Genetic Algorithm for the Set Cover Problem and Its Application to Large-Scale Wireless Sensor Networks

Abstract: Operating mode scheduling is crucial for the lifetime of wireless sensor networks (WSNs). However, the growing scale of networks has made such a scheduling problem more challenging, as existing set cover and evolutionary algorithms become unable to provide satisfactory efficiency due to the curse of dimensionality. In this paper, a Kuhn–Munkres (KM) parallel genetic algorithm is developed to solve the set cover problem and is applied to the lifetime maximization of large-scale WSNs. The proposed algorithm schedules the sensors into a number of disjoint complete cover sets and activates them in batch for energy conservation. It uses a divide-and-conquer strategy of dimensionality reduction, and the polynomial KM algorithm a are hence adopted to splice the feasible solutions obtained in each subarea to enhance the search efficiency substantially. To further improve global efficiency, a redundant-trend sensor schedule strategy was developed. Additionally, we meliorate the evaluation function through penalizing incomplete cover sets, which speeds up convergence. Eight types of experiments are conducted on a distributed platform to test and inform the effectiveness of the proposed algorithm. The results show that it offers promising performance in terms of the convergence rate, solution quality, and success rate.