身為一個熱愛美食、喜歡在城市裡挖掘驚喜的人，臺中公益路一直是我最常出沒的地方之一。這條路可說是「臺中人的美食戰場」，從精緻西餐到創意火鍋，從日式丼飯到義式早午餐，每走幾步，就會有完全不同的特色料理餐廳。

這次我特別花了一整個月，實際造訪了公益路上十間口碑不錯的餐廳。有的是網友熱推的打卡名店，也有隱藏在巷弄裡的小驚喜。我以環境氛圍、口味表現、價格CP值與再訪意願為基準，整理出這篇實測評比。希望能幫正在猶豫去哪裡吃飯的你，找到那一間「吃完會想再來」的餐廳。

評比標準與整理方向

這次我走訪的10家餐廳橫跨不同料理類型，從高質感牛排館到巷弄系早午餐，每一間都有自己獨特的風格。為了讓整體比較更客觀，我依照以下四大面向進行評比，並搭配實際用餐體驗來打分。

整體而言，我希望這份評比不只是「哪家好吃」，而是幫你在不同情境下（約會、家庭聚餐、朋友小聚、商業午餐）都能快速找到合適的選擇。畢竟，美食不只是味覺的滿足，更是一段段與朋友共享的生活記憶。

10間臺中公益路餐廳評比懶人包

公益路向來是臺中人聚餐的首選地段，從火鍋、燒肉到中式料理與早午餐，每走幾步就有驚喜。以下是我實際造訪過的10間代表性餐廳清單，橫跨平價、創意、高級各路風格。

一頭牛日式燒肉｜炭香濃郁的和牛饗宴，約會聚餐首選

走在公益路上，很難不被 一頭牛日式燒肉 的木質外觀吸引。低調卻不失質感的門面，搭配昏黃燈光與暖色調的內裝，讓人一進門就感受到濃濃的日式職人氛圍。店內空間不大，但桌距規劃得宜，每桌皆設有獨立排煙設備，烤肉時完全不怕滿身油煙味。

餐點特色

一頭牛的靈魂，絕對是他們招牌的「三國和牛拼盤」。
嚴選的和牛部位，共八個部位、十樣餐點，讓人能從牛頭一路品嘗到牛尾。
油花分布均勻、切片厚薄恰好，經過炭火烤炙後香氣四溢，焦香與油脂在口中交融，入口即化的滑順感令人難忘。
值得一提的是，一頭牛的菜單設計十分彈性
想要一次體驗完整套餐也可以，偏好客製口味則能自由單點組合，不受套餐限制，想吃什麼就點什麼。
而且每桌都能選擇「自行燒烤」或「專人代烤」服務，烤肉管家的火侯掌握與節奏讓整體體驗更輕鬆愉快。
除了主角和牛，旬味野炊飯 與 主廚冰淇淋 也是隱藏版亮點，前者粒粒分明、香氣撲鼻；後者以香草與焙茶為基底，隨季節更換口味，完美收尾。整體服務親切熱情，特別是壽星還能享有 生日畫盤驚喜，讓慶祝時刻更添儀式感。

用餐體驗

整體節奏掌握得非常好。店員會在你剛想烤下一片肉時貼心遞上夾子、幫忙換烤網，讓人完全不用分心。整場用餐過程就像一場表演，從視覺、嗅覺到味覺都被滿足。
如果是第一次約會或慶祝特別節日，這裡的氛圍既不尷尬又不吵鬧，是營造氣氛的理想選擇。

綜合評分

地址：408臺中市南屯區公益路二段162號

電話：04-23206800

官網：http://www.marihuana.com.tw/yakiniku/index.html

小結語

一頭牛日式燒肉不僅是「吃肉的地方」，更像是一場五感盛宴。從進門那一刻到最後一道甜點，都能感受到他們對細節的用心。
若要在公益路找一間能讓人「邊吃邊微笑」的燒肉店，一頭牛 絕對值得列入你的必訪清單。

TANG Zhan 湯棧｜文青系火鍋代表，麻香湯底與視覺美感並重

在公益路這條美食戰線上，TANG Zhan 湯棧 是讓人一眼就會想走進去的那一種。
黑灰調的現代外觀、搭配微霧玻璃與招牌的「湯棧」燈字，呈現出一種低調的時尚感。
店內設計延續品牌主題，以「湯」為靈魂打造整體體驗，從裝潢到香氣，都有濃厚的溫潤氣息。

餐點特色

湯棧最有名的當然是它的「麻香鍋」。
湯底以雞骨與多種辛香料慢熬，香氣濃郁卻不嗆辣，入口後會在喉間留下柔和的花椒香。
「招牌麻油雞鍋」與「黃金牛奶鍋」也是人氣選項，特別是在冬天，溫潤的湯底配上滑嫩肉片，讓人每一口都覺得暖心。
他們的「滷肉飯」和「香蔥豆腐皮」更是許多老客人必點的靈魂配角，簡單卻有記憶點。

