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International Papers


  • Ahn H, Jung I, Shin S. J, Park J, Rhee S, Kim JK, Kwon HB, Kim S. Transcriptional network analysis reveals drought resistance specific biological mechanisms underlying AP2/ERF transgenic rice species. Frontiers in Plant Science. 2017.
  • Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S, TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. Bioinformatics. 2017.
  • Jung I, Ahn H, Shin SJ, Kim J, Kwon HB, Jung W, Kim S. Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. BMC Systems Biology. 2016.
  • Shin SJ, Ahn H, Jung I, Rhee S, Kim S, Kwon HB. Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L. Genes & Genomics. 2016.
  • Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee J, Ryu H, Kim S. Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice. BMC Medical Genomics. 2016.
  • Kim KY, Hwang YJ, Jung MK, Choe J, Kim Y, Kim S, Lee CJ, Ahn H, Lee J, Kowall NW, Kim YK, Kim JI, Lee SB, Ryu H. A multifunctional protein EWS regulates the expression of Drosha and microRNAs. Cell Death Differ. 2013.

Conference Papers

  • Ahn H, Chae H, Kim S, Integration of heterogeneous time series gene expression data by clustering on time dimension, 2017 IEEE International Conference on Big Data and Smart Computing (BigComp 2017), Jeju, Korea.
  • Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S, TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes. The 27th International Conference on Genome Informatics (GIW 2016), Shanghai, China
  • Jung I, Ahn H, Shin SJ, Kim J, Kwon HB, Jung W, Kim S. Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. The 27th International Conference on Genome Informatics (GIW 2016), Shanghai, China
  • Lee CJ, Ahn H, Lee SB, Shin JY, Park WY, Kim JI, Lee JH, Ryu H, Kim S. Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of EWS KO mice. The 5th Translational Bioinformatics Conference (TBC 2015), Tokyo, Japan.

Domestic Papers

  • 강동원, 안홍렬, 정우석, 김선. 이질적 시계열 유전자 발현 데이터의 통합 분석 문제의 정의 및 애기장대에서의 저온 스트레스 반응 유전자 검출 알고리즘 개발, 한국정보과학회 2015년 동계학술발표회 논문집, Vol.2015, No.12, pp.648-650.
  • 손승현, 안홍렬, 김선. 딥러닝을 통한 유전자 온톨로지 거리의 추론, 한국정보과학회 2017 한국소프트웨어종합학술대회 논문집, Vol.2017, pp.994-956.

SIX GRAPHS OF BIG DATA

from http://aojajena.wordpress.com/2013/08/12/six-graphs-of-big-data/

SIX GRAPHS OF BIG DATA

This post is about Big Data. We will talk about the value and economical benefits of Big Data, not the atoms that constitute it [Big Data]. For the atoms you can refer to Wearable Technology orGetting Ready for the Internet of Things by Alex Sukholeyster, or just logging of the click stream… and you will get plenty of data, but it will be low-level, atom level, not much useful.
The value starts at the higher levels, when we use social connections of the people, understand their interests and consumptions, know their movement, predict their intentions, and link it all together semantically. In other words, we are talking about six graphs: Social, Interest, Consumption, Intention, Mobile and Knowledge. Forbes mentions five of them in Strategic Big Data insight. Gartner provided report “The Competitive Dynamics of the Consumer Web: Five Graphs Deliver a Sustainable Advantage”, it is paid resource unfortunately. It would be fine to look inside, but we can move forward with our vision, then compare to Gartner’s and analyze the commonality and variability. I foresee that our vision is wider and more consistent!

