News

10
Dec

Please see our publication page

12/10/2018
The SFB group has been very productive in both bioinformatics/computational biology and artificial intelligence. There are too many papers published at top journals and conferences to be highlighted individually. Please refer to our publication page for our recent work: https://sfb.kaust.edu.sa/Pages/Articles.aspx.
https://sfb.kaust.edu.sa/Pages/Articles.aspx
03
Aug

Our work on promoter- and enhancer-level regression analysis of combinatorial drug treament accepted by Bioinformatics

8/3/2017
​​Congratulates Trisevgeni on her work on the genome-scale regression analysis for promoters and enhancers after combinatorial drug treatment  which was accepted by Bioinformatics.
https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx503/4082269/Genome-scale-regression-analysis-reveals-a-linear
24
Jul

Our work on developing deep learning method for binding affnity prediction accepted by Bioinformatics

7/24/2017
​​Congratulates Ramzan, Hiro, and Yu on their work on developing a novel method that combines the strength of probabilistic graphical models, Hilbert space embedding, and deep learning to model binding affinity of transcription factors which was accepted by Bioinformatics.
https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx480/4042128/Sequence2Vec-A-novel-embedding-approach-for
17
May

SFB Group graduated its fourth PhD student - Dr. Majed Alzahrani!

5/17/2017
​Fourth PhD graduated from SFB Group
06
May

Our work on online multi-task learning accepted by TKDE

5/6/2017
​​Congratulates Peng Yang on his work on developing a robust online multi-task learning with correlative and personalized structures, which was accepted by IEEE Transactions on Knowledge and Data Engineering (TKDE).
09
Apr

SFB Group graduated its third PhD student - Dr. Ibrahim Alabdulmohsin!

4/9/2017
​Third PhD graduated from SFB Group
01
Apr

Our work on mining growth phenotype data accepted by Bioinformatics

4/1/2017
​​Congratulates Majed and Hiro on their work on developing a novel constant-column biclustering algorithm for mining co-fit genes from genome-scale growth phenotype data which was accepted by Bioinformatics.
21
Dec

Our work on multi-instance dictionary learning accepted by Pattern Recognition

12/21/2016
​Congratulates Jingyan on his work on multi-instance dictionary learning via multivariate performance optimization which was accepted by Pattern Recognition.
25
Aug

Congratulates Xuefeng for his tenure-track AP position at Tsinghua!

8/25/2016
​Congratulates Xuefeng Cui of the SFB group on getting his tenure-track assistant professor position at Institute for Interdisciplinary Information Sciences at Tsinghua University, China. Xuefeng joined the SFB Group in June 2014 as a postdoc fellow and did a great job on protein bioinformatics research. His new PI position starts on September 1, 2016. 
http://iiis.tsinghua.edu.cn/en/xfcui/
16
Jul

Congratulates Jingyan for his Research Scientist position at NYU Abu Dhabi!

7/16/2016
​Congratulates Jingyan Wang of the SFB group on getting his research scientist position at NYU Abu Dhabi. Jingyan joined the SFB Group in July 2014 as a postdoc fellow and did a great job on machine learning research. His new research scientist position starts on July 16, 2016.
27
Apr

SFB Group graduated its second PhD student - Dr. Abdullah Khamis!

4/27/2016
Second PhD graduated from SFB Group
20
Apr

Our work on protein homology detection through cross-modal learning accepted by ISMB2016 and Bioinformatics

4/20/2016
Our work on protein homology detection through cross-modal learning accepted by ISMB2016 and Bioinformatics
17
Apr

Our biosynthesis pathway design server, MRE, published in NAR

4/17/2016
Our biosynthesis pathway design server, MRE, published in NAR
http://www.cbrc.kaust.edu.sa/mre/
18
Dec

SFB Group graduated its first PhD student - Dr. Ahmed Abbas!

12/18/2015

Congratulates the SFB group on graduating its first Ph.D. student. Dr. Ahmed Abbas joined the SFB Group in October 2010. He got his Ph.D. degree in Computer Science in December 2015. His thesis title is "Zero-in-on key open problems in automated NMR protein structure determination". He is now an Assistant Professor at Ain Shams University, Egypt.