用餐體驗

整體氛圍比一般火鍋店更有質感。
桌距寬敞、燈光柔和，店員動作俐落又親切。即使客滿，也不會感覺吵雜或壓迫。
不論是一個人想靜靜吃鍋、或是朋友聚餐，湯棧都能給你剛剛好的距離與溫度。
值得一提的是，上菜速度快、湯底續湯毫不手軟，細節服務到位。

綜合評分

地址：408臺中市南屯區公益路二段248號

電話：04-22580617

官網：https://www.facebook.com/TangZhan.tw/

小結語

NINI 尼尼臺中店｜明亮寬敞的義式早午餐天堂

如果說前兩間是肉食愛好者的天堂，那 NINI 尼尼臺中店 絕對是想放鬆、聊聊天的好地方。餐廳外觀以白色系與大片玻璃窗為主，陽光灑進室內，讓人一踏入就有種度假般的輕盈感。假日早午餐時段特別熱鬧，建議提早訂位。

餐點特色

NINI 的菜單融合義式與臺灣人口味，選擇多樣且份量十足。主打的 松露燉飯 濃郁卻不膩口，米芯保留微Q口感；而 香蒜海鮮義大利麵 則以新鮮白蝦、花枝與淡菜搭配微辣蒜香，口感層次豐富。
此外，他們的薄餅披薩相當受歡迎，餅皮薄脆、餡料新鮮，是三五好友共享的好選擇。

用餐體驗

店內氣氛輕鬆不拘謹，無論是一個人帶電腦工作、或朋友聚餐，都能找到舒服角落。餐點上桌速度穩定，服務人員態度親切、補水與收盤都非常主動。整體節奏讓人覺得「時間變慢了」，很適合想遠離忙碌日常的人。

綜合評分

地址：40861臺中市南屯區公益路二段18號

電話：04-23288498

官網：https://nini.com.tw/

小結語

加分100%浜中特選昆布鍋物｜平價卻用心的湯頭系火鍋，家庭聚餐好選擇

在公益路這條高質感餐廳林立的戰場上，加分100%浜中特選昆布鍋物 走的是截然不同的路線。它沒有浮誇的裝潢、也沒有高價位的套餐，但靠著實在的湯頭與親切的服務，默默吸引許多回頭客。每到用餐時間，總能看到家庭或情侶三兩成群地圍著鍋邊聊天。

餐點特色

主打 北海道浜中昆布湯底，湯頭清澈卻不單薄，越煮越能喝出海藻與柴魚的自然香氣。
我這次點的是「牛奶昆布鍋」，入口時奶香與昆布香完美融合，搭配新鮮的牛五花肉片，滑順又不膩。
菜盤走健康取向，蔬菜比例高，連玉米、南瓜、豆皮都能吃出甜味；附餐的烏龍麵Q彈有嚼勁，吃完十分有飽足感。

用餐體驗

整體氛圍偏家庭取向，桌距寬敞、座位舒適，帶小孩來也不覺擁擠。店員態度親切，補湯、收盤都很勤快，給人一種「被照顧著」的安心感。
最難得的是，即使價位不高，食材新鮮度仍維持得很好，能感受到店家對品質的堅持。

綜合評分

地址：403臺中市西區公益路288號

電話：0910855180

官網：https://giafine100.com/

小結語

加分100%浜中特選昆布鍋物是一間「不浮誇、但會讓人想再訪」的火鍋店。它不追求豪華擺盤，而是用最簡單的湯頭與新鮮食材，傳遞出家常卻不平凡的溫度。
如果你想在公益路找一間可以放心帶家人一起吃的鍋物店，這裡絕對會讓人感到「加分」不少。

印月餐廳｜中式料理的藝術演繹，宴客與家庭聚會首選

說到臺中公益路的中式料理代表，印月餐廳 絕對是榜上有名。這間開業多年的餐廳以「中菜西吃」的概念聞名，把傳統中式料理以現代手法重新詮釋。從建築外觀到餐具擺設，每個細節都散發著低調的典雅氣息。
走進印月，挑高的空間、柔和的燈光與木質桌椅構成沉穩的氛圍。
不論是家庭聚餐、商務宴客，還是節日慶祝，都能找到恰到好處的格調。

餐點特色

印月最令人印象深刻的是他們將傳統中菜融入創意手法。
這次我品嚐的「松露雞湯」香氣濃郁、層次分明，一口下去既有中式的溫潤感，又帶出西式松露的奢華香氣。
「蒜香牛肋條」則是另一道招牌菜，外酥內嫩、油香十足，咬下去肉汁在口中散開，搭配特調醬汁非常過癮。
此外，他們的創意港點如「麻辣小籠包」與「金沙流沙包」也深受年輕客群喜愛，既保留經典又玩出新意。