Social Graph

This is mostly analyzed and discussed graph. It is about connections between people. There are fundamental researches about it, like Six degrees of separation. Since LiveJournal times (since 1999), the Social Graph concept has been widely adopted and implemented. Facebook and its predecessors for non-professionals, LinkedIn mainly for professionals, and then others such as Twitter, Pinterest. There is a good overview about Social Graph Concepts and Issues on ReadWrite. There is good practical review of social graph by one of its pioneers, Brad Fitzpatrick, calledThoughts on the Social Graph. Mainly he reports a problem of absence of a single graph that is comprehensive and decentralized. It is a pain for integrations because of all those heterogeneous authentications and “walled garden” related issues.
Regarding implementation of the Social Graph, there are advices from the successful implementers, such as Pinterest. Official Pinterest engineering blog revealed how to Build a Follower Model from scratch. We can look at the same thing [Social Graph] from totally different perspective – technology. The modern technology provider Redis features tutorial how to Build a Twitter clone in PHP and (of course) Redis. So situation with Social Graph is less or more established. Many build it, but nobody solved the problem of having single consistent independent graph (probably built from other graphs).

Interest Graph

It is representation of the specific things in which an individual is interested. Read more aboutInterest Graph on Wikipedia. This is the next hot graph after the social. Indeed, the Interest Graph complements the Social one. Social Commerce see the Interest + Social Graphs together. People provide the raw data on their public and private profiles. Crawling and parsing of that data, plus special analysis is capable of building the Interest Graph for each of you. Gravity Labs created a special technology for building the Interest Graph. They call it Interest Graph Builder. There is an overview (follow previous link) and a demo. There are ontologies, entities, entity matching etc. Interesting insight about the Future of Interest Graph is authored by Pinterest’s head of engineering. The idea is to improve the Amazon’s recommendation engine, based on the classifiers (via pins). Pinterest knows the reasoning, “why” users pinned something, while Amazon doesn’t know. We are approaching Intention Graph.

Intention Graph

Not much could be said about intentions. It is about what we do and why we do.  Social and Interests are static in comparison to Intentions. This is related to prescriptive analytics, because it deals with the reasoning and motivation, “why” it happens or will happen. It seems that other graphs together could reveal much more about intentions, than trying to figure them [Intentions] out separately.
Intention Graph is tightly bound to the personal experience, or personal UX. It was foreseen in far 1999, by Harvard Business Review, as Experience Economy. Many years were spent, but not much implemented towards personal UX. We still don’t stage a personal ad hoc experience from goods and services exclusively for each user. I predict that Social + Interest + Consumption + Mobile graphs will allow us to build useful Intention Graph and achieve capabilities to build/deliver individual experiences. When the individual is within the service, then we are ready to predict some intentions, but it is true when Service Design was done properly.

Consumption Graph

One of the most important graphs of Big Data. Some call it Payment Graph. But Consumption is a better name, because we can consume without payment, Consumption Graph is relatively easy for e-commerce giants, like Amazon and eBay, but tricky for 3rd parties, like you. What if you want to know what user consumes? There are no sources of such information. Both Amazon and eBay are “walled gardens”. Each tracks what you do (browse, buy, put into wish list etc.), how you do it (when log in, how long staying within, sequence of your activities etc.), they send you some notifications/suggestions and measure how do you react, and many other tricks how to handle descriptive, predictive and prescriptive analytics. But what if user buys from other e-stores? There is a same problem like with Social Graph. IMHO there should be a mechanism to grab user’s Consumption Graph from sub-graphs (if user identifies herself).
Well, but there is still big portion of retail consumption. How to they build your Consumption Graph? Very easy, via loyalty cards. You think about discounts by using those cards, while retailers think about your Consumption Graph and predicts what to do with all of users/client together and even individually. There is the same problem of disconnected Consumption Graphs as in e-commerce, because each store has its own card. There are aggregators like Key Ring. Theoretically, they simplify the life of consumer by shielding her from all those cards. But in reality, the back-end logic is able to build a bigger Consumption Graph for retail consumption! Another aspect: consumption of goods vs. consumption of services and experiences, is there a difference? What is a difference between hard goods and digital goods? There are other cool things about retail, like tracking clients and detecting their sex and age. It is all becoming the Consumption Graph. Think about that yourself:)
Anyway, Consumption Graph is very interesting, because we are digitizing this World. We are printing digital goods on 3D printers. So far the shape and look & feel is identical to the cloned product (e.g. cup), but internals are different. As soon as 3D printer will be able to reconstruct thecrystal structure, it will be brand new way of consumption. It is thrilling and wide topic, hence I am going to discuss it separately. Keep in touch to not miss it.