12
Nov

Our work on multivariate performance optimization from multi-view data accepted by AAAI-16

11/12/2015
Congratulates Jingyan on his work on optimizing multivariate performance measures from multi-view data which was accepted as a regular paper by AAAI-16.
30
Oct

Our work on translational bursting published in Integrative Biology

10/30/2015
Congratulates Hiro on his work on studying the effects of translational burst size distributions on the stability of gene expression which was accepted by Integrative Biology.
http://pubs.rsc.org/en/Content/ArticleLanding/2015/IB/C5IB00107B#!divAbstract
17
Sep

Our work on collective estimation of multiple bivariate functions published in JASA

9/17/2015
Congratulates Xin on his joint work with Prof. Jianhua Huang at Texas A&M University on collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling that was published in JASA.
http://www.tandfonline.com/doi/abs/10.1080/01621459.2015.1099535
12
Aug

Our drug repositioning framework published in Bioinformatics

8/12/2015

Congratulates Hammad on his computational drug repositioning framework which has been accepted by Bioinformatics and highlighted in Nature Middle East.

http://bioinformatics.oxfordjournals.org/content/early/2015/09/03/bioinformatics.btv477.long
14
Jul

Our work on structural alignment of interaction interfaces presented at ISMB2015

7/14/2015
Congratulates Xuefeng on presenting his work on structural alignment of biomolecular interaction interfaces at ISMB2015 conference. The work was accepted by ISMB2015 as a full paper and was published by Bioinformatics. 
http://bioinformatics.oxfordjournals.org/content/31/12/i133.long
29
Jun

Our work on parameter estimation methods for gene circuits published in Briefings in Bioinformatics

6/29/2015
Congratulates Ming, Hiro, and Xiaolei on their work on parameter estimation methods for gene circuit modeling from time-series mRNA data which was published in Briefings in Bioinformatics.
http://bib.oxfordjournals.org/content/early/2015/03/26/bib.bbv015.full
05
Sep

Jingyan's paper is accepted by Knowledge-Based Systems

9/5/2013

​Jingyan Wang's paper has been accepted by Knowledge-Based Systems (IF: 4.104)

1. J. Wang, H. Bensmail, and X. Gao. Discriminative Sparse Coding on Multi-Manifolds. Knowledge-Based Systems. Accepted.

19
Aug

Two papers published at Pattern Recognition

8/19/2013
Two papers have been published at Pattern Recognition (IF: 2.632)
1. J. Wang, H. Bensmail, and X. Gao. Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification. Pattern Recognition. (2013). 46(12): 3249-3255.
2. J. Wang, H. Bensmail, and X. Gao. Multiple graph regularized nonnegative matrix factorization. Pattern Recognition (2013). 46(10): 2840-2847.
26
Jul

Kuwahara's paper published at Scientific Reports

7/26/2013

Hiroyuki Kuwahara and Xin Gao coauthored a paper, "Stochastic effects as a force to increase the complexity of signaling networks", that was accepted by Scientific Reports (Nature Publishing Group).

23
Apr

Two papers accepted by ISMB2013

4/23/2013

Two papers are accepted by ISMB2013 (The 21st International Conference on Intelligent Systems for Molecular Biology), to be held in Berlin, Germany, during July 21-23, 2013.

1. H. Kuwahara, M. Fan, S. Wang, and X. Gao. A framework for scalable parameter estimation of gene circuit models using structural information. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013. (Acceptance rate 16%)
2. B. Xie, B. Jankovic, V. Bajic, L. Song, and X. Gao. Poly(A) motif prediction using spectral latent features from human DNA sequences. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2013), Berlin, Germany, July 2013. (Acceptance rate 16%)

23
Feb

International Conference on Biomolecular Dynamics: Experiment Meets Computation to be held at KAUST during Feb 23-25

2/23/2013

Xin Gao will chair the International Conference on Biomolecular Dynamics: Experiment Meets Computation to be held at KAUST during Feb 23-25.

http://cemse.kaust.edu.sa/Biomolecular%20Dynamics/Pages/default.aspx
07
Jan

BH peak selection published at PLOS One

1/7/2013

Ahmed Abbas' new NMR peak selection method that is based on the Benjamini-Hochberg algorithm is published by PLOS One. 

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053112
15
Sep

Protein function annotation methods published at Bioinformatics

9/15/2012

Mario Messih's protein function annotation methods that are based on domain order and recurrence is published at Bioinformatics.

http://bioinformatics.oxfordjournals.org/content/28/18/i444.full
16
Jul

LagSVD accepted by Briefings in Bioinformatics

7/16/2012

Paper "Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles" is accepted for publication at Briefings in Bioinformatics (IF: 5.202).

23
May

SECOM is accepted for publication at PLoS ONE

5/23/2012

Article "SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification" is accepted for publication at PLoS ONE. (IF: 4.411)

08
Feb

WaVPeak published at Bioinformatics

2/8/2012

Our novel peak picking method WaVPeak published at Bioinformatics as a full length research article.

http://bioinformatics.oxfordjournals.org/content/early/2012/02/10/bioinformatics.bts078.abstract
01
Feb

Two papers accepted by BMC Bioinformatics

2/1/2012

Two articles "Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY" and "ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval" are accepted for publication on BMC Bioinformatics (IF: 3.03).

18
Jan

ProClusEnsem published at Computers in Biology and Medicine

1/18/2012

Article "ProClusEnsem: predicting membrane protein types by fusing different models of pseudo amino acid composition" is accepted for publication at Computers in Biology and Medicine (IF: 1.112).