用餐體驗

服務方面完全對得起餐廳的高級定位。從入座、點餐到上菜節奏，都拿捏得恰如其分。每道菜都會有服務人員細心介紹食材與吃法，讓人感受到「被款待」的尊榮感。
雖然價位偏中高，但在這樣的氛圍與品質下，物有所值。

綜合評分

地址：408臺中市南屯區公益路二段818號

電話：0422511155

官網：https://wein818.com/

小結語

印月餐廳是一間「不只吃飯，更像品味生活」的地方。
它成功地讓中式料理不再只是圓桌菜，而是能展現質感、講究細節的美食體驗。
若你在找一間能同時滿足味蕾與體面的餐廳，印月 絕對是公益路上的不敗經典。

KoDō 和牛燒肉｜極致職人精神，專為儀式感與頂級味覺而生

若要形容 KoDō 和牛燒肉 的用餐體驗，一句話足以總結——「像在欣賞一場關於肉的表演」。
隱身在公益路一隅，KoDō 的外觀低調典雅，店內以深色木質調與間接照明營造出沉穩氛圍。
從踏入店門那一刻開始，服務人員的態度、動線、聲音控制，全都精準到位，讓人彷彿走進日式劇場。

餐點特色

這裡主打 日本A5和牛冷藏肉，以「精切厚燒」的方式呈現。
我點的「壽喜燒風和牛套餐」是本日最驚艷的一道——服務人員現場以鐵鍋輕煎，再淋上特製壽喜燒醬汁，香氣瞬間瀰漫整桌。
肉片油花細緻、入口即化，搭配生蛋液後更添柔滑口感。
另一道「冷藏肋眼心」則保留了和牛的彈性與甜度，每一口都能感受到油脂與炭火交織出的層次。
即使是配角如「季節小菜」與「日式和風飯」也毫不馬虎，整體呈現出高級卻不造作的平衡。

用餐體驗

KoDō 的最大特色是「儀式感」。
每位店員的動作都有節奏，從擺盤、火候、換網到講解，都像排練過無數次的演出。
在這裡用餐，會自然地放慢速度，專注於每一口肉帶來的細膩變化。
特別推薦搭配店內的紅酒或日本威士忌，風味更加圓潤。

綜合評分

地址：403臺中市西區公益路260號

電話：0423220312

官網：https://www.facebook.com/kodo2018/

小結語

KoDō 和牛燒肉不是日常餐廳，而是一場體驗。
從環境、服務到食材，每個細節都讓人感受到對「完美」的執著。
若你想在公益路找一間能讓人留下深刻印象、適合紀念日慶祝的餐廳，KoDō 絕對是值得收藏的一次「味覺儀式」。

永心鳳茶｜在茶香裡用餐的優雅時光，臺味早午餐的新詮釋

走進 永心鳳茶公益店，彷彿進入一間有氣質的茶館。
柔和的燈光灑在復古綠牆上，搭配大理石桌面與金色餐具，整體氛圍既典雅又帶有一絲文青氣息。
這裡不只是喝茶的地方，更像是把「臺灣味」以早午餐的形式重新演繹。

餐點特色

永心鳳茶的餐點結合中式靈魂與西式擺盤，無論是「炸雞腿飯」還是「紅玉紅茶拿鐵」，都能讓人感受到熟悉卻不平凡的味道。
炸雞腿外酥內嫩，搭配自製酸菜與溏心蛋，鹹香中帶著層次感。
「鳳茶甜點拼盤」則以茶為靈魂——伯爵茶蛋糕、烏龍茶奶酪、紅茶雪酥，每一口都有細緻的香氣變化。
最特別的是他們的茶飲，從臺灣高山紅茶到金萱冷泡茶，每一壺都現泡現倒，香氣清雅。
對我而言，這不只是一頓飯，更是一段放鬆的午後儀式。

用餐體驗

店內服務人員態度溫和，對茶品介紹詳盡。上餐節奏剛好，不急不徐。
整體氛圍很「耐坐」，許多客人吃完正餐後仍會續點一壺茶聊天。
音樂輕柔、光線柔和，是那種可以靜靜待上兩小時的地方。

綜合評分

地址：40360臺中市西區公益路68號三樓(勤美誠品)

電話：0423221118

官網：https://linktr.ee/yonshin

小結語

永心鳳茶讓人重新定義「臺味」。
它不走傳統路線，而是把熟悉的元素以更細緻、更現代的方式呈現。
無論是姊妹下午茶、親子餐聚，或是想一個人沉澱片刻，永心鳳茶 都是一處能讓人慢下來、品味生活的好地方。