Mobile Graph

This graph is built from mobile data. It does not mean the data comes from mobile phones. Today may be majority of data is still generated by the smartphones, but tomorrow it will not be the truth. Check out Wearable Technology to figure out why. Second important notion is about the views onto the understanding of the Mobile Graph. Marketing based view described on Floatpoint is indeed about the smartphones usage. It is considered that Mobile Graph is a map of interactions (with contexts how people interact) such as Web, social apps/bookmarks/sharing, native apps, GPS and location/checkins, NFC, digital wallets, media authoring, pull/push notifications. I would view the Mobile Graph as a user-in-motion. Where user resides at each moment (home, office, on the way, school, hospital, store etc.), how user relocates (fast by car, slow by bike, very slow by feet; or uniformly or not, e.g. via public transport), how user behaves on each location (static, dynamic, mixed), what other users’ motions take place around (who else traveled same route, or who also reside on same location for that time slot) and so on. I am looking at the Motion Graph more as to the Mesh Network.
Why dynamic networking view makes more sense? Consider users as people and machines. Recall about IoT and M2M. Recall the initiatives by Ford and Nokia for resolving the gridlock problems in real-time. Mobile Graphs is better related to the motion, mobility, i.e. to the essence of the word “mobile”. If we consider it from motion point of view and add/extend with the marketing point of view, we will get pretty useful model for the user and society. Mobile Graph is not for oneself. At least it is more efficient for many than for one.

Knowledge Graph

This is a monster one. It is about the semantics between all digital and physical things. Why Google rocks still? Because they built the Knowledge Graph. You can see it action here. Check out interesting tips & tricks here. Google’s Knowledge Graph is a tool to find the UnGoogleable. There is a post on Blumenthals that Google’s Local Graph is much better than Knowledge, but this probably will be eliminated with time. IMHO their Knowledge Graph is being taught iteratively.
As Larry Page said many times, Google is not a search engine or ads engine, but the company that is building the Artificial Intelligence. Ray Kurzweil joined Google to simulate the human brain and recreate kind of intelligence. Here is a nice article How Larry Page and Knowledge Graph helped to seduce Ray Kurzweil to join Google. “The Knowledge Graph knows that Santa Cruz is a place, and that this list of places are related to Santa Cruz”.
We can look at those graphs together. Social will be in the middle, because we (people) like to be in the center of the Universe:) The Knowledge Graph could be considered as meta-graph, penetrating all other graphs, or as super-graph, including multiple parts from other graphs. Even now, the Knowledge Graph is capable of handling dynamics (e.g. flight status).

Other Graphs

There are other graphs in the world of Big Data. The technology ecosystems are emerging around those graphs. The boost is expected from the Biotech. There is plenty of gene data, but lack of structured information on top of it. Brand new models (graphs) to emerge, with ease of understanding those terabytes of data. Circos was invented in the field of genomic data, to simplify understanding of data via visualization. More experiments could be found on Visual Complexity web site. We are living in the different World than a decade ago. And it is exciting. Just plan your strategies correspondingly. Consider Big Data strategically.

헌팅턴병(Huntington’s Disease, HD)이란



헌팅턴 무도병(Huntington's chorea)이라고도 알려져 있는 헌팅턴병(Huntington's disease)은 드물게 발병하는 우성 유전병이다. 어린 시절부터 노년 사이의 어느 때라도 발병할 수 있지만, 보통은 30 세에서 50 세 사이에 발병한다.