三希樓｜老饕級江浙功夫菜，穩重又帶人情味的中式饗宴

位於公益路上的 三希樓 是許多臺中老饕的口袋名單。
它沒有浮誇的裝潢，卻有一種低調的自信。從大門進入，就能聞到淡淡的醬香與蒸氣味，那是正宗江浙菜的靈魂。
整體裝潢以深木色為主，搭配圓桌與包廂設計，非常適合家庭聚餐或請客宴會。

餐點特色

三希樓的菜色以 江浙與港式料理 為主，兼顧傳統與現代風味。
我這次點了「東坡肉」與「蝦仁炒飯」，兩道都展現了主廚深厚的火候功力。
東坡肉油亮卻不膩，入口即化、鹹甜交織；蝦仁炒飯粒粒分明、香氣十足，每一口都吃得到鑊氣。
此外，「小籠包」皮薄多汁，是幾乎每桌必點的招牌；港點類如「金牌流沙包」與「干貝燒賣」也都表現穩定。

用餐體驗

三希樓的服務給人一種老派但貼心的感覺。
店員上菜節奏掌握得很好，會主動幫忙分菜、收盤，態度沉穩而不打擾。
最讓我印象深刻的是，這裡的客群非常多元——有帶長輩的家庭、公司聚餐，也有情侶共度節日，卻都能在同一空間裡感到自在。

綜合評分

地址：408臺中市南屯區公益路二段95號

電話：0423202322

官網：https://www.sanxilou.com.tw/

小結語

三希樓是一間「吃得出功夫」的餐廳。
它不追求創新，而是用穩定的味道與真材實料，抓住每一位饕客的胃。
如果你想在公益路上找一間能兼顧長輩口味、氣氛又不拘謹的中餐廳，三希樓 絕對是最穩妥的選擇。

一笈壽司｜低調奢華的無菜單日料，職人手藝詮釋旬味極致

在熱鬧的公益路上，一笈壽司 低調得幾乎不顯眼。
外觀簡約，沒有華麗招牌，只有小小的木質門面與柔黃燈光。
一推開門，迎面而來的是日式杉木香氣與寧靜的氛圍，吧檯座位整齊排列，主廚站在中間，彷彿舞臺上的演出者。

餐點特色

一笈壽司採 Omakase（無菜單料理） 形式，每一餐都由主廚根據當日食材設計。
我這次選擇中價位套餐（約 $1200），共十多道料理，從前菜、小鉢、刺身、握壽司到甜點一氣呵成。
「比目魚鰭邊握」是整場最驚豔的瞬間——主廚以火槍輕炙，油脂瞬間釋放，入口後化成柔滑香氣。
「甜蝦海膽軍艦」則完美展現鮮度與層次感，海膽甘甜、甜蝦緊實。
搭配主廚親自調配的醬汁，每一口都像在品嚐季節的節奏。

用餐體驗

整場用餐約90分鐘，節奏緩慢但沉穩。
主廚會邊料理邊與客人互動，介紹魚種產地與食材處理方式。
雖然整體空間不大，但氣氛極佳——柔和的音樂、清酒的香氣、刀刃切魚時的聲音，讓人完全沉浸其中。
特別喜歡他們最後的甜點「焙茶奶酪」，收尾清爽優雅，為整場體驗畫下完美句點。

綜合評分

地址：408臺中市南屯區公益路二段25號

電話：0423206368

官網：https://www.facebook.com/YIJI.sushi/

小結語

一笈壽司是一間真正讓人「放慢呼吸」的餐廳。
這裡沒有多餘擺盤，也不靠噱頭，而是以主廚對食材的尊重與技術堆疊出一場味覺饗宴。
若你想在公益路體驗日本料理最純粹的精神，一笈壽司 絕對值得你預約、靜靜期待。

茶六燒肉堂｜人氣爆棚的和牛燒肉聖地，肉香與幸福感同時滿分

若要票選公益路上「最難訂位」的餐廳，茶六燒肉堂 絕對名列前茅。
不管平日或假日，用餐時段幾乎一位難求。外觀以木質格柵搭配大面玻璃設計，呈現出年輕又有質感的風格。店內空間明亮、桌距適中，播放著輕快的音樂，整體氛圍熱鬧中帶點高級感，是許多年輕人聚餐、慶生的首選地。

餐點特色

茶六主打 和牛燒肉套餐，價格約落在 $700–$1000 間，份量與品質兼具。
我這次點的是「厚切牛舌套餐」，肉片厚實彈牙，略帶脆感，搭配鹽蔥提味剛剛好。
另一道「和牛拼盤」也相當受歡迎，油花分布均勻、香氣濃郁，輕烤幾秒即可入口即化。
套餐附餐部分也相當用心：沙拉新鮮、味噌湯濃郁，最後還有一份「茶香冰淇淋」作結尾，香氣清爽，完美收尾。