[편집]원인

염색체 4p16.3에 위치하는 헌팅턴(Huntington) 유전자에는 CAG 세 개의 코돈이 반복되어 나타나는 특이한 서열이 존재하는데, 정상인은 19회 정도 반복하지만 헌팅턴병 환자에게서는 40회 이상 나타난다. 또한 이러한 반복 횟수는 헌팅턴병이 발병하는 나이와 반비례한다. 소아 헌팅턴병(Juvenile Huntington's disease)의 경우에는 최대 200회 이상의 반복이 나타나는데, 이 때문에 일반 환자에 비해 증상이 조기에 나타난다.[1]

[편집]증상

운동 증상은 대개 안면 경련과 함께 시작되고, 나중에는 떨림이 신체 다른 부위에까지 퍼져서 환자의 의사와 상관없이 비틀리는 운동으로 발전한다.(무도병이란 의미의 chorea는 무용술이란 의미의 choreography와 어원이 같다. 무도병의 비틀리는 움직임이 때로는 약간 무용 같아 보이기도 하기 때문이다.) 점차 경련이나 비틀리는 운동이 환자의 걷기, 말하기, 그리고 다른 자발적인 운동을 더욱 더 방해하게 된다. 특히 새로운 운동습관을 형성하는 능력이 쇠퇴한다.
이 장애는 광범위한 뇌손상과 관련되는데, 특히 미상핵조가비핵, 그리고 담창구의 손상을 가져오며 대뇌피질에도 어느 정도 손상을 입게 된다. 병의 진행에 따라 환자가 사망했을 때 의 총 무게는 정상이었을 때보다 15 ~ 20 % 정도 감소하기도 한다. 가장 큰 손상을 입는 것은 GABA를 신경전달물질로 분비하는뉴런들이다. 그렇지만 GABA 수용기를 자극하는 약물들은 헌팅턴병의 증세를 거의 또는 전혀 없애주지 못한다. 헌팅턴병 환자들은 또한 여러 가지 심리적 장애를 겪는데, 여기엔 우울증, 기억장애, 불안, 환각과 망상, 판단력의 쇠퇴, 알코올 중독, 약물 남용, 그리고 완전한 무반응성에서부터 분별없는 난잡함에 걸친 성격 장애가 포함된다. 어떤 경우에는 심리적 장애가 운동 장애보다 먼저 발달하기도 한다. 일단 증세가 나타나면, 심리적 증상과 운동 증상이 모두 약 15년에 걸쳐 진행되면서 점차 악화되어 결국 사망에 이르게 된다.
출처 : http://health.naver.com/medical/disease/detail.nhn?selectedTab=detail&diseaseSymptomTypeCode=AA&diseaseSymptomCode=AA000134&cpId=CP00038907#con