用餐體驗

茶六的服務效率相當高。店員親切、換網勤快、補水速度快，整場用餐流程流暢無壓力。
雖然客人很多，但環境維持得乾淨整潔，動線規劃良好。
最令人印象深刻的是他們的 整體節奏拿捏得剛剛好 ——餐點上桌快、氣氛熱絡，卻不會讓人覺得匆忙。
不論是朋友聚會、家庭聚餐，甚至是情侶約會，都能找到各自的樂趣。

綜合評分

地址：403臺中市西區公益路268號

電話：0423281167

官網：https://inline.app/booking/-L93VSXuz8o86ahWDRg0:inline-live-karuizawa/-LUYUEIOYwa7GCUpAFWA

小結語

茶六燒肉堂用「穩定品質＋輕奢氛圍」抓住了臺中年輕族群的心。
不論是第一次約會還是老朋友重聚，都能在這裡找到屬於燒肉的快樂節奏。
若你在公益路只想挑一家「保證不踩雷」的燒肉店，茶六燒肉堂 絕對是首選。

吃完10家公益路餐廳後的心得與結語

吃完這十家餐廳後，臺中公益路不只是一條美食街，而是一段生活風景線。

有的餐廳講究細膩與儀式感，像 一頭牛日式燒肉 與 一笈壽司，讓人感受到食材最純粹的美好

有的則以親切與溫度打動人心，像 加分昆布鍋物、永心鳳茶，讓人明白吃飯不只是為了飽足，而是一種被照顧的幸福。

而像茶六燒肉堂、TANG Zhan 湯棧 這類人氣名店，則用穩定的品質與熱絡的氛圍，成為許多臺中人心中「想吃肉就去那裡」的代名詞。

這十家店，構成了公益路最動人的縮影

有華麗的，也有溫柔的；有傳統的，也有創新的。

 每一家都在自己的風格裡發光，讓人吃到的不只是料理，而是一種生活的溫度與節奏。

對我而言，這不僅是一場美食旅程，更是一趟關於「臺中味道」的回憶之旅。

FAQ：關於臺中公益路美食常見問題

Q1：公益路哪一區的餐廳最集中？
 最熱鬧的區段大約在「公益路與黎明路口」一帶，這裡聚集了許多知名餐廳，從高級燒肉到早午餐通通有。
像 一頭牛日式燒肉、TANG Zhan 湯棧、茶六燒肉堂 都在這附近，交通方便、停車也相對容易。

Q2：需要提前訂位嗎？
 公益路的熱門餐廳幾乎都建議 提早3～5天訂位，尤其是假日或節慶期間。
特別是 一頭牛日式燒肉、KoDō 和牛燒肉、一笈壽司 這幾家，若臨時前往幾乎很難有位。

最後的話

若要用一句話形容這趟美食之旅，我會說：
「在公益路，吃飯不是選擇，而是一種享受。」
這條路上的每一次用餐，都像一段城市裡的小旅行。
下次當你不確定想吃什麼時，不妨沿著公益路走一圈，或許下一家，正好就是你新的最愛。

三希樓好吃嗎？

如果你也和我一樣喜歡用味蕾探索一座城市，那就把這篇公益路美食攻略收藏起來吧。一笈壽司尾牙預算好掌控嗎？

無論是約會、慶生、家庭聚餐，或只是想犒賞一下辛苦的自己——這條路上永遠會有一間剛剛好的餐廳在等你。一笈壽司適合請客嗎？

下一餐，不妨從這10家開始。印月餐廳值得推薦嗎？

打開手機、約上朋友，讓公益路成為你生活裡最容易抵達的小確幸。三希樓飲料值得加點嗎？

如果你有私心愛店，也歡迎留言分享，KoDō 和牛燒肉婚前派對適合嗎？

你的推薦，可能讓我下一趟美食旅程變得更精彩。印月餐廳肉質如何？

Researchers used DNA sequences from high-resolution experiments to train a neural network called BPNet, whose “black box” innerworkings were then uncovered to reveal sequence patterns and organizing principles of the genome’s regulatory code. Credit: Illustration courtesy of Mark Miller, Stowers Institute for Medical Research Opening the Black Box To Uncover the Rules of the Genome’s Regulatory Code Researchers at the Stowers Institute for Medical Research, in collaboration with colleagues at Stanford University and Technical University of Munich, have developed advanced explainable artificial intelligence (AI) in a technical tour de force to decipher regulatory instructions encoded in DNA. In a report published online on February 18, 2021, in Nature Genetics, the team found that a neural network trained on high-resolution maps of protein-DNA interactions can uncover subtle DNA sequence patterns throughout the genome and provide a deeper understanding of how these sequences are organized to regulate genes. Neural networks are powerful AI models that can learn complex patterns from diverse types of data such as images, speech signals, or text to predict associated properties with impressive high accuracy. However, many see these models as uninterpretable since the learned predictive patterns are hard to extract from the model. This black-box nature has hindered the wide application of neural networks to biology, where the interpretation of predictive patterns is paramount. One of the big unsolved problems in biology is the genome’s second code—its regulatory code. DNA bases (commonly represented by letters A, C, G, and T) encode not only the instructions for how to build proteins, but also when and where to make these proteins in an organism. The regulatory code is read by proteins called transcription factors that bind to short stretches of DNA called motifs. However, how particular combinations and arrangements of motifs specify regulatory activity is an extremely complex problem that has been hard to pin down. BPNet: A Next-Gen Neural Network Now, an interdisciplinary team of biologists and computational researchers led by Stowers Investigator Julia Zeitlinger, PhD, and Anshul Kundaje, PhD, from Stanford University, have designed a neural network—named BPNet for Base Pair Network—that can be interpreted to reveal regulatory code by predicting transcription factor binding from DNA sequences with unprecedented accuracy. The key was to perform transcription factor-DNA binding experiments and computational modeling at the highest possible resolution, down to the level of individual DNA bases. This increased resolution allowed them to develop new interpretation tools to extract the key elemental sequence patterns such as transcription factor binding motifs and the combinatorial rules by which motifs function together as a regulatory code. “This was extremely satisfying,” says Zeitlinger, “as the results fit beautifully with existing experimental results, and also revealed novel insights that surprised us.” For example, the neural network models enabled the researchers to discover a striking rule that governs the binding of the well-studied transcription factor called Nanog. They found that Nanog binds cooperatively to DNA when multiples of its motifs are present in a periodic fashion such that they appear on the same side of the spiraling DNA helix. Discovering Unexpected Patterns with Nanog “There has been a long trail of experimental evidence that such motif periodicity sometimes exists in the regulatory code,” Zeitlinger says. “However, the exact circumstances were elusive, and Nanog had not been a suspect. Discovering that Nanog has such a pattern, and seeing additional details of its interactions, was surprising because we did not specifically search for this pattern.” “This is the key advantage of using neural networks for this task,” says Žiga Avsec, PhD, first author of the paper. Avsec and Kundaje created the first version of the model when Avsec visited Stanford during his doctoral studies in the lab of Julien Gagneur, PhD, at the Technical University in Munich, Germany. “More traditional bioinformatics approaches model data using pre-defined rigid rules that are based on existing knowledge. However, biology is extremely rich and complicated,” says Avsec. “By using neural networks, we can train much more flexible and nuanced models that learn complex patterns from scratch without previous knowledge, thereby allowing novel discoveries.“ BPNet Learns Like a Face Recognition System BPNet’s network architecture is similar to that of neural networks used for facial recognition in images. For instance, the neural network first detects edges in the pixels, then learns how edges form facial elements like the eye, nose, or mouth, and finally detects how facial elements together form a face. Instead of learning from pixels, BPNet learns from the raw DNA sequence and learns to detect sequence motifs and eventually the higher-order rules by which the elements predict the base-resolution binding data. Once the model is trained to be highly accurate, the learned patterns are extracted with interpretation tools. The output signal is traced back to the input sequences to reveal sequence motifs. The final step is to use the model as an oracle and systematically query it with specific DNA sequence designs, similar to what one would do to test hypotheses experimentally, to reveal the rules by which sequence motifs function in a combinatorial manner. “The beauty is that the model can predict way more sequence designs that we could test experimentally,” Zeitlinger says. “Furthermore, by predicting the outcome of experimental perturbations, we can identify the experiments that are most informative to validate the model.” Indeed, with the help of CRISPR gene editing techniques, the researchers confirmed experimentally that the model’s predictions were highly accurate. Since the approach is flexible and applicable to a variety of different data types and cell types, it promises to lead to a rapidly growing understanding of the regulatory code and how genetic variation impacts gene regulation. Both the Zeitlinger Lab and the Kundaje Lab are already using BPNet to reliably identify binding motifs for other cell types, relate motifs to biophysical parameters, and learn other structural features in the genome such as those associated with DNA packaging. To enable other scientists to use BPNet and adapt it for their own needs, the researchers have made the entire software framework available with documentation and tutorials. Reference: “Base-resolution models of transcription-factor binding reveal soft motif syntax” by Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje and Julia Zeitlinger, 18 February 2021, Nature Genetics. DOI: 10.1038/s41588-021-00782-6 Other contributors to the study included Melanie Weilert, Sabrina Krueger, PhD, Khyati Dalal, Robin Fropf, PhD, and Charles McAnany, PhD, from Stowers; and Avanti Shrikumar, PhD, and Amr Alexandari from Stanford University. This work was supported in part by the Stowers Institute for Medical Research and the National Human Genome Research Institute (awards R01HG009674 and U01HG009431 to A.K. and R01HG010211 to J.Z.) and National Institute of General Medical Sciences (DP2GM123485 to A.K.) of the National Institutes of Health (NIH). Additional support included the German Bundesministerium für Bildung und Forschung (project MechML 01IS18053F to Z.A.) and a Stanford BioX Fellowship and Howard Hughes Medical Institute International Student Research Fellowship (to A.S). Sequencing was performed at the Stowers Institute for Medical Research and University of Kansas Medical Center Genomics Core supported by the NIH awards from the National Institute of Child Health and Human Development (U54HD090216), Office of the Director (Instrumentation S10OD021743), and National Institute of General Medical Sciences (COBRE P30GM122731). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Lay Summary of Findings DNA is well known for encoding proteins. It also contains another code—a regulatory code—that directs when and where to make proteins in an organism. In a report published online February 18, 2021, in Nature Genetics, researchers from the lab of Julia Zeitlinger, PhD, an investigator at the Stowers Institute for Medical Research, and collaborators from Stanford University and Technical University of Munich describe how they have used explainable artificial intelligence to help decipher the genome’s regulatory code. The researchers developed a neural network whose inner workings can be uncovered to reveal regulatory DNA sequence patterns and their higher-level organizing principles from high-resolution genomics data. The Zeitlinger Lab anticipates that the predictive models, rules, and maps generated using this type of approach will lead to a better understanding of natural and disease-associated genetic variation in regulatory regions of DNA.