헌팅턴병은 상염색체 우성으로 유전되는 질환(상염색체 우성 유전질환)이다. 선천성(유전성) 질환인 질병은 뇌의 특정 부위에 침범하여 점차적으로 퇴행을 초래하여 성격장애, 불수의적 이상운동, 치매에 이르게 한다.
상염색체 우성 유전이란 질병 유전자의 단일 카피(아버지 또는 어머니로부터 받은) 다른 정상 유전자보다 '우성적으로(Dominating)' 발현되는 것으로, 영향 받은 부모로부터 자녀에게 질환을 전달할 위험률은 50%이며, 확률을 각각의 임신마다 독립적으로 작용하며, 성별에 영향을 받지 않는다.
헌팅턴병은 4 염색체의 짧은 (4p16.3) 위치하고 있는 '헌팅틴(Huntingtin)'으로 알려진 유전자의 돌연변이에 의해 생기는 병으로 상염색체 우성으로 유전되는 질환이다.
인간의 세포 안에는 개인의 유전 정보를 가지고 있는 46개의 염색체가 있다. 46개의 염색체는 22쌍의 상염색체와 1쌍의 성염색체로 구성된다. 성염색체의 경우 남성은 X Y 염색체, 여성은 X X 염색체로 이루어져 있으며, 각각의 염색체는 'p'라고 불리는 짧은 (단완) 'q'라고 불리는 (장완)으로 구성되어 있다.
염색체를 염색하게 되면 모양의 염색대(band) 관찰되는데, 각각의 염색대(band)에는 번호가 매겨져 있다. 예를 들면 4p16.3이란 4 염색체의 단완에 있는 16.3 염색대(band) 의미하는 것이다.
헌팅틴(Huntingtin) 유전자는 전체에 분포되어 있는 신경세포(뉴런) 단백질 생산에 관여한다. 그러나 헌팅틴(Huntingtin) 유전자에 의해 생산되는 단백질의 기능은 아직 완전히 밝혀지지 않았다. 질환을 가진 개인들의 헌팅틴 유전자는 특정 유전학적 지시를 수행하는 암호화된 '빌딩 블럭(building blocks)' 오류가 있는 것으로 알려졌다. 각각의 유전자 안에는 4개의 기본적인 화학물질(뉴클레오타이드 염기, Nucleotide) 다른 배열로 구성되어 있다.
헌팅턴병을 가진 환자의 뉴클레오타이 염기(Nucleotide, 염기는 아데닌-adenine, 사이토신-cytosine, 구아닌-guanine, 티민-thymine으로 구성) 보면 3 염기서열(CAG; cytosine, adenine, guanine) 반복이 정상인보다 비정상적으로 증가되어 있음을 있다(CAG 삼염기 반복 확장, 사이토신-cytosine, 아데닌-adenine, 구아닌-guanine으로 구성되어 암호화된 비정상적으로 유전자를 반복하고 있다. 이때 확장되어진 반복의 길이는 증상 발현의 나이에 영향을 미친다).
예를 들어, 질병을 가진 개인들은 헌팅틴 유전자 내에 35 이상의 CAG 반복 서열을 가지며, 대부분 39개보다 많다. 그러나 질환이 없는 개인들은 유전자내에 대략 20개의 반복 서열을 가지는 경향이 있다. 확장된 CAG 반복서열은 불안정하고, 세대를 거듭함에 따라 확장된다. , 반복 확장된 길이에 따라 증상의 발현 시기가 달라지고, 이러한 염기서열의 반복은 세대를 거듭함에 따라 확장되어 헌팅턴병 증상의 발현 시기가 점점 빨라진다. 이를 유전적 전구증상(Anticipation)이라 한다. 추가적으로, 일부 연구자들의 헌팅틴 유전자의 확장된 CAG 반복서열은 아버지로부터 전달받았을 불안정(unstable)하다는 보고도 있다.

헌팅턴병의 특이한 증상과 신체적인 특성은 뇌의 특정 지역의 신경 세포(뉴런) 변성의 결과에 따라 구분된다. 헌팅턴병이 발현되는 뇌의 특정 지역이란 깊숙이 있으며 운동 조절 역할을 하는 뇌기저핵(Basal ganglia) 뇌의 바깥부분에 위치하면서 의식적인 사고와 운동에 관여하는 대뇌피질(Cerebrum cortex)이다.
헌팅턴병은 대략 미국에서 10,000에서 1명의 비율로 영향을 나타내어 대략 30,000명의 미국인이 헌팅턴병을 가지고 있고, 다른 200,000명은 아마도 질환에 위험이 있다. 질환은 남성과 여성에게서 동일하게 나타나 성별의 차이는 없으나, 백인에게서 발병률이 높다는 보고가 있다. 서유럽인들 100,000명당 3~7, 아프리카와 아시아인들 1,000,000명당 1명꼴로 발병한다. 질환에 대한 국내의 정확한 역학조사 자료는 없으며, 서울대학교병원에서 2001년까지 '비정상 유전자 검사' 확진된 환자가 60여명이었다.
헌팅턴병에서 드문 유년기 형태는 대략적으로 모든 사례에서 10% 차지한다. 형태는 2 가량의 어린이에게서 나타날 있다.

출처 : http://kimsline.egloos.com/10249108