Horseshoe Bat. Credit: University of East Anglia A coronavirus related to the virus that causes COVID-19 in humans has been found in UK horseshoe bats – according to new collaborative research from the University of East Anglia, ZSL (Zoological Society of London), and Public Health England (PHE). However, there is no evidence that this novel virus has been transmitted to humans, or that it could in the future, unless it mutates. UEA researchers collected fecal samples from more than 50 lesser horseshoe bats in Somerset, Gloucestershire, and Wales and sent them for viral analysis at Public Health England. Genome sequencing found a novel coronavirus in one of the bat samples, which the team have named ‘RhGB01’.  It is the first time that a sarbecovirus (SARS-related coronavirus) has been found in a lesser horseshoe bat and the first to be discovered in the UK.  There is no evidence that this novel virus has been transmitted to humans, or that it could in the future, unless it mutates. The research team say that these bats will almost certainly have harbored the virus for a very long time. And it has been found now, because this is the first time that they have been tested.  Importantly, this novel virus is unlikely to pose a direct risk to humans, unless it mutates. A mutation could happen if a human infected with COVID-19 passes it to an infected bat, so anyone coming into contact with bats or their droppings, for example, those engaged in caving or bat protection, should wear appropriate PPE. Prof Diana Bell, an expert in emerging zoonotic diseases from UEA’s School of Biological Sciences, said: “Horseshoe bats are found across Europe, Africa, Asia, and Australia and the bats we tested lie at the western extreme of their range. “Similar viruses have been found in other horseshoe bat species in China, South East Asia, and Eastern Europe. “Our research extends both the geographic and species ranges of these types of viruses and suggests their more widespread presence across more than 90 species of horseshoe bats.  “These bats will almost certainly have harbored this virus for a very long time – probably many thousands of years. We didn’t know about it before because this is the first time that such tests have been carried out in UK bats.  “We already know that there are different coronaviruses in many other mammal species too,” she said. “This is a case of ‘seek and you will find’. “Research into the origins of SARS-CoV-2, the virus that causes COVID-19 in humans, has focused on horseshoe bats – but there are some 1,400 other bat species and they comprise 20 percent of known mammals.  “Our findings highlight the need for robust genotype testing for these types of viruses in bat populations around the world. And it raises an important question about what other animals carry these types of viruses.” Prof Andrew Cunningham, from the Zoological Society of London, said: “Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection have been underestimated.  “This UK virus is not a threat to humans because the receptor binding domain (RBD) – the part of the virus that attaches to host cells to infect them – is not compatible with being able to infect human cells.  “But the problem is that any bat harboring a SARS-like coronavirus can act as a melting pot for virus mutation. So if a bat with the RhGB01 infection we found were to become infected with SARS-CoV-2, there is a risk that these viruses would hybridize and a new virus emerges with the RBD of SARS-CoV-2, and so be able to infect people. “Preventing transmission of SARS-CoV-2 from humans to bats, and hence reducing opportunities for virus mutation, is critical with the current global mass vaccination campaign against this virus.” Prof Bell added: “The main risks would be for example a bat rehabilitator looking after a rescued animal and infecting it with SARS-CoV2 – which would provide an opportunity for genetic recombination if it is already carrying another sarbecovirus.  “Anyone coming into contact with bats or their droppings, such as bat rescuers or cavers, should wear appropriate PPE – in order to reduce the risk of a mutation occurring. “We need to apply stringent regulations globally for anyone handling bats and other wild animals,” she added.  The new virus falls within the subgroup of coronaviruses called sarbecoviruses which contains both SARS-CoV-2 (responsible for the current pandemic) and SARS-CoV (responsible for the initial 2003 SARS outbreak in humans). Further analysis compared the virus with those found in other horseshoe bat species in China, South East Asia, and Europe and showed that its closest relative was discovered in a Blasius’s bat from Bulgaria in 2008. The UK discovery was made by undergraduate ecology student Ivana Murphy, from UEA’s School of Biological Sciences, who collected bat droppings as part of her final year research dissertation. Jack Crook conducted the genetic analyses in partnership with other researchers at PHE.   A total of 53 bats were captured, and their feces were collected in sterile bags. The research was conducted under strict Health and Safety protocols. Full PPE was worn and Ivana was regularly tested for COVID-19 to avoid any chance of cross contamination. The bats were released immediately after their droppings had been collected. Ivana said: “More than anything, I’m worried that people may suddenly start fearing and persecuting bats, which is the last thing I would want and would be unnecessary. As like all wildlife, if left alone they do not pose any threat.” Reference: “Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe” by Jack M. Crook, Ivana Murphy, Daniel P. Carter, Steven T. Pullan, Miles Carroll, Richard Vipond, Andrew A. Cunningham and Diana Bell, 19 July 2021, Scientific Reports.  DOI: 10.1038/s41598-021-94011-z

A male spider catapulting off a female during mating. These male spiders catapult at impressive speeds to flee their mates before they get eaten. After males of the orb-weaving spider Philoponella prominens mate with a female, they quickly launch themselves away, researchers report today (April 25, 2022) in the journal Current Biology. Using a mechanism that hadn’t been described before, the male spiders use a joint in their first pair of legs to immediately undertake a split-second catapult action, flinging themselves away from their partners at impressive speeds clocked at up to 88 centimeters per second (cm/s) or 2 miles per hour. “We found that mating was always ended by a catapulting, which is so fast that common cameras could not record the details clearly,” says Shichang Zhang of Hubei University in Wuhan, China. The reason the males catapult themselves is simple: to avoid being eaten by the female in an act of sexual cannibalism. The few males the researchers saw that didn’t catapult were promptly captured, killed, and consumed by their female partners. When the researchers prevented males from catapulting, they met the same fate. This photograph shows two Philoponella prominens spiders mating. Credit: Shichang Zhang Zhang and colleagues made this discovery while studying sexual selection in this spider, which lives in communal groups of up to 300 individuals in a web complex with many individual webs within it. Of 155 successful matings, they report that 152 ended with the male catapulting. All those catapulting males survived their sexual encounters. The three males that didn’t catapult were killed. Another 30 prevented by the researchers from catapulting also got killed and eaten by the female. The researchers say that the findings show clearly that the catapulting behavior is required to avoid sexual cannibalism. This video shows a male spider catapulting off a female during mating. Credit: Shichang Zhang With high-resolution video cameras, the researchers calculated an average peak speed of catapulting spiders of about 65 cm/s (1.5 mph). Speeds ranged from about 30 cm/s (0.7 mph) to almost 90 cm/s (2 mph). They also accelerated at an average of about 200 m/s2. As they soar through the air, the males also spin around 175 times per second on average. The males manage to catapult at these speeds by folding their tibia-metatarsus joint against the female. When released, hydraulic pressure allows for rapid expansion. The joint in question lacks extensor muscles in spiders, they explain. This photograph shows two Philoponella prominens spiders mating. Credit: Shichang Zhang “We observed that males that could not perform the catapulting were cannibalized by the female,” Zhang says. “It suggests that this behavior evolved to fight against female’s sexual cannibalism under strong predation pressure of females. “Females may use this behavior to judge the quality of a male during mating,” he adds. “If a male could not perform catapulting, then kill it, and if a male could perform it multiple times, then accept its sperm.” In future studies, they hope to explore the role of catapulting ability in male mating success. Reference: “Male spiders avoid sexual cannibalism with a catapult mechanism” by Shichang Zhang, Yangjié Liu, Yubing Ma, Hao Wang, Yao Zhao, Matjaž Kuntner and Daiqin Li, 25 April 2022, Current Biology. DOI: 10.1016/j.cub.2022.03.051 This work was supported by the grants from the National Natural Science Foundation of China, the Ministry of Education AcRF grants from Singapore, and the Slovenian Research Agency.